Author: "Department of Ecology and Evolutionary Biology" - Searchworks@Jio Institute Digital Library Search Results

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18,458 results on '"Department of Ecology and Evolutionary Biology"'

1. Advancing Diversity and Inclusivity in Ocean Sciences by Re-Envisioning Overlooked Barriers in Scientific Diving Training

Author: Barber, Paul, Department of Ecology and Evolutionary Biology, University of California, Barber-Choi, Jeannie, Betancourt, Austin, Cuker, Benjamin, Davis, Alexandra, Fong, Caitlin, Fong, Peggy, Gibson, Deidre, and Smith, Tyler
Subjects: Earth Sciences, Oceanography, Life Below Water
Abstract: Self-contained underwater breathing apparatus (scuba) is an essential tool in some marine science fields. However, financial costs and racial disparities in swimming participation can be a barrier to entry for many aspiring marine scientists of color. Scientific diving programs could improve access to scientific diving training by offering training as part of their standard undergraduate curriculum and by maintaining a stock of scuba gear for use during courses. Similarly, the American Academy of Underwater Scientists (AAUS) could make training more accessible by re-envisioning components of the swim test and by building water safety skills into AAUS training—all without compromising safety. Combined, these two actions would expand pathways for students of color to careers in marine science, adding much needed diversity to the field.
Published: 2023

2. DNA extraction (Qiagen DNEasy Blood and Tissue Kit) v1

Author: Imani D Russell, Joanna G. Larson [Department of Ecology and Evolutionary Biology, Rudolf von May, Iris A. Holmes, Timothy Y. James, and Alison R. Davis Rabosky
Abstract: Protocol for extracting DNA from amphibian skin swabs using the Qiagen DNeasy blood and Tissue Kit.
Published: 2019

3. Nesting and habitat selection in cavity nesting birds: final project report

Author: Paine, Charles R.; Martin, Thomas E.; University of Arizona, Department of Ecology and Evolutionary Biology; Arizona Game and Fish Department, Heritage Fund, Arizona Game and Fish Department; University of Arizona, Paine, Charles R.; Martin, Thomas E.; University of Arizona, Department of Ecology and Evolutionary Biology; Arizona Game and Fish Department, Heritage Fund, and Arizona Game and Fish Department; University of Arizona
Abstract: 44 pages
Published: 2012

4. Dispersal of sweet pignut hickory in a year of low fruit production, and the influence of predation by a curculionid beetle

Author: Department of Ecology and Evolutionary Biology, University of Michigan, 48109, Ann Arbor, MI, USA, Ann Arbor, Boucher, Douglas H., Sork, Victoria L., Department of Ecology and Evolutionary Biology, University of Michigan, 48109, Ann Arbor, MI, USA, Ann Arbor, Boucher, Douglas H., and Sork, Victoria L.
Abstract: The rate at which fallen hickory nuts are removed from beneath the parent tree, and the effect on this rate of the seed predator Conotrachelus affinis, was studied in an oak-hickory forest in southeastern Michigan, USA, during a year in which few nuts were produced. The trees responded to Conotrachelus, which destroyed half the nut crop, by aborting inviable nuts during the summer. The seed dispersers, mostly gray squirrels, removed fallen nuts rapidly, showing the ability to distinguish viable nuts and remove them preferentially. The number of nuts removed in a week varies directly with the number available, and removal rate increases when many viable nuts are falling. The death of most seeds before dispersal, and the squirrels' efficiency at foraging on nuts and recovering them after burial, imply that successful hickory reproduction takes place only in years of heavy nut production.
Published: 2006

5. Soil respiration in northern forests exposed to elevated atmospheric carbon dioxide and ozone

Author: School of Natural Resoures and the Environment, and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109-1115, USA, Ecosystem Science Center, School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Ave., Houghton, MI, 49931, USA, USDA Forest Service North Central Research Station, Rhinelander, WI, 54501, USA, Ann Arbor, Pregitzer, Kurt S., Loya, Wendy, Kubiske, Mark E., Zak, Donald, School of Natural Resoures and the Environment, and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109-1115, USA, Ecosystem Science Center, School of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Ave., Houghton, MI, 49931, USA, USDA Forest Service North Central Research Station, Rhinelander, WI, 54501, USA, Ann Arbor, Pregitzer, Kurt S., Loya, Wendy, Kubiske, Mark E., and Zak, Donald
Abstract: The aspen free-air CO 2 and O 3 enrichment (FACTS II???FACE) study in Rhinelander, Wisconsin, USA, is designed to understand the mechanisms by which young northern deciduous forest ecosystems respond to elevated atmospheric carbon dioxide (CO 2) and elevated tropospheric ozone (O 3) in a replicated, factorial, field experiment. Soil respiration is the second largest flux of carbon (C) in these ecosystems, and the objective of this study was to understand how soil respiration responded to the experimental treatments as these fast-growing stands of pure aspen and birch??+??aspen approached maximum leaf area. Rates of soil respiration were typically lowest in the elevated O 3 treatment. Elevated CO 2 significantly stimulated soil respiration (8???26%) compared to the control treatment in both community types over all three growing seasons. In years 6???7 of the experiment, the greatest rates of soil respiration occurred in the interaction treatment (CO 2??+??O 3), and rates of soil respiration were 15???25% greater in this treatment than in the elevated CO 2 treatment, depending on year and community type. Two of the treatments, elevated CO 2 and elevated CO 2??+??O 3, were fumigated with 13 C-depleted CO 2, and in these two treatments we used standard isotope mixing models to understand the proportions of new and old C in soil respiration. During the peak of the growing season, C fixed since the initiation of the experiment in 1998 (new C) accounted for 60???80% of total soil respiration. The isotope measurements independently confirmed that more new C was respired from the interaction treatment compared to the elevated CO 2 treatment. A period of low soil moisture late in the 2003 growing season resulted in soil respiration with an isotopic signature 4???6??? enriched in 13 C compared to sample dates when the percentage soil moisture was higher. In 2004, an extended period of low soil moisture during August and early September, punctuated by a significant rain
Published: 2006

6. Do Physiological Integration and Soil Heterogeneity Influence the Clonal Growth and Foraging of Schoenoplectus pungens?

Author: Department of Ecology and Evolutionary Biology, University of Michigan, 48109, Ann Arbor, MI, USA, Ann Arbor, Poor, Allison, Hershock, Chad, Goldberg, Deborah E., Rosella, Kristin, Department of Ecology and Evolutionary Biology, University of Michigan, 48109, Ann Arbor, MI, USA, Ann Arbor, Poor, Allison, Hershock, Chad, Goldberg, Deborah E., and Rosella, Kristin
Abstract: Physiological integration and foraging behavior have both been proposed as advantages for clonal growth in heterogeneous environments. We tested three predictions concerning their short- and long-term effects on the growth of the clonal perennial sedge Schoenoplectus pungens (Pers.) Volk. ex Schinz and R. Keller: (1) growth would be greatest for clones with connected rhizomes and on heterogeneous soil, (2) clones would preferentially place biomass in the nutrient-rich patches of a spatially heterogeneous environment, and (3) physiological integration would decrease a clone???s ability to forage. We tested our predictions by growing S. pungens clones for 2??years in an experimental garden with two severing treatments (connected and severed rhizomes) crossed with two soil treatments (homogeneous and heterogeneous nutrient distribution). Severing treatments were only carried out in the first year. As predicted, severing significantly decreased total biomass and per capita growth rate in year one and individual ramet biomass both in year one and the year after severing stopped. This reduction in growth was most likely caused by severing damage, because the total biomass and growth rate in severed treatments did not vary with soil heterogeneity. Contrary to our prediction, total biomass and number of ramets were highest on homogeneous soil at the end of year two, regardless of severing treatment, possibly because ramets in heterogeneous treatments were initially planted in a nutrient-poor patch. Finally, as predicted, S. pungens concentrated ramets in the nutrient-rich patches of the heterogeneous soil treatment. This foraging behavior seemed enhanced by physiological integration in the first year, but any possible enhancement disappeared the year after severing stopped. It seems that over time, individual ramets become independent, and parent ramets respond independently to the conditions of their local microsite when producing offspring, a life-history pattern that may
Published: 2006

7. Anthropogenic N deposition and the fate of 15 NO 3??? in a northern hardwood ecosystem

Author: School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109-1115, USA; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109-1115, USA, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109-1115, USA; Department of Biological Sciences, University of New England, Biddeford, ME, 04005, USA, School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931-1295, USA, Ann Arbor, Zak, Donald R., Pregitzer, Kurt S., Holmes, William E., Burton, Andrew J., Zogg, Gregory P., School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109-1115, USA; Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, 48109-1048, USA, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109-1115, USA, School of Natural Resources and Environment, University of Michigan, Ann Arbor, MI, 48109-1115, USA; Department of Biological Sciences, University of New England, Biddeford, ME, 04005, USA, School of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI, 49931-1295, USA, Ann Arbor, Zak, Donald R., Pregitzer, Kurt S., Holmes, William E., Burton, Andrew J., and Zogg, Gregory P.
Abstract: Human activity has substantially increased atmospheric NO 3??? deposition in many regions of the Earth, which could lead to the N saturation of terrestrial ecosystems. Sugar maple (Acer saccharum Marsh.) dominated northern hardwood forests in the Upper Great Lakes region may be particularly sensitive to chronic NO 3??? deposition, because relatively moderate experimental increases (three times ambient) have resulted in substantial N leaching over a relatively short duration (5???7 years). Although microbial immobilization is an initial sink (i.e., within 1???2 days) for anthropogenic NO 3??? in this ecosystem, we have an incomplete understanding of the processes controlling the longer-term (i.e., after 1 year) retention and flow of anthropogenic N. Our objectives were to determine: (i) whether chronic NO 3??? additions have altered the N content of major ecosystem pools, and (ii) the longer-term fate of 15 NO 3??? in plots receiving chronic NO 3??? addition. We addressed these objectives using a field experiment in which three northern hardwood plots receive ambient atmospheric N deposition (ca. 0.9 g N m???2 year???1) and three plots which receive ambient plus experimental N deposition (3.0 g NO 3??? -N m???2 year???1). Chronic NO 3??? deposition significantly increased the N concentration and content (g N/m 2) of canopy leaves, which contained 72% more N than the control treatment. However, chronic NO 3??? deposition did not significantly alter the biomass, N concentration or N content of any other ecosystem pool. The largest portion of 15 N recovered after 1 year occurred in overstory leaves and branches (10%). In contrast, we recovered virtually none of the isotope in soil organic matter (SOM), indicating that SOM was not a sink for anthropogenic NO 3??? over a 1 year duration. Our results indicate that anthropogenic NO 3??? initially assimilated by the microbial community is released into soil solution where it is subsequently taken up by ove
Published: 2006

8. Analysis of conditional contingency using ACTUS2 with examples from studies of animal behavior

Author: Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA, Unidade de Investiga????o em Eco-Etologia, Instituto Superior de Psicologia Aplicada, Rua Jardim do Tabaco 44, 1100 Lisbon, Portugal, Ann Arbor, Almada, F., Robalo, J., Estabrook, George F., Almada, V., Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1048, USA, Unidade de Investiga????o em Eco-Etologia, Instituto Superior de Psicologia Aplicada, Rua Jardim do Tabaco 44, 1100 Lisbon, Portugal, Ann Arbor, Almada, F., Robalo, J., Estabrook, George F., and Almada, V.
Abstract: In this paper we present ACTUS2, the second version of ACTUS (Analysis of Contingency Tables??Using Simulation). ACTUS2 has many new features, including analysis of data in which dependencies that make some combinations of properties impossible are hypothesized. Because ACTUS2 explicitly simulates such hypotheses, it can be used without loss of accuracy to analyze small amounts of data in large tables with many zeros or very low frequencies. We illustrate these features with two studies of animal behavior: interactions of male individuals with other individuals in groups of captive, mature Triturus marmoratus pygmaeus (newts); and agonistic interactions between pairs of male juvenile Diplodus sargus (the sparid fish, white sea-bream). Both significantly frequent, and significantly infrequent, co-occurrences that had biologically meaningful interpretations were revealed.
Published: 2006

9. Installation of bat gates at Lake Mead National Recreation Area

Author: University of Arizona, Department of Ecology and Evolutionary Biology; Arizona Game and Fish Department, Heritage Fund, Boyles, Michael J., Arizona Game and Fish Department; University of Arizona, University of Arizona, Department of Ecology and Evolutionary Biology; Arizona Game and Fish Department, Heritage Fund, Boyles, Michael J., and Arizona Game and Fish Department; University of Arizona
Abstract: 7 pages
Published: 2000

10. Status of native and introduced species of aquatic herpetofauna at San Bernardino National Wildlife Refuge

Author: Schwalbe, Cecil R.; University of Arizona, Department of Ecology and Evolutionary Biology; Cooperative National Park Resources Studies Unit (Tucson, Ariz.); Arizona Game and Fish Department, Heritage Fund, Rosen, Philip C., Arizona Game and Fish Department; University of Arizona, Schwalbe, Cecil R.; University of Arizona, Department of Ecology and Evolutionary Biology; Cooperative National Park Resources Studies Unit (Tucson, Ariz.); Arizona Game and Fish Department, Heritage Fund, Rosen, Philip C., and Arizona Game and Fish Department; University of Arizona
Abstract: 77 pages
Published: 1998

11. Status of native and introduced species of aquatic herpetofauna at San Bernardino National Wildlife Refuge

Author: Schwalbe, Cecil R.; University of Arizona, Department of Ecology and Evolutionary Biology; Cooperative National Park Resources Studies Unit (Tucson, Ariz.); Arizona Game and Fish Department, Heritage Fund, Rosen, Philip C., Arizona Game and Fish Department; University of Arizona, Schwalbe, Cecil R.; University of Arizona, Department of Ecology and Evolutionary Biology; Cooperative National Park Resources Studies Unit (Tucson, Ariz.); Arizona Game and Fish Department, Heritage Fund, Rosen, Philip C., and Arizona Game and Fish Department; University of Arizona
Abstract: 24 pages
Published: 1997

12. Ecology and status of shovelnose snakes (Chionactis) and leafnose snakes (Phyllorhynchus) at and near Organ Pipe Cactus National Monument, Arizona

Author: Holm, Peter A.; Lowe, Charles H.; University of Arizona Department of Ecology and Evolutionary Biology; Arizona Game and Fish Department, Heritage Fund, Rosen, Philip C., Arizona Game and Fish Department; University of Arizona, Holm, Peter A.; Lowe, Charles H.; University of Arizona Department of Ecology and Evolutionary Biology; Arizona Game and Fish Department, Heritage Fund, Rosen, Philip C., and Arizona Game and Fish Department; University of Arizona
Abstract: 70 pages
Published: 1996

13. Population ecology of the Sonoran mud turtle (Kinosternon sonoriense) at Quitobaquito Springs, Organ Pipe Cactus National Monument, Arizona

Author: Lowe, Charles H.; University of Arizona, Department of Ecology and Evolutionary Biology; Arizona Game and Fish Department, Heritage Fund, Rosen, Philip C., Arizona Game and Fish Department, Lowe, Charles H.; University of Arizona, Department of Ecology and Evolutionary Biology; Arizona Game and Fish Department, Heritage Fund, Rosen, Philip C., and Arizona Game and Fish Department
Abstract: 67 pages
Published: 1996

14. Status and conservation of sensitive herpetofauna in the Madrean riparian habitat of Scotia Canyon, Huachuca Mountains, Arizona

Author: Lowe, Charles H.; University of Arizona, Department of Ecology and Evolutionary Biology; Arizona Game and Fish Department, Heritage Fund, Holm, Peter A., Arizona Game and Fish Department; University of Arizona, Lowe, Charles H.; University of Arizona, Department of Ecology and Evolutionary Biology; Arizona Game and Fish Department, Heritage Fund, Holm, Peter A., and Arizona Game and Fish Department; University of Arizona
Abstract: 57 pages
Published: 1995

15. Ecology of the Mexican rosy boa and the Ajo Mountain whipsnake

Author: Parizek, David A.; University of Arizona, School of Renewable Natural Resources; University of Arizona, Department of Ecology and Evolutionary Biology; Arizona Game and Fish Department Heritage Fund, Arizona Game and Fish Department; University of Arizona, UA- School of Renewable Natural Resources, Parizek, David A.; University of Arizona, School of Renewable Natural Resources; University of Arizona, Department of Ecology and Evolutionary Biology; Arizona Game and Fish Department Heritage Fund, Arizona Game and Fish Department; University of Arizona, and UA- School of Renewable Natural Resources
Abstract: 99 pages
Published: 1995

16. Characterizing amplitude and frequency modulation cues in natural soundscapes: A pilot study on four habitats of a biosphere reserve

Author: François-Michel Le Tourneau, Etienne Thoret, Christian Lorenzi, Léo Varnet, Yves Boubenec, Régis Ferrière, Bernie Krause, Laboratoire des systèmes perceptifs (LSP), Département d'Etudes Cognitives - ENS Paris (DEC), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), éQuipe d'AppRentissage de MArseille (QARMA), Laboratoire d'Informatique et Systèmes (LIS), Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Perception, Représentations, Image, Son, Musique (PRISM), Aix Marseille Université (AMU)-Ecole supérieure d'Art d'Aix en Provence (ESA AIX)-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, CREDA - Centre de Recherche Et de Documentation sur les Amériques - UMR 7227 (CREDA), Université Sorbonne Nouvelle - Paris 3-Centre National de la Recherche Scientifique (CNRS), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), ANR-16-CONV-0002,ILCB,ILCB: Institute of Language Communication and the Brain(2016), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), ANR-10-IDEX-0001,PSL,Paris Sciences et Lettres(2010), ANR-17-EURE-0017,FrontCog,Frontières en cognition(2017), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Department of Ecology and Evolutionary Biology, and CREDAL - Centre de recherche et de documentation de l'Amérique latine - UMR 7169 (CREDAL)
Subjects: 0106 biological sciences, Soundscape, Acoustics and Ultrasonics, Range (biology), Pilot Projects, 010501 environmental sciences, 010603 evolutionary biology, 01 natural sciences, Arts and Humanities (miscellaneous), Animals, Humans, Temporal scales, Ecosystem, 0105 earth and related environmental sciences, Elevation, Biosphere, Bayes Theorem, Vegetation, 15. Life on land, Sound, Habitat, Salient, Environmental science, Cues, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Cartography
Abstract: International audience; Natural soundscapes correspond to the acoustical patterns produced by biological and geophysical sound sources at different spatial and temporal scales for a given habitat. This pilot study aims to characterize the temporal-modulation information available to humans when perceiving variations in soundscapes within and across natural habitats. This is addressed by processing soundscapes from a previous study [Krause, Gage, and Joo. (2011). Landscape Ecol. 26, 1247] via models of human auditory processing extracting modulation at the output of cochlear filters. The soundscapes represent combinations of elevation, animal, and vegetation diversity in four habitats of the biosphere reserve in the Sequoia National Park (Sierra Nevada, USA). Bayesian statistical analysis and support vector machine classifiers indicate that: (i) amplitude-modulation (AM) and frequency-modulation (FM) spectra distinguish the soundscapes associated with each habitat; and (ii) for each habitat, diurnal and seasonal variations are associated with salient changes in AM and FM cues at rates between about 1 and 100 Hz in the low (1-3 kHz) audio-frequency range. Support vector machine classifications further indicate that soundscape variations can be classified accurately based on these perceptually inspired representations.
Published: 2020

17. Tracking of marine predators to protect Southern Ocean ecosystems

Author: Marthán N Bester, Birgitte I. McDonald, Karine Delord, Ben Raymond, Jaimie Cleeland, Steven L. Chown, Jean-Benoît Charrassin, Daniel P. Costa, Norman Ratcliffe, Michael E. Goebel, Henri Weimerskirch, Bruno Danis, Rachael Alderman, Simon D. Goldsworthy, Akiko Kato, Keith W. Nicholls, Peter G. Ryan, Nick Gales, Luciano Dalla Rosa, Andrew D. Lowther, Pierre A. Pistorius, Rochelle Constantine, P J Nico de Bruyn, Christian Lydersen, Mike Double, Jefferson T. Hinke, Stuart Corney, Arnaud Tarroux, Kieran Lawton, Yan Ropert-Coudert, Colin Southwell, Kerstin Jerosch, Silvia Olmastroni, Richard A. Phillips, Dominik A Nachtsheim, David R. Thompson, Robert J. M. Crawford, Ian D. Jonsen, Kimberly T. Goetz, Mary-Anne Lea, José C. Xavier, Sébastien Descamps, Charles-André Bost, Michael A. Fedak, Grant Ballard, Robert Harcourt, Mônica M. C. Muelbert, Klemens Pütz, Christophe Guinet, Simon Wotherspoon, Kit M. Kovacs, Iain J. Staniland, Leigh G. Torres, Luis A. Hückstädt, Phil O'b. Lyver, Ari S. Friedlaender, Arnoldus Schytte Blix, Azwianewi B. Makhado, Mercedes Santos, Roger Kirkwood, Peter L. Boveng, John L. Bengtson, Erling S. Nordøy, Barbara Wienecke, Mark A. Hindell, Ryan R. Reisinger, Wayne Z. Trivelpiece, Joachim Plötz, Knowles Kerry, Ben Arthur, Akinori Takahashi, Virginia Andrews-Goff, Horst Bornemann, M. E. I. Marquez, Clive R. McMahon, Gerald L. Kooyman, Anton Van de Putte, Ewan D. Wakefield, Lars Boehme, Philip N. Trathan, Louise Emmerson, Antarctic Wildlife Research Unit, University of Tasmania [Hobart, Australia] (UTAS), Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), CESAB-FRB [France], Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Ecology and Evolutionary Biology (University of California Santa Cruz), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), Department of Ecology and Evolutionary Biology [Santa Cruz], Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung (AWI), School of Biological Sciences [Victoria, Australia] (Monash University), Monash University [Victoria, Australia], Marine Biology Laboratory, Université libre de Bruxelles (ULB), Institute for Marine and Antarctic Studies [Hobart] (IMAS), National Institute of Water and Atmospheric Research [Wellington] (NIWA), Marine Mammal Institute, Oregon State University (OSU), BEDIC, OD Nature [Brussels, Belgium], Royal Belgian Institute for Natural Sciences [Belgium], Department of Primary Industries [Australia], Department of Primary Industries, Parks, Water and Environment, Australian Antarctic Division (AAD), Australian Government, Department of the Environment and Energy, PRBO Conservation Science, Department of Zoology and Entomology [Pretoria], University of Pretoria [South Africa], The Arctic University of Norway [Tromsø, Norway] (UiT), Scottish Oceans Institute, University of St Andrews [Scotland], School of Biological Sciences [Auckland, New Zealand], University of Auckland [Auckland], Antarctic Climate and Ecosystems Cooperative Research Centre (ACE-CRC), Department of Environment, Agriculture and Fisheries [South Africa] (Oceans and Coasts), Laboratório de Ecologia e Conservação da Megafauna Marinha [Rio Grande, Brazil], Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Norvegian Polar Research Institute (NPRI), Norwegian Polar Institute, Institute of Marine Sciences, Long Marine Laboratory, South Australian Research and Development Institute [Australia], Department of Biological Sciences [North Ryde], Macquarie University, Antarctic Ecosystem Research Division, National Oceanic and Atmospheric Administration (NOAA)-National Marine Fisheries Service, Scholander Hall, Scripps Institution of Oceanography [CA, USA], Scripps Institution of Oceanography (SIO - UC San Diego), University of California [San Diego] (UC San Diego), University of California (UC)-University of California (UC)-University of California [San Diego] (UC San Diego), FRAM Centre, Norwegian Polar Institute, Fram Centre, Manaaki Whenua – Landcare Research [Lincoln], Instituto Antartico Argentino, Moss Landing Marine Laboratories [CA, USA] (San José State University), San Jose State University [San Jose] (SJSU), University of Sydney Institute of Marine Science (USIMS), The University of Sydney, Universidade Federal do Rio Grande, British Antarctic Survey (BAS), Natural Environment Research Council (NERC), University of Tromsø (UiT), Dipartimento di Scienze Ambientali 'G. Sarfatti', Università degli Studi di Siena = University of Siena (UNISI), National Research Foundation Centre of Excellence at the Percy FitzPatrick Institute, Antarctic Research Trust, British Antarctic Survey NERC [UK], DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology [South Africa], Nelson Mandela University [Port Elizabeth], Instituto Antártico Argentino, National Insitute of Polar Research, National Institute of Polar Research [Tokyo] (NiPR), Southwest Fisheries Science Center (SWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Institute of Biodiversity, Animal Health and Comparative Medicine, School of Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Natural Environment Research Council - British Antarctic Survey [Cambridge, UK], Department of Biological Sciences, Macquarie University (Australia), Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of California [Santa Cruz] (UCSC), University of California-University of California, Institute for Marine and Antarctic Studies [Horbat] (IMAS), The Arctic University of Norway (UiT), Universidade Federal do Rio Grande do Sul (UFRGS), Scripps Institution of Oceanography, San Jose State University [San José] (SJSU), and Nelson Mandela University
Subjects: 0106 biological sciences, Conservation of Natural Resources, Aquatic Organisms, Food Chain, bird, 010504 meteorology & atmospheric sciences, General Science & Technology, Oceans and Seas, Climate Change, Fishing, Population Dynamics, Animal Identification Systems, Climate change, Antarctic Regions, climate chang, mammal, 01 natural sciences, Predation, long-term change, Birds, bird, climate chang, econtinental shelf, exploitation, long-term change, mammal, predator tracking, Animals, Ecosystem, Ice Cover, 14. Life underwater, econtinental shelf, Life Below Water, Exploitation of natural resources, 0105 earth and related environmental sciences, Mammals, geography, Multidisciplinary, geography.geographical_feature_category, Continental shelf, predator tracking, 010604 marine biology & hydrobiology, Fishes, Biodiversity, Fishery, Climate Action, 13. Climate action, Predatory Behavior, Ecological significance, [SDE]Environmental Sciences, Environmental science, exploitation, Sciences exactes et naturelles
Abstract: International audience; Southern Ocean ecosystems are under pressure from resource exploitation and climate change1,2. Mitigation requires the identification and protection of Areas of Ecological Significance (AESs), which have so far not been determined at the ocean-basin scale. Here, using assemblage-level tracking of marine predators, we identify AESs for this globally important region and assess current threats and protection levels. Integration of more than 4,000 tracks from 17 bird and mammal species reveals AESs around sub-Antarctic islands in the Atlantic and Indian Oceans and over the Antarctic continental shelf. Fishing pressure is disproportionately concentrated inside AESs, and climate change over the next century is predicted to impose pressure on these areas, particularly around the Antarctic continent. At present, 7.1% of the ocean south of 40°S is under formal protection, including 29% of the total AESs. The establishment and regular revision of networks of protection that encompass AESs are needed to provide long-term mitigation of growing pressures on Southern Ocean ecosystems.
Published: 2020

18. A continuous-time state-space model for rapid quality-control of Argos locations from animal-borne tags

Author: Philip D. Doherty, Robert Harcourt, Brendan J. Godley, Scott D. Whiting, Christophe Guinet, Daniel P. Costa, Toby A. Patterson, Stephen C. Votier, Patrick W. Robinson, Matthew J. Witt, Sarah S. Kienle, Clive R. McMahon, Xavier Hoenner, Mark A. Hindell, W. James Grecian, Ian D. Jonsen, University of St Andrews. School of Biology, University of St Andrews. Scottish Oceans Institute, University of St Andrews. Sea Mammal Research Unit, Dept of Biological Sciences [Australia], Macquarie University [Sydney], CSIRO Oceans and Atmosphere [Hobart], Department of Ecology and Evolutionary Biology [Santa Cruz], University of California [Santa Cruz] (UCSC), University of California-University of California, Environment and Sustainability Institute [UK], University of Exeter, South Atlantic Environmental Research Institute [UK], Falkland Islands Joint Nature Conservation Committee [UK], Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Ecology and Evolutionary Biology (University of California Santa Cruz), Environment and Sustainability Institute [Penryn, UK], Department of Biodiversity, Conservation and Attractions [Australia], Parks and Wildlife Service of Northern Territory, Antartic Wildlife Research Unit, School of Zoology, University of Tasmania, Department of Biological Sciences, Macquarie University, Macquarie University, Department of Biological Sciences, Institute for Marine and Antarctic Studies [Horbat] (IMAS), and University of Tasmania [Hobart, Australia] (UTAS)
Subjects: 0106 biological sciences, FOS: Computer and information sciences, Ocean observations, Computer science, Reliability (computer networking), QH301 Biology, Animal-borne sensors, NDAS, Satellite system, 010603 evolutionary biology, 01 natural sciences, Quantitative Biology - Quantitative Methods, Statistics - Applications, Template model builder, QH301, Bio-telemetry, Global Positioning System, Applications (stat.AP), 14. Life underwater, Pinniped, SDG 14 - Life Below Water, lcsh:QH301-705.5, Ecology, Evolution, Behavior and Systematics, Quantitative Methods (q-bio.QM), Remote sensing, State-space representation, business.industry, 010604 marine biology & hydrobiology, Methodology Article, Template Model Builder, Filter (signal processing), Kalman filter, Seabird, Sea turtle, foieGras R package, lcsh:Biology (General), Animal ecology, FOS: Biological sciences, [SDE]Environmental Sciences, business
Abstract: State-space models are important tools for quality control of error-prone animal movement data. The near real-time (within 24 h) capability of the Argos satellite system aids dynamic ocean management of human activities by informing when animals enter intensive use zones. This capability also facilitates use of ocean observations from animal-borne sensors in operational ocean forecasting models. Such near real-time data provision requires rapid, reliable quality control to deal with error-prone Argos locations. We formulate a continuous-time state-space model for the three types of Argos location data (Least-Squares, Kalman filter, and Kalman smoother), accounting for irregular timing of observations. Our model is deliberately simple to ensure speed and reliability for automated, near real-time quality control of Argos data. We validate the model by fitting to Argos data collected from 61 individuals across 7 marine vertebrates and compare model-estimated locations to GPS locations. Estimation accuracy varied among species with median Root Mean Squared Errors usually < 5 km and decreased with increasing data sampling rate and precision of Argos locations. Including a model parameter to inflate Argos error ellipse sizes resulted in more accurate location estimates. In some cases, the model appreciably improved the accuracy of the Argos Kalman smoother locations, which should not be possible if the smoother uses all available information. Our model provides quality-controlled locations from Argos Least-Squares or Kalman filter data with slightly better accuracy than Argos Kalman smoother data that are only available via reprocessing. Simplicity and ease of use make the model suitable both for automated quality control of near real-time Argos data and for manual use by researchers working with historical Argos data., 25 pages, 10 figures
Published: 2020
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19. Variations of leaf longevity in tropical moist forests predicted by a trait-driven carbon optimality model

Author: Pacala, Stephen [Princeton Univ., NJ (United States). Department of Ecology and Evolutionary Biology]
Published: 2017
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20. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer

Author: Sullivan, Matthew [Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721, USA; Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA; Department of Molecular & Cellular Biology, University of Arizona, Tucson, AZ 85721, USA; Present Address: Departments of Microbiology, Ohio State University, Columbus, OH 43210, USA; Present Address: Department of Evolution, Ecology, and Organismal Biology, Ohio State University, Columbus, OH 43210, USA. ; Present Address: Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA]
Published: 2016
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21. Oxytocin Experiments Shed Light on Mechanisms Shaping Prosocial and Antisocial Behaviors in Non-human Mammals

Author: Daniel T. Blumstein, Matthew B. Petelle, Hélène Cristofari, Emily L. Jerome, Jennifer E. Smith, Mills College, Partenaires INRAE, Department of Ecology and Evolutionary Biology, University of California, University of the Free State [South Africa], Institut National de la Recherche Agronomique (INRA), Dept Ecol & Evolutionary Biol, University of Toronto, The Rocky Mountain Biological Laboratory, USA to the Participants in the Development and Mechanisms Underlying Inter-individual Variation in Pro-social Behavior Symposium, National Science Foundation : IOS-1634027, IDBR-0754247, DEB-1119660, DEB-1557130, DBI 0242960, 0731346, Society for Integrative and Comparative Biology (Division of Animal Behavior), and Society for Integrative and Comparative Biology (Division of Comparative Endocrinology) Society for Integrative and Comparative Biology (Division of Neurobiology, Neuroethology, and Sensory Biology) Society for Integrative and Comparative Biology (Division of Ecology and Evolution) American Philosophical Society for fellowships GAANN fellowship GK-12 fellowship UCLA Department of Ecology and Evolutionary Biology Universite Toulouse III Paul Sabatier National Geographic Society UCLA (Faculty Senate and the Division of Life Sciences) RMBL research fellowship
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], media_common.quotation_subject, Pilot Projects, Context (language use), Plant Science, Oxytocin, 03 medical and health sciences, Behavioral traits, 0302 clinical medicine, Oxytocics, medicine, Animals, Biological evidence, Social Behavior, media_common, Mammals, Behavior, Animal, Salience (language), 030104 developmental biology, Prosocial behavior, Non-human, Animal Science and Zoology, Psychology, hormones, hormone substitutes, and hormone antagonists, 030217 neurology & neurosurgery, Reputation, medicine.drug, Cognitive psychology
Abstract: Oxytocin has gained a reputation in popular culture as a simple "love drug" or "cuddle hormone", yet emerging biological evidence indicates that the effects of oxytocin are complex, mediating a suite of behavioral traits that range from ultrasocial to antisocial. Here we provide a comprehensive review to assess the salience of oxytocin in the lives of free-living social mammals. We reviewed the literature to understand the potential effects of oxytocin in promoting prosocial and antisocial behaviors in non-human mammals. Our review highlights a strong bias for studies of model organisms in highly-controlled settings, and emerging evidence for oxytocin's antisocial, context-specific and sex-specific effects. We discuss the results of the review in the context of insights gained from a pilot study aimed to investigate the potential for oxytocin to promote social cohesion in free-living yellow-bellied marmots (Marmota flaviventer). Our field experiment offers an example of the diverse issues that arise when conducting oxytocin manipulations in ecologically relevant contexts. Our synthesis highlights the challenges associated with acquiring adequate sample sizes for field-based, manipulative studies that require standardized measures of social behavior. Taken together, our findings lead us to join others in calling for revision of a simplistic view of oxytocin's role in regulating patterns of behavior. We draw from classical approaches used to study the mechanistic basis of behavior and offer a useful guide for disentangling these effects while appreciating the complex actions of oxytocin in shaping mammalian social behavior.
Published: 2017

22. Animal-Borne Telemetry: An Integral Component of the Ocean Observing Toolkit

Author: Rob Harcourt, Ana M. M. Sequeira, Xuelei Zhang, Fabien Roquet, Kosei Komatsu, Michelle Heupel, Clive McMahon, Fred Whoriskey, Mark Meekan, Gemma Carroll, Stephanie Brodie, Colin Simpfendorfer, Mark Hindell, Ian Jonsen, Daniel P. Costa, Barbara Block, Mônica Muelbert, Bill Woodward, Mike Weise, Kim Aarestrup, Martin Biuw, Lars Boehme, Steven J. Bograd, Dorian Cazau, Jean-Benoit Charrassin, Steven J. Cooke, Paul Cowley, P. J. Nico de Bruyn, Tiphaine Jeanniard du Dot, Carlos Duarte, Víctor M. Eguíluz, Luciana C. Ferreira, Juan Fernández-Gracia, Kimberly Goetz, Yusuke Goto, Christophe Guinet, Mike Hammill, Graeme C. Hays, Elliott L. Hazen, Luis A. Hückstädt, Charlie Huveneers, Sara Iverson, Saifullah Arifin Jaaman, Kongkiat Kittiwattanawong, Kit M. Kovacs, Christian Lydersen, Tim Moltmann, Masaru Naruoka, Lachlan Phillips, Baptiste Picard, Nuno Queiroz, Gilles Reverdin, Katsufumi Sato, David W. Sims, Eva B. Thorstad, Michele Thums, Anne M. Treasure, Andrew W. Trites, Guy D. Williams, Yoshinari Yonehara, Mike A. Fedak, Department of Biological Sciences [North Ryde], Macquarie University, The University of Western Australia Oceans Institute and School of Biological Sciences [Australia], The University of Western Australia (UWA), First Institute of Oceanography [China], Equipe Physique de l'Ocean Austral (DMPA), Graduate School of Frontier Sciences [Kashiwa], The University of Tokyo, Australian Institute of Marine Science (AIMS), University of Sydney Institute of Marine Science (USIMS), The University of Sydney, Ocean Tracking network, Dalhousie University, Australian Institute of Marine Science [Perth] (AIMS Perth), Environmental Research Division [USA], NOAA Southwest Fisheries Science Center [USA], James Cook University (JCU), Institute for Marine and Antarctic Studies [Horbat] (IMAS), University of Tasmania (UTAS), LaSIGE [Lisboa], Universidade de Lisboa (ULISBOA)-Faculdade de Ciências, Stanford Woods Institute for the Environment [USA], Stanford Woods Institute for the Environment, Instituto de Oceanografia, Universidade Federal do Rio Grande, NOAA Integrated Ocean Observing System (IOOS), National Oceanic and Atmospheric Administration (NOAA), Office of Naval Research [USA], National Institute of Aquatic Resources, Technical University of Denmark [Lyngby] (DTU), NERC Sea Mammal Research Unit (NERC Sea Mammal Research Unit), NERC, Sea Mammal Research Unit (SMRU), University of Saint Andrews, Lab-STICC_ENSTAB_CID_TOMS, Laboratoire des sciences et techniques de l'information, de la communication et de la connaissance (Lab-STICC), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT), Fish Ecology and Conservation Physiology Laboratory, Carleton University, South African Institute for Aquatic Biodiversity (SAIAB), South African Institute for Aquatic Biodiversity, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR), Department of Global Change Research, Institut Mediterrani d´Estudis Avançats (IMEDEA), Institut Mediterrani d'Estudis Avancats (IMEDEA), Consejo Superior de Investigaciones Científicas [Spain] (CSIC)-Universidad de las Islas Baleares (UIB)-Consejo Superior de Investigaciones Científicas [Spain] (CSIC)-Universidad de las Islas Baleares (UIB), CSIC-UIB, IFISC, CSIRO Indian Ocean Marine Research Centre [Australia], Instituto de Fısica Interdisciplinar y Sistemas Complejos IFISC (CSIC-UIB), Universitat de les Illes Balears (UIB), Atmosphere and Ocean Research Institute, University of Tokyo, Centre d'études biologiques de Chizé (CEBC), Centre National de la Recherche Scientifique (CNRS), Fisheries and Oceans Canada, Maurice Lamontagne Institute, School of Life and Environmental Sciences [Australia], School of Life and Environmental Sciences Deakin University, Department of Ecology and Evolutionary Biology (University of California Santa Cruz), University of California [Santa Cruz] (UCSC), University of California-University of California, South Australian Research and Development Institute, Malaysia Institute of Oceanography, University of Malaysia, Phuket Marine Biological Center (PMBC), FRAM Centre, Norwegian Polar Institute, Integrated Marine Observing System, Aeronautical Technology Directorate [Japan], Japan Aerospace Exploration Agency, Centro de Investigação em Biodiversidade e Recursos Genéticos/Research Network in Biodiversity and Evolutionary Biology [Portugal], Campus Agrário de Vairão, Universidade do Porto, Processus et interactions de fine échelle océanique (PROTEO), Laboratoire d'Océanographie et du Climat : Expérimentations et Approches Numériques (LOCEAN), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), National Insitute of Polar Research, National Institute of Polar Research [Tokyo] (NiPR), Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, Chester Beatty Laboratories, Norwegian Institute for Nature Research (NINA), Department of Oceanography and Marine Research Institute, University of Cape Town, Fisheries Centre (Marine Mammal Research Unit), University of British Columbia (UBC), Department of Marine Sciences [Gothenburg], University of Gothenburg (GU), Department of Ecology and Evolutionary Biology [Santa Cruz], Scottish Oceans Institute, University of St Andrews [Scotland], École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne), Sorbonne Université (SU), Department of Zoology and Entomology University of Pretoria, Red Sea Research Centre (RSRC), King Abdullah University of Science and Technology (KAUST), National Institute of Water & Atmospheric Research Ltd [New Zealand], Marine Biological Association of the UK, The University of Tokyo (UTokyo), Southwest Fisheries Science Center (SWFSC), NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Marine Fisheries Service (NMFS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), University of Tasmania [Hobart, Australia] (UTAS), Sea Mammal Research Unit [University of St Andrews] (SMRU), School of Biology [University of St Andrews], University of St Andrews [Scotland]-University of St Andrews [Scotland]-Natural Environment Research Council (NERC), Department of Zoology and Entomology [Pretoria], University of Pretoria [South Africa], Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de las Islas Baleares (UIB)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Universidad de las Islas Baleares (UIB), National Institute of Water and Atmospheric Research [Wellington] (NIWA), Universidade do Porto, Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP)-Institut de Recherche pour le Développement (IRD)-Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS)-Sorbonne Université (SU), Institute for Marine and Antarctic Studies [Hobart] (IMAS), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC)-University of California (UC), Danmarks Tekniske Universitet = Technical University of Denmark (DTU), École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-École Nationale d'Ingénieurs de Brest (ENIB)-Université de Bretagne Sud (UBS)-Université de Brest (UBO)-École Nationale Supérieure de Techniques Avancées Bretagne (ENSTA Bretagne)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique (IMT Atlantique), Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Muséum national d'Histoire naturelle (MNHN)-Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut Pierre-Simon-Laplace (IPSL (FR_636)), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-École polytechnique (X)-Centre National d'Études Spatiales [Toulouse] (CNES)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), National Research Foundation [South Africa] (NRF), Institut National de la Recherche Agronomique (INRA)-La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), and Universidade do Porto = University of Porto
Subjects: 0106 biological sciences, 010504 meteorology & atmospheric sciences, lcsh:QH1-199.5, Home range, [SDV]Life Sciences [q-bio], Big data, Ocean Engineering, Aquatic Science, lcsh:General. Including nature conservation, geographical distribution, movement analysis, Oceanography, 01 natural sciences, [INFO.INFO-NI]Computer Science [cs]/Networking and Internet Architecture [cs.NI], Telemetry, Ecosystem, SDG 14 - Life Below Water, 14. Life underwater, Animal telemetry, lcsh:Science, Animal movement, ComputingMilieux_MISCELLANEOUS, 0105 earth and related environmental sciences, Water Science and Technology, Remote sensing, Abiotic component, Global and Planetary Change, geography, ocean observing, geography.geographical_feature_category, business.industry, Continental shelf, 010604 marine biology & hydrobiology, [SDV.BA]Life Sciences [q-bio]/Animal biology, EOV, Sampling (statistics), animal movement, Habitat, 13. Climate action, [SDE]Environmental Sciences, Environmental science, lcsh:Q, business, animal telemetry
Abstract: International audience; Animal telemetry is a powerful tool for observing marine animals and the physical environments that they inhabit, from coastal and continental shelf ecosystems to polar seas and open oceans. Satellite-linked biologgers and networks of acoustic receivers allow animals to be reliably monitored over scales of tens of meters to thousands of kilometers, giving insight into their habitat use, home range size, the phenology of migratory patterns and the biotic and abiotic factors that drive their distributions. Furthermore, physical environmental variables can be collected using animals as autonomous sampling platforms, increasing spatial and temporal coverage of global oceanographic observation systems. The use of animal telemetry, therefore, has the capacity to provide measures from a suite of essential ocean variables (EOVs) for improved monitoring of Earth's oceans. Here we outline the design features of animal telemetry systems, describe current applications and their benefits and challenges, and discuss future directions. We describe new analytical techniques that improve our ability to not only quantify animal movements but to also provide a powerful framework for comparative studies across taxa. We discuss the application of animal telemetry and its capacity to collect biotic and abiotic data, how the data collected can be incorporated into ocean observing systems, and the role these data can play in improved ocean management.
Published: 2019

23. Genetic basis of amphibian larval development along a latitudinal gradient: Gene diversity, selection and links with phenotypic variation in transcription factor C/EBP‐1

Author: María Quintela, Jacob Höglund, Alex Richter-Boix, Patrik Rödin-Mörch, Anssi Laurila, Emilien Luquet, Yvonne Meyer-Lucht, Fríða Jóhannesdóttir, Department of Ecology and Genetics [Uppsala] (EBC), Uppsala University, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE), Department of Ecology and Evolutionary Biology, Cornell University, Ecology and Genetics Research, University of Oulu, Department of Population Genetics, Institute of Marine Research (IMR) Bergen, Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology [Ithaca], Cornell University [New York], Institute of Marine Research [Bergen] (IMR), and University of Bergen (UiB)-University of Bergen (UiB)
Subjects: 0106 biological sciences, 0301 basic medicine, Ranidae, Climatic adaptation, Biology, Polymorphism, Single Nucleotide, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Negative selection, daptation, Gene Frequency, Genetics, Animals, Selection, Genetic, Allele, Codon, Gene, Alleles, Genetic Association Studies, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), Geography, climate change, Genetic Variation, 15. Life on land, Ecological genetics, life history evolution, ecological genetics, Phenotype, 030104 developmental biology, Evolutionary biology, Larva, Ectotherm, Linear Models, amphibians, Adaptation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Transcription Factors
Abstract: International audience; Ectotherm development rates often show adaptive divergence along climatic gradients, but the genetic basis for this variation is rarely studied. Here, we investigated the genetic basis for phenotypic variation in larval development in the moor frog Rana arvalis from five regions along a latitudinal gradient from Germany to northern Sweden. We focused on the C/EBP‐1 gene, a transcription factor associated with larval development time. Allele frequencies at C/EBP‐1 varied strongly among geographic regions. Overall, the distribution of alleles along the gradient was in concordance with the dual postglacial colonization routes into Scandinavia, with a large number of alleles exclusively present along the southern colonization route. Only three of 38 alleles were shared between the routes. Analysis of contemporary selection on C/EBP‐1 showed divergent selection among the regions, likely reflecting adaptation to the local environmental conditions, although this was especially strong between southern and northern regions coinciding also with lineages from different colonization routes. Overall, the C/EBP‐1 gene has historically been under purifying selection, however, two specific amino acid positions showed significant signals of positive selection. These positions showed divergence between southern and northern regions, and we suggest that they are functionally involved in the climatic adaptation of larval development. Using phenotypic data from a common garden experiment, we found evidence for specific C/EBP‐1 alleles being correlated with larval development time, suggesting a functional role in adaptation of larval development to large‐scale climatic variation. This article is protected by copyright. All rights reserved.
Published: 2019

24. Alloparental care in the sea: Brood parasitism and adoption within and between two species of coral reef Altrichthys damselfish?

Author: Giacomo Bernardi, Bruce E. Lyon, Gary C. Longo, Kimberly Tenggardjaja, Alexis M. Jackson, Nicole L. Crane, Angela L. Quiros, Juliette Tariel, Department of Ecology and Evolutionary Biology [Santa Cruz], University of California [Santa Cruz] (UCSC), University of California-University of California, Department of Ecology and Evolutionary Biology (University of California Santa Cruz), Équipe 1 - Biodiversité et Adaptation dans les Hydrosystèmes (BAH), Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés (LEHNA), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)-Centre National de la Recherche Scientifique (CNRS), Department of Biology, Cabrillo College, The Nature Conservancy, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), and Université de Lyon-Université de Lyon-École Nationale des Travaux Publics de l'État (ENTPE)
Subjects: 0106 biological sciences, 0301 basic medicine, Genotype, Offspring, Parasitism, Zoology, damselfish, Biology, 010603 evolutionary biology, 01 natural sciences, Nesting Behavior, 03 medical and health sciences, Nest, Altrichthys, Adoption, Genetics, Animals, 14. Life underwater, Damselfish, ComputingMilieux_MISCELLANEOUS, reproductive and urinary physiology, Ecology, Evolution, Behavior and Systematics, brood parasitism, Brood parasite, Parenting, Coral Reefs, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], fungi, Fishes, biology.organism_classification, Brood, 030104 developmental biology, behavior/social evolution, behavior and behavior mechanisms, Pomacentrus smithi, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Paternal care
Abstract: The evolution of parental care opens the door for the evolution of brood parasitic strategies that allow individuals to gain the benefits of parental care without paying the costs. Here we provide the first documentation for alloparental care in coral reef fish and we discuss why these patterns may reflect conspecific and interspecific brood parasitism. Species-specific barcodes revealed the existence of low levels (3.5% of all offspring) of mixed interspecific broods, mostly juvenile Amblyglyphidodon batunai and Pomacentrus smithi damselfish in Altrichthys broods. A separate analysis of conspecific parentage based on microsatellite markers revealed that mixed parentage broods are common in both species, and the genetic patterns are consistent with two different modes of conspecific brood parasitism, although further studies are required to determine the specific mechanisms responsible for these mixed parentage broods. While many broods had offspring from multiple parasites, in many cases a given brood contained only a single foreign offspring, perhaps a consequence of the movement of lone juveniles between nests. In other cases, broods contained large numbers of putative parasitic offspring from the same parents and we propose that these are more likely to be cases where parasitic adults laid a large number of eggs in the host nest than the result of movements of large numbers of offspring from a single brood after hatching. The evidence that these genetic patterns reflect adaptive brood parasitism, as well as possible costs and benefits of parasitism to hosts and parasites, are discussed.
Published: 2019

25. Active pollination drives selection for reduced pollen‐ovule ratios

Author: David M. Althoff, Wendy L. Clement, Teresa Terrazas, Atsushi Kawakita, J. Nathaniel Holland, David H. Hembry, Olle Pellmyr, Kari A. Segraves, Edward Allen Herre, Finn Kjellberg, University of Idaho [Moscow, USA], Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Smithsonian Tropical Research Institute, The University of Tokyo (UTokyo), Cornell University [New York], Department of Ecology and Evolutionary Biology, University of Arizona, Universidad Nacional Autónoma de México (UNAM), The College of New Jersey (TCNJ), Syracuse University, Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Department of Ecology and Evolutionary Biology [University of Arizona], and Universidad Nacional Autónoma de México = National Autonomous University of Mexico (UNAM)
Subjects: 0106 biological sciences, pollination, Pollination, media_common.quotation_subject, Yucca, Flowers, Plant Science, Insect, Biology, medicine.disease_cause, 010603 evolutionary biology, 01 natural sciences, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, Pollinator, Pollen, Botany, Genetics, medicine, Animals, Symbiosis, Ovule, Ecology, Evolution, Behavior and Systematics, media_common, sister-group comparisons, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Mating system, biology.organism_classification, Brood, mating systems, pollen production, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, 010606 plant biology & botany
Abstract: International audience; PREMISE: Variation in pollen-ovule ratios is thought to reflect the degree of pollen transfer efficiency—the more efficient the process, the fewer pollen grains needed. Few studies have directly examined the relationship between pollen-ovule ratio and pollen transfer efficiency. For active pollination in the pollination brood mutualisms of yuccas and yucca moths, figs and fig wasps, senita and senita moths, and leafflowers and leafflower moths, pollinators purposefully collect pollen and place it directly on the stigmatic surface of conspecific flowers. The tight coupling of insect reproductive interests with pollination of the flowers in which larvae develop ensures that pollination is highly efficient.METHODS: We used the multiple evolutionary transitions between passive pollination and more efficient active pollination to test if increased pollen transfer efficiency leads to reduced pollen-ovule ratios. We collected pollen and ovule data from a suite of plant species from each of the pollination brood mutualisms and used phylogenetically controlled tests and sister-group comparisons to examine whether the shift to active pollination resulted in reduced pollen-ovule ratios.RESULTS: Across all transitions between passive and active pollination in plants, actively pollinated plants had significantly lower pollen-ovule ratios than closely related passively pollinated taxa. Phylogenetically corrected comparisons demonstrated that actively pollinated plant species had an average 76% reduction in the pollen-ovule ratio.CONCLUSIONS: The results for active pollination systems support the general utility of pollen-ovule ratios as indicators of pollination efficiency and the central importance of pollen transfer efficiency in the evolution of pollen-ovule ratio.
Published: 2019

26. Science Advances

Author: Tiegs, Scott D., Costello, David M., Isken, Mark W., Woodward, Guy, McIntyre, Peter B., Gessner, Mark O., Chauvet, Eric, Griffiths, Natalie A., Flecker, Alex S., Acuña, Vicenç, Albariño, Ricardo, Allen, Daniel C., Alonso, Cecilia, Andino, Patricio, Arango, Clay, Aroviita, Jukka, Barbosa, Marcus V. M., Barmuta, Leon A., Baxter, Colden V., Bell, Thomas D. C., Bellinger, Brent, Boyero, Luz, Brown, Lee E., Bruder, Andreas, Bruesewitz, Denise A., Burdon, Francis J., Callisto, Marcos, Canhoto, Cristina, Capps, Krista A., Castillo, María M., Clapcott, Joanne, Colas, Fanny, Colón-Gaud, Checo, Cornut, Julien, Crespo-Pérez, Verónica, Cross, Wyatt F., Culp, Joseph M., Danger, Michael, Dangles, Olivier, de Eyto, Elvira, Derry, Alison M., Villanueva, Veronica Díaz, Douglas, Michael M., Elosegi, Arturo, Encalada, Andrea C., Entrekin, Sally, Espinosa, Rodrigo, Ethaiya, Diana, Ferreira, Verónica, Ferriol, Carmen, Flanagan, Kyla M., Fleituch, Tadeusz, Follstad Shah, Jennifer J., Frainer, André, Friberg, Nikolai, Frost, Paul C., Garcia, Erica A., García Lago, Liliana, García Soto, Pavel Ernesto, Ghate, Sudeep, Giling, Darren P., Gilmer, Alan, Gonçalves, José Francisco, Gonzales, Rosario Karina, Graça, Manuel A. S., Grace, Mike, Grossart, Hans-Peter, Guérold, François, Gulis, Vlad, Hepp, Luiz U., Higgins, Scott, Hishi, Takuo, Huddart, Joseph, Hudson, John, Imberger, Samantha, Iñiguez-Armijos, Carlos, Iwata, Tomoya, Janetski, David J., Jennings, Eleanor, Kirkwood, Andrea E., Koning, Aaron A., Kosten, Sarian, Kuehn, Kevin A., Laudon, Hjalmar, Leavitt, Peter R., Lemes da Silva, Aurea L., Leroux, Shawn J., LeRoy, Carri J., Lisi, Peter J., MacKenzie, Richard, Marcarelli, Amy M., Masese, Frank O., McKie, Brendan G., Oliveira Medeiros, Adriana, Meissner, Kristian, Miliša, Marko, Mishra, Shailendra, Miyake, Yo, Moerke, Ashley, Mombrikotb, Shorok, Mooney, Rob, Moulton, Tim, Muotka, Timo, Negishi, Junjiro N., Neres-Lima, Vinicius, Nieminen, Mika L., Nimptsch, Jorge, Ondruch, Jakub, Paavola, Riku, Pardo, Isabel, Patrick, Christopher J., Peeters, Edwin T. H. M., Pozo, Jesus, Pringle, Catherine, Prussian, Aaron, Quenta, Estefania, Quesada, Antonio, Reid, Brian, Richardson, John S., Rigosi, Anna, Rincón, José, Rîşnoveanu, Geta, Robinson, Christopher T., Rodríguez-Gallego, Lorena, Royer, Todd V., Rusak, James A., Santamans, Anna C., Selmeczy, Géza B., Simiyu, Gelas, Skuja, Agnija, Smykla, Jerzy, Sridhar, Kandikere R., Sponseller, Ryan, Stoler, Aaron, Swan, Christopher M., Szlag, David, Teixeira-de Mello, Franco, Tonkin, Jonathan D., Uusheimo, Sari, Veach, Allison M., Vilbaste, Sirje, Vought, Lena B. M., Wang, Chiao-Ping, Webster, Jackson R., Wilson, Paul B., Woelfl, Stefan, Xenopoulos, Marguerite A., Yates, Adam G., Yoshimura, Chihiro, Yule, Catherine M., Zhang, Yixin X., Zwart, Jacob A., School of Biological and Chemical Sciences, Queen Mary University of London (QMUL), Leibniz-Institut für Gewässerökologie und Binnenfischerei (IGB), Leibniz Association, Laboratoire Ecologie Fonctionnelle et Environnement (ECOLAB), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées, ICRA, Catalan Institute for Water Research, ICRA, Pontificia Universidad Catolica del Ecuador, Wetland ecology department (Seville, Espagne), Doñana biological station - CSIC (SPAIN), Swiss Federal Institute of Aquatic Science and Technology - EAWAG (SWITZERLAND), Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences – Uppsala, Sweden, Burdon, Universidade Federal de Minas Gerais [Belo Horizonte] (UFMG), Marine and environmental research centre - IMAR-CMA (Coimbra, Portugal), University of Coimbra [Portugal] (UC), GRET, Sécurité et Qualité des Produits d'Origine Végétale (SQPOV), Institut National de la Recherche Agronomique (INRA)-Avignon Université (AU), Laboratorio de Limnología [Bariloche], Instituto Nacional de Investigaciones en Biodiversidad y Medioambiente [Bariloche] (INIBIOMA-CONICET), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Comahue [Neuquén] (UNCOMA)-Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Comahue [Neuquén] (UNCOMA), Faculty of Science and Technology, University of the Basque Country, Polska Akademia Nauk (PAN), Norwegian Institute for Water Research (NIVA), Limnology of Stratified Lakes, IGB-Neuglobsow, Laboratoire Interdisciplinaire des Environnements Continentaux (LIEC), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Faculty of Agriculture, Kyushu University, University of Bath [Bath], Yamanashi University, Department of Forest Ecology and Management, Swedish University of Agricultural Sciences (SLU), University of Vienna [Vienna], University of Zagreb, VTT Information technology, Technical Research Centre of Finland, Instituto de Ciencias Marinas y Limnológicas, Universidate de Vigo, Hospital Universitario La Paz, Department of Biology, Universidad Autonoma de Madrid (UAM), Universidad del Zulia (LUZ), Department of River Ecology and Conservation, Senckenberg Research Institute and Natural History Museum Frankfurt, Gelnhausen, Germany, University of Southampton, Research Institute of New-Type Urbanization, Avignon Université (AU)-Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique - CNRS (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), Université Toulouse III - Paul Sabatier - UT3 (FRANCE), Oakland University (USA), Kent State University, Imperial College London, Cornell University, Department of Ecology and Evolutionary Biology, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Climate Change Science Institute [Oak Ridge] (CCSI), Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC-UT-Battelle, LLC, Instituto Catalán de Investigación del Agua - ICRA (SPAIN) (ICRA), Consejo Nacional de Investigaciones Científicas y Técnicas [Buenos Aires] (CONICET)-Universidad Nacional del Comahue [Neuquén] (UNCOMA), DEPARTMENT OF BIOLOGY UNIVERSITY OF OKLAHOMA NORMAN USA, Partenaires IRSTEA, Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA)-Institut national de recherche en sciences et technologies pour l'environnement et l'agriculture (IRSTEA), University of the Republic of Uruguay, Central Washington University, Finnish Environment Institute (SYKE), Federal University of Tocantins, University of Tasmania [Hobart, Australia] (UTAS), Idaho State University, Watershed Protection Department, Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), School of Geography, University of Leeds, Leeds, UK, Swiss Federal Insitute of Aquatic Science and Technology [Dübendorf] (EAWAG), Colby College, Department of Aquatic Sciences and Assessment, University of Georgia [USA], EI Colegio de la Frontera Sur (ECOSUR), Consejo Nacional de Ciencia y Tecnología [Mexico] (CONACYT), Cawthron Institute, Risques, Ecosystèmes, Vulnérabilité, Environnement, Résilience (RECOVER), Aix Marseille Université (AMU)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Georgia Southern University, University System of Georgia (USG), Pontifical Catholic University of Ecuador, Montana State University (MSU), Wilfrid Laurier University (WLU), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Polska Akademia Nauk = Polish Academy of Sciences (PAN), Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Terre et Environnement de Lorraine (OTELo), Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Universidade de Vigo, Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Department of Ecology and Evolutionary Biology [CALS], College of Agriculture and Life Sciences [Cornell University] (CALS), Cornell University [New York]-Cornell University [New York], Laboratoire Ecologie Fonctionnelle et Environnement (LEFE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Observatoire Midi-Pyrénées (OMP), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT), Pontificia Universidad Católica del Ecuador, Universidade Federal do Tocantins (UFT), University of Leeds, Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Universidad Autónoma de Madrid (UAM), and Entomology
Subjects: Aquatic Ecology and Water Quality Management, riparian zones, ORGANIC-MATTER DECOMPOSITION, Biodiversité et Ecologie, Oceanografi, hydrologi och vattenresurser, Carbon Cycle, CARBON, ekosysteemit, Oceanography, Hydrology and Water Resources, biomes, biomit, ddc:570, carbon cycle, Humans, STREAMS, Life Science, Human Activities, Riparian zones, TEMPERATURE, Institut für Biochemie und Biologie, Ecosystem, ComputingMilieux_MISCELLANEOUS, SDG 15 - Life on Land, aquatic ecosystems, Science & Technology, WIMEK, hiilen kierto, vesiekosysteemit, Aquatic Ecology, Aquatische Ecologie en Waterkwaliteitsbeheer, rivers, Multidisciplinary Sciences, ekosysteemit (ekologia), Biomonitoring, articles, Science & Technology - Other Topics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ecosystems, joet, Environmental Monitoring
Abstract: River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth’s biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented “next-generation biomonitoring” by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale. This research was supported by awards to S.D.T. from the Ecuadorian Ministry of Science [Secretaría de Educación Superior Ciencia, Tecnología e Innovación (SENESCYT)] through the PROMETEO scholar exchange program, the Oakland University Research Development Grant program, and a Huron Mountain Wildlife Foundation research grant. N.A.G. was supported by the U.S. Department of Energy’s Office of Science, Biological and Environmental Research. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725. We are grateful for open-access-publishing funds from Kresge Library at Oakland University and Queen’s University Belfast. This research was supported by awards to S.D.T. from the Ecuadorian Ministry of Science [Secretaría de Educación Superior Ciencia, Tecnología e Innovación (SENESCYT)] through the PROMETEO scholar exchange program, the Oakland University Research Development Grant program, and a Huron Mountain Wildlife Foundation research grant. N.A.G. was supported by the U.S. Department of Energy’s Office of Science, Biological and Environmental Research. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725. We are grateful for open-access-publishing funds from Kresge Library at Oakland University and Queen’s University Belfast.
Published: 2019

27. Skaar Ridge revisited: Insights into a Permian high latitude peat swamp forest ecosystem from Antarctica

Author: Harper, Carla J., Decombeix, Anne-Laure, Ryberg, Patricia, Serbet, Rudolph, Schwendemann, Andrew B, Taylor, Edith L, Department of Ecology and Evolutionary Biology, University of Kansas, University of Kansas [Lawrence] (KU), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Park University, Department of Ecology and Evolutionary Biology, university of Kansas, International Palaeontological Association, and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Permian, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2018

28. Clade diversification dynamics and the biotic and abiotic controls of speciation and extinction rates

Author: Robin Aguilée, Fanny Gascuel, Amaury Lambert, Regis Ferriere, Aguilée, Robin, Initiative d'excellence - Université Fédérale de Toulouse - - UNITI2011 - ANR-11-IDEX-0002 - IDEX - VALID, Memory in living systems: an integrated approach - - MEMOLIFE2010 - ANR-10-LABX-0054 - LABX - VALID, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre interdisciplinaire de recherche en biologie (CIRB), Labex MemoLife, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Probabilités, Statistique et Modélisation (LPSM (UMR_8001)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, International Center for Interdisciplinary and Global Environmental Studies (iGLOBES) UMI 3157 CNRS, ENS - PSL University, University of Arizona, Center for Interdisciplinary Research in Biology (Collège de France), CNRS Mission pour l’Interdisciplinarité Pépinière de site PSL 'Eco-Evo-Devo', Laboratory of Excellence 'TULIP' (PIA-10-LABX-41), Laboratory of Excellence 'MemoLife' (PIA-10-LABX-54), Partner University Fund for ENS-University of Arizona cooperation., ANR-11-IDEX-0002,UNITI,Université Fédérale de Toulouse(2011), ANR-10-LABX-0054,MEMOLIFE,Memory in living systems: an integrated approach(2010), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Probabilités, Statistiques et Modélisations (LPSM (UMR_8001)), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université de Paris (UP), Department of Ecology and Evolutionary Biology, University of Arizona, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Ecole Superieure de Physique et de Chimie Industrielles de la Ville de Paris (ESPCI Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Collège de France (CdF (institution))-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)
Subjects: Genetic Speciation, Science, Extinction, Biological, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, Article, competitive exclusion, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Computer Simulation, lcsh:Science, hybridization, landscape dynamics, Phylogeny, macroevolution, Geography, genetic incompatibilities, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], geographic isolation, Biodiversity, diversity dependence, lcsh:Q, extinction rate, adaptive radiation, speciation rate, individual-based model
Abstract: How ecological interactions, genetic processes, and environmental variability jointly shape the evolution of species diversity remains a challenging problem in biology. We developed an individual-based model of clade diversification to predict macroevolutionary dynamics when resource competition, genetic differentiation, and landscape fluctuations interact. Diversification begins with a phase of geographic adaptive radiation. Extinction rates rise sharply at the onset of the next phase. In this phase of niche self-structuring, speciation and extinction processes, albeit driven by biotic mechanisms (competition and hybridization), have essentially constant rates, determined primarily by the abiotic pace of landscape dynamics. The final phase of diversification begins when intense competition prevents dispersing individuals from establishing new populations. Species’ ranges shrink, causing negative diversity-dependence of speciation rates. These results show how ecological and microevolutionary processes shape macroevolutionary dynamics and rates; they caution against the notion of ecological limits to diversity, and suggest new directions for the phylogenetic analysis of diversification., The history and patterns of species diversity are shaped by a variety of ecological and evolutionary factors. Here, the authors develop a computational model to predict clade diversification dynamics and rates of speciation and extinction under the influences of resource competition, genetic differentiation, and random landscape fluctuation.
Published: 2018

29. Under pressure? Epicormic shoots and traumatic growth zones in high-latitude Triassic trees from East Antarctica

Author: Anne-Laure Decombeix, Rudolph Serbet, Edith L. Taylor, Department of Ecology and Evolutionary Biology, University of Kansas, University of Kansas [Lawrence] (KU), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Department of Ecology and Evolutionary Biology
Subjects: 0106 biological sciences, 010506 paleontology, growth, Growing season, Antarctic Regions, Plant Science, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Latitude, Trees, epicormics, Paleontology, gymnosperm, [SDV.EE.ECO]Life Sciences [q-bio]/Ecology, environment/Ecosystems, Forest ecology, Mesozoic, Ecosystem, History, Ancient, 0105 earth and related environmental sciences, fossil, Plant Stems, Fossils, frost ring, fungi, high latitude, Original Articles, 15. Life on land, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Fremouw Formation, Triassic, Taxon, Epicormic shoot, Habitat, Antarctica, Anatomy, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Plant Shoots, Tree, wood
Abstract: International audience; Background and Aims: Investigating the biology of trees that were growing at high latitudes during warmer geological periods is key to understanding the functioning of both past and future forest ecosystems. The aim of this study is to report the first co-occurrence of epicormic shoots and traumatic growth zones in fossil trees from the Triassic of Antarctica and to discuss their biological and environmental implications.Methods : Permineralized woods bearing scars of epicormic shoots were collected from the Triassic Fremouw Formation in Gordon Valley, Central Transantarctic Mountains, Antarctica in 2010. Samples from different portions of three specimens were prepared using standard thin section and hydrofluoric (HF) acid peel techniques, and anatomical details were studied in transmitted light.Key Results: The fossil woods represent the outer part of trunks, with at least 40 growth rings that are 0.2–4.8 mm in width. Anatomical comparisons suggest that they represent a new tree taxon for the Triassic of Antarctica. Numerous small epicormic shoots can be seen crossing the wood almost horizontally and are locally branched. Each specimen also contains several occurrences of traumatic growth zones located in the early wood, in the cells produced either at the very start of the growing season or slightly later.Conclusions: This is the first report of epicormic shoots and traumatic growth zones in the wood of a Triassic tree from Antarctica. Their co-occurrence indicates that these trees from Gordon Valley were subjected to environmental stresses not seen in Triassic trees previously described from this region. This suggests that they had a different biology and/or were growing in a different habitat, which offers a new glimpse into the diversity of high-latitude trees in the Triassic greenhouse climate.
Published: 2018

30. Mapping local and global variability in plant trait distributions

Author: Fernando Valladares, Thomas Hickler, Benjamin Blonder, Kirk R. Wythers, Peter B. Reich, Kerry A. Brown, Ethan E. Butler, Andrés González-Melo, Enio E. Sosinski, Vanessa Minden, Nicolas Gross, Josep Peñuelas, Peter M. van Bodegom, Steven Jansen, Daniel C. Laughlin, Yusuke Onoda, Giandiego Campetella, Nathan J. B. Kraft, Bruno Enrico Leone Cerabolini, Ming Chen, Patrick Meir, Peter E. Thornton, Farideh Fazayeli, Tomas F. Domingues, Lawren Sack, Bernard Amiaud, Sandra Díaz, Dylan Craven, Ben Bond-Lamberty, Quentin D. Read, Ülo Niinemets, Gerhard Boenisch, Habacuc Flores-Moreno, Franciska T. de Vries, Chaeho Byun, Christian Wirth, Abhirup Datta, Marko J. Spasojevic, Koen Kramer, Brandon S. Schamp, Wenxuan Han, Arindam Banerjee, Joseph M. Craine, Mathew Williams, Jens Kattge, Nadejda A. Soudzilovskaia, Wesley N. Hattingh, Johannes H. C. Cornelissen, Estelle Forey, Owen K. Atkin, Hiroko Kurokawa, Department of Forest Resources, University of Minnesota, St. Paul, MN, USA, Department of Biostatistics [Baltimore], Johns Hopkins University (JHU), University of Minnesota [Twin Cities] (UMN), University of Minnesota System, Guangzhou Institute of Geochemistry, Chinese Academy of Sciences [Beijing] (CAS), University of Minnesota, Department of Computer Science and Engineering, Australian National University (ANU), German Centre for Integrative Biodiversity Research, Ecologie et Ecophysiologie Forestières [devient SILVA en 2018] (EEF), Institut National de la Recherche Agronomique (INRA)-Université de Lorraine (UL), Environmental Change Institute, University of Oxford, Oxford, UK, Max Planck Institute for Biogeochemistry (MPI-BGC), Max-Planck-Gesellschaft, Joint Global Change Research Institute, University Research Court, Department of Geography and Geology, Kingston University, Kingston upon Thames, UK, Seoul National University [Seoul] (SNU), University of Camerino, Department of Theoretical and Applied Sciences [Insubria], University of Insubria, Varese, Jonah Ventures, School of Earth and Environmental Sciences [Manchester] (SEES), University of Manchester [Manchester], Insituto Multidisciplinario de Biologia Vegetal, Universidad Nacional de Córdoba [Argentina], Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Étude et compréhension de la biodiversité (ECODIV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Centre d'Études Biologiques de Chizé - UMR 7372 (CEBC), Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre d'Etudes Biologiques de Chizé [France] (USC 1339 INRA), Institut National de la Recherche Agronomique (INRA), College of Resources and Environmental Sciences, Ministry of Agriculture, Key Laboratory of Arable Land Conservation (North China), China Agricultural University (CAU), Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences [Changchun Branch] (CAS), School of Animal, Plant & Environmental Sciences, University of the Witwatersrand [Johannesburg] (WITS), Department of Physical Geography and Ecosystem Science [Lund], Lund University [Lund], Universität Ulm - Ulm University [Ulm, Allemagne], Alterra - Green World Research, Wageningen University and Research [Wageningen] (WUR), Department of Ecology and Evolutionary Biology, University of California, Los Angeles, California, Tohoku University [Sendai], Department of Botany, University of Wyoming, Laramie, WY, USA, University of Wyoming, Laramie, Research School of Biology, Institute of Biology and Environmental Science, Carl von Ossietzky University Oldenburg, Kyoto University [Kyoto], Global Ecology Unit CREAF-CEAB-CSIC, Universitat Autònoma de Barcelona (UAB), Department of Forestry, Michigan State University, East Lansing, Department of Ecology and Evolutionary Biology, University of California, Department of Biology, Algoma University, Marie, OA, Canada, Algoma University, Institute of Environmental Sciences [Leiden] (CML), Leiden University, Laboratorio de Planejamento Ambiental, Oak Ridge National Laboratory [Oak Ridge] (ORNL), UT-Battelle, LLC, Climate Change Science Institute [Oak Ridge] (CCSI), UT-Battelle, LLC-UT-Battelle, LLC, Escuela Superior de Ciencias Experimentales y Tecnológicas, Departamento de Biología y Geología, Universidad Rey Juan Carlos [Madrid] (URJC), School of Geosciences [Edinburgh], University of Edinburgh, Department of Systematic Botany and Functional Biodiversity, Universität Leipzig [Leipzig], Department of Forest Resources, University of Minnesota System-University of Minnesota System, European Project: 609398,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,AGREENSKILLSPLUS(2014), Biology, Butler, Ethan E., Datta, Abhirup, Systems Ecology, Environmental Change Institute, University of Oxford, Università degli Studi di Camerino = University of Camerino (UNICAM), Universitá degli Studi dell’Insubria = University of Insubria [Varese] (Uninsubria), Institut National de la Recherche Agronomique (INRA)-La Rochelle Université (ULR)-Centre National de la Recherche Scientifique (CNRS), Kyoto University, University of California (UC), Universiteit Leiden, Universität Leipzig, INRA - CEBC, Institut National de la Recherche Agronomique (INRA)-Université de La Rochelle (ULR)-Centre National de la Recherche Scientifique (CNRS), Wageningen University and Research Centre [Wageningen] (WUR), Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Universitat Autònoma de Barcelona [Barcelona] (UAB), University of Minnesota [Twin Cities], Department of Energy (US), National Science Foundation (US), University of Minnesota, European Commission, Natural Environment Research Council (UK), Generalitat de Catalunya, Wageningen University and Research Centre, National Natural Science Foundation of China, and Australian Research Council
Subjects: 0106 biological sciences, Bayes theorem, Data base, 010504 meteorology & atmospheric sciences, Biodiversité et Ecologie, répartition territoriale, échelle globale, statistique spatiale, 01 natural sciences, Filosofie, spatial statistics, Leaf area, Bayes' theorem, Models, échelle locale, ComputingMilieux_MISCELLANEOUS, Priority journal, 2. Zero hunger, changement climatique, Multidisciplinary, Geography, Phosphorus, Vegetation, Plants, Statistical, PE&RC, global, Bayesian modeling, Climate, Global, Plant traits, Spatial statistics, PNAS Plus, [SDE]Environmental Sciences, Trait, Centre for Crop Systems Analysis, Statistical model, Cartography, CIENCIAS NATURALES Y EXACTAS, Nitrogen, Otras Ciencias Biológicas, Bayesian probability, plant traits, climate, Quantitative trait locus, Environment, 010603 evolutionary biology, Article, Ciencias Biológicas, Biodiversity and Ecology, Quantitative Trait, Quantitative Trait, Heritable, Spatial analysis, Heritable, Ecosystem, 0105 earth and related environmental sciences, Spatial Analysis, Models, Statistical, Plant Dispersal, diversité végétale fonctionnelle, Leaf litter, Plant, 15. Life on land, Nonhuman, modèle bayésien, Philosophy, Evergreen, 13. Climate action, Concentration (parameters), Prediction, Scale (map), Bayesian modelling, Model
Abstract: Our ability to understand and predict the response of ecosystems to a changing environment depends on quantifying vegetation functional diversity. However, representing this diversity at the global scale is challenging. Typically, in Earth system models, characterization of plant diversity has been limited to grouping related species into plant functional types (PFTs), with all trait variation in a PFT collapsed into a single mean value that is applied globally. Using the largest global plant trait database and state of the art Bayesian modeling, we created fine-grained global maps of plant trait distributions that can be applied to Earth system models. Focusing on a set of plant traits closely coupled to photosynthesis and foliar respiration—specific leaf area (SLA) and dry mass-based concentrations of leaf nitrogen (Nm) and phosphorus (Pm), we characterize how traits vary within and among over 50,000 ∼50×50-km cells across the entire vegetated land surface. We do this in several ways—without defining the PFT of each grid cell and using 4 or 14 PFTs; each model’s predictions are evaluated against out-of-sample data. This endeavor advances prior trait mapping by generating global maps that preserve variability across scales by using modern Bayesian spatial statistical modeling in combination with a database over three times larger than that in previous analyses. Our maps reveal that the most diverse grid cells possess trait variability close to the range of global PFT means., This research was supported as part of the Energy Exascale Earth System Model (E3SM) project, funded by the US Department of Energy, Office of Science, Office of Biological and Environmental Research (Grant DE-SC0012677 to P.B.R. and A.B.). O.K.A. acknowledges the support of the Australian Research Council (CE140100008). This research was also funded by programs from the NSF Long-Term Ecological Research (Grant DEB-1234162) and Long-Term Research in Environmental Biology (Grant DEB-1242531). A.B., F.F., and P.B.R. acknowledge funding from NSF Grant IIS-1563950. P.B.R. also acknowledges support from two University of Minnesota Institute on the Environment discovery grants. This study has been supported by the TRY initiative on plant traits (www.try-db.org). The TRY database is hosted at the Max Planck Institute for Biogeochemistry (Jena, Germany) and supported by DIVERSITAS/Future Earth, the German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, and the EU H2020 project BACI (Grant 640176). B.B. acknowledges a Natural Environment Research Council (NERC) independent research fellowship NE/M019160/1. J.P. acknowledges the financial support from the European Research Council Synergy Grant ERC-SyG-2013-610028 IMBALANCE-P, the Spanish Government Grant CGL2013-48074-P, and the Catalan Government Grant SGR 2014-274. B.B.-L. was supported by the Earth System Modeling program of the US Department of Energy, Office of Science, Office of Biological and Environmental Research. K.K. acknowledges the contribution of the Wageningen University and Research Investment theme Resilience for the project Resilient Forest (KB-29-009-003). P.M. acknowledges support from ARC Grant FT110100457 and NERC Grant NE/F002149/1. W.H. acknowledges support from the National Natural Science Foundation of China (Grant 41473068) and the “Light of West China” Program of the Chinese Academy of Sciences.
Published: 2017

31. Connecting genomic patterns of local adaptation and niche suitability in teosintes

Author: Brandon S. Gaut, Luis E. Eguiarte, Maud I. Tenaillon, Jonás A. Aguirre-Liguori, J. P. Jaramillo-Correa, Valeria Souza, Alejandra Vázquez-Lobo, Salvador Montes-Hernández, Departamento de Ecologia Evolutiva, Instituto de Ecologıa, Universidad Nacional Autónoma de México (UNAM), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Centro de Investigacion en Biodiversidad y Conservacion, Universidad Autonoma del Estado de Morelos (UAEM), Department of Ecology and Evolutionary Biology [Irvine], University of California [Irvine] (UCI), University of California-University of California, Campo Experimental Bajıo, Instituto Nacional de Investigaciones Forestales, Agricolas y Pecuarias [Mexico] (INIFAP), CONACYT-ANUIES 207571 (SEP-CONACYT-ANUIES-ECOS Nord France), Department of Ecology and Evolutionary Biology, and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, Climate, [SDV]Life Sciences [q-bio], Population, Niche, Biology, Polymorphism, Single Nucleotide, Zea mays, Ecological speciation, 03 medical and health sciences, central abundance hypothesis, Genetic variation, Genetics, ecological speciation, education, Ecology, Evolution, Behavior and Systematics, Ecosystem, Local adaptation, 2. Zero hunger, Ecological niche, Genetic diversity, education.field_of_study, Geography, Ecology, Genetic Variation, Cline (biology), 15. Life on land, Adaptation, Physiological, 030104 developmental biology, niche centroid, Linear Models, Genome, Plant, conditional neutrality, local adaptation
Abstract: The central abundance hypothesis predicts that local adaptation is a function of the distance to the centre of a species' geographic range. To test this hypothesis, we gathered genomic diversity data from 49 populations, 646 individuals and 33,464 SNPs of two wild relatives of maize, the teosintes Zea mays ssp. parviglumis and Zea. mays. ssp. mexicana. We examined the association between the distance to their climatic and geographic centroids and the enrichment of SNPs bearing signals of adaptation. We identified candidate adaptive SNPs in each population by combining neutrality tests and cline analyses. By applying linear regression models, we found that the number of candidate SNPs is positively associated with niche suitability, while genetic diversity is reduced at the limits of the geographic distribution. Our results suggest that overall, populations located at the limit of the species' niches are adapting locally. We argue that local adaptation to this limit could initiate ecological speciation processes and facilitate adaptation to global change.
Published: 2017

32. The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Author: BADOUIN, Hélène, Gouzy, Jerome, GRASSA, Christopher, Murat, Florent, Staton, S Evan, Cottret, Ludovic, Lelandais-briere, Christine, Owens, Gregory L, Carrere, Sebastien, mayjonade, Baptiste, Legrand, Ludovic, Gill, Navdeep, Kane, Nolan C, Bowers, John E, Hubner, Sariel, Bellec, Arnaud, Berard, Aurélie, Berges, Helene, BLANCHET, Nicolas, Boniface, Marie-Claude, Brunel, Dominique, Catrice, Olivier, Chaidir, Nadia, Claudel, Clotilde, Donnadieu, Cecile, Faraut, Thomas, Fievet, Ghislain, Helmstetter, Nicolas, King, Matthew, Knapp, Steven J, Lai, Zhao, Le Paslier, Marie-Christine, Lippi, Yannick, LORENZON, Lolita, Mandel, Jennifer R, Marage, Gwenola, MARCHAND, Gwenaëlle, MARQUAND, Elodie, MESTRIES, Emmanuelle, Morien, Evan, Nambeesan, Savithri, Nguyen, Thuy, Pegot - Espagnet, Prune, Pouilly, Nicolas, Raftis, Frances, Sallet, Erika, Schiex, Thomas, Thomas, Justine, Vandecasteele, Céline, Vares, Didier, Vear, Felicity, Vautrin, Sonia, Crespi, Martin, Mangin, Brigitte, Burke, John M, Salse, Jerome, Munos, Stephane, Vincourt, Patrick, Rieseberg, Loren H, Langlade, Nicolas, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Botany and Biodiversity Research Centre, University of British Columbia (UBC), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, Department of Plant Biology, Miller Plant Sciences, University of Georgia [USA], Department of Biotechnology, Tel-Hai Academic College, Galilee Research Institute (Migal), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Etude du Polymorphisme des Génomes Végétaux (EPGV), Dow AgroSciences LLC, Biogemma, GeT PlaGe, Genotoul, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT], Department of Plant Sciences, University of California, Department of Biology, Northern Arizona University [Flagstaff], Center for Genomics and Bioinformatics, Indiana University [Bloomington], Indiana University System-Indiana University System, Department of Biological Sciences, The Open University [Milton Keynes] (OU), UMR : AGroécologie, Innovations, TeRritoires, Ecole Nationale Supérieure Agronomique de Toulouse, Department of Horticulture, University of Wisconsin-Madison, The Wellcome Trust Sanger Institute [Cambridge], Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), French National Research Agency : SUNYFUEL/ANR-07-GPLA-0022, SUNRISE/ANR-11-BTBR-0005 Midi-Pyrenees Region, European Fund for Regional Development, French Fund for Competitiveness Clusters (FUI), Genoscope SystemSun project, Genome Canada, Genome BC's Applied Genomics Research in Bioproducts or Crops (ABC) Competition, NSF Plant Genome Program : DBI-082045, International Consortium for Sunflower Genomics Resources, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Tel-Hai College, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, AGroécologie, Innovations, teRritoires (AGIR), Institut National de la Recherche Agronomique (INRA)-Institut National Polytechnique (Toulouse) (Toulouse INP), ANR-07-GPLA-0022,SUNYFUEL,Improving sunflower yield and quality for biofuel production by genomics and genetics(2007), ANR-11-BTBR-0005,SUNRISE,Ressources génétiques de tournesol pour l'amélioration de la stabilité de production d'huile sous c(2011), Institut National de la Recherche Agronomique (INRA)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020]), Galilee Research Institute [Israël] (MIGAL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT), University of California (UC), Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), University of British Columbia ( UBC ), Génétique Diversité et Ecophysiologie des Céréales ( GDEC ), Université Blaise Pascal - Clermont-Ferrand 2 ( UBP ) -Institut National de la Recherche Agronomique ( INRA ), UMR 1403 Institut des Sciences des Plantes de Paris Saclay, Institut National de la Recherche Agronomique ( INRA ) -Université Paris Diderot - Paris 7 ( UPD7 ), Department of Ecology and Evolutionary Biology ( Faculty of Biology ), University of Georgia, Galilee Research Institute ( Migal ), Centre National de Ressources Génomiques Végétales ( CNRGV ), Institut National de la Recherche Agronomique ( INRA ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), GenPhySE - UMR 1388 ( Génétique Physiologie et Systèmes d'Elevage ), Institut National de la Recherche Agronomique ( INRA ) -École nationale supérieure agronomique de Toulouse [ENSAT]-ENVT, The Open University [Milton Keynes] ( OU ), University of Wisconsin-Madison [Madison], Wellcome Trust Sanger Institute, and Unité de Mathématiques et Informatique Appliquées de Toulouse ( MIAT INRA )
Subjects: [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, sunflower, Acclimatization, résistance au stress, génome végétal, Flowers, genome evolution, résilience, Evolution, Molecular, Gene Expression Regulation, Plant, Stress, Physiological, Gene Duplication, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Plant Oils, Sunflower Oil, genome, food and beverages, Genetic Variation, Genomics, Sequence Analysis, DNA, tournesol, genêtic variation, stress biotique, diversité génétique, Helianthus, Transcriptome, Genome, Plant
Abstract: The domesticated sunflower, Helianthus annuus L., is a global oil crop that has promise for climate change adaptation, because it can maintain stable yields across a wide variety of environmental conditions, including drought. Even greater resilience is achievable through the mining of resistance alleles from compatible wild sunflower relatives, including numerous extremophile species. Here we report a high-quality reference for the sunflower genome (3.6 gigabases), together with extensive transcriptomic data from vegetative and floral organs. The genome mostly consists of highly similar, related sequences and required single-molecule real-time sequencing technologies for successful assembly. Genome analyses enabled the reconstruction of the evolutionary history of the Asterids, further establishing the existence of a whole-genome triplication at the base of the Asterids II clade and a sunflower-specific whole-genome duplication around 29 million years ago. An integrative approach combining quantitative genetics, expression and diversity data permitted development of comprehensive gene networks for two major breeding traits, flowering time and oil metabolism, and revealed new candidate genes in these networks. We found that the genomic architecture of flowering time has been shaped by the most recent whole-genome duplication, which suggests that ancient paralogues can remain in the same regulatory networks for dozens of millions of years. This genome represents a cornerstone for future research programs aiming to exploit genetic diversity to improve biotic and abiotic stress resistance and oil production, while also considering agricultural constraints and human nutritional needs.
Published: 2016

33. Improving marine disease surveillance through sea temperature monitoring, outlooks and projections

Author: C. Mark Eakin, Gang Liu, Maya L. Groner, Jeffrey Maynard, C. Drew Harvell, Scott F. Heron, Andrew P. Dobson, Gareth J. Williams, Bette L. Willis, Kathleen Reardon, Ruben van Hooidonk, Jeffrey D. Shields, Robert P. Glenn, Department of Ecology and Evolutionary Biology [Ithaca], Cornell University [New York], Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Cooperative Institute for Marine and Atmospheric Studies (CIMAS), Rosenstiel School of Marine and Atmospheric Science (RSMAS), University of Miami [Coral Gables]-University of Miami [Coral Gables], NOAA Atlantic Oceanographic and Meteorological Laboratory (AOML), National Oceanic and Atmospheric Administration (NOAA), NOAA Center for Satellite Applications and Research (STAR), NOAA National Environmental Satellite, Data, and Information Service (NESDIS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), College of Marine and Environmental Sciences [Cairns], James Cook University (JCU), ARC Centre of Excellence for Coral Reef Studies (CoralCoE), School of Ocean Sciences, Bangor University, Centre for Veterinary Epidemiological Research, University of Prince Edward Island, Department of Ecology and Evolutionary Biology [Princeton], Princeton University, Coral Reef Watch, National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Environmental Satellite, Data, and Information Service (NESDIS), Marine Geophysical Laboratory, Dept. of Marine Fisheries and Resources, Marine Biology Division, Hadhramout University of Science and Technology, Department of Marine Resources (DMR), State of Maine, Virginia Institute of Marine Science (VIMS), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), and Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE)
Subjects: 0106 biological sciences, Conservation of Natural Resources, Homarus americanus, Time Factors, marine disease, Fisheries, Climate change, 010603 evolutionary biology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, medicine, Animals, Resource management, resource management, 14. Life underwater, Maine, Atlantic Ocean, Epizootic, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Disease surveillance, biology, Ecology, 010604 marine biology & hydrobiology, Temperature, predictive tools, Outbreak, American lobster, Articles, biology.organism_classification, medicine.disease, epizootic shell disease, Nephropidae, Fishery, climate change, 13. Climate action, Software deployment, Sustainability, Host-Pathogen Interactions, Seasons, General Agricultural and Biological Sciences, Research Article, Environmental Monitoring, Forecasting
Abstract: International audience; To forecast marine disease outbreaks as oceans warm requires new environmental surveillance tools. We describe an iterative process for developing these tools that combines research, development and deployment for suitable systems. The first step is to identify candidate host–pathogen systems. The 24 candidate systems we identified include sponges, corals, oysters, crustaceans, sea stars, fishes and sea grasses (among others). To illustrate the other steps, we present a case study of epizootic shell disease (ESD) in the American lobster. Increasing prevalence of ESD is a contributing factor to lobster fishery collapse in southern New England (SNE), raising concerns that disease prevalence will increase in the northern Gulf of Maine under climate change. The lowest maximum bottom temperature associated with ESD prevalence in SNE is 128C. Our seasonal outlook for 2015 and long-term projections show bottom temperatures greater than or equal to 128C may occur in this and coming years in the coastal bays of Maine. The tools presented will allow managers to target efforts to monitor the effects of ESD on fishery sustainability and will be iteratively refined. The approach and case example highlight that temperature-based surveillance tools can inform research, monitoring and management of emerging and continuing marine disease threats.
Published: 2016

34. Plankton networks driving carbon export in the oligotrophic ocean

Author: Guidi, Lionel, Brum, Jennifer R, Coelho, Luis Pedro, Espinoza, Julio Cesar Ignacio, Malviya, Shruti, Sunagawa, Shinichi, Dimier, Céline, Kandels-Lewis, Stefanie, Picheral, Marc, Poulain, Julie, Searson, Sarah, Chaffron, Samuel, Tara Oceans Consortium Coordinators, Stemmann, Lars, Not, Fabrice, Hingamp, Pascal, Speich, Sabrina, Follows, Mick, Karp-Boss, Lee, Boss, Emmanuel, Ogata, Hiroyuki, Pesant, Stephane, Bittner, Lucie, Weissenbach, Jean, Wincker, Patrick, Acinas, Silvia G, Bork, Peer, de Vargas, Colomban, Iudicone, Daniele, Sullivan, Matthew B, Raes, Jeroen, Karsenti, Eric, Bowler, Chris, Eveillard, Damien, Gorsky, Gabriel, Larhlimi, Abdelhalim, Roux, Simon, Darzi, Youssef, Audic, Stephane, Berline, Léo, Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Oceanography, University of Hawai‘i [Mānoa] (UHM), Department of Applied Biological Sciences (DBIT), Department of Microbiology and Immunology, Rega Institute, Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'Informatique de Nantes Atlantique (LINA), Mines Nantes (Mines Nantes)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen d'océanologie (MIO), Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS), Biological Oceanography Division, CSIR National Institute of Oceanography [India] (NIO), Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, Ohio State University [Columbus] (OSU), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Structural and Computational Biology, European Molecular Biology Laboratory [Heidelberg] (EMBL), Directors’ Research European Molecular Biology, Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Diversité et Interactions au sein du Plancton Océanique (DIPO), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Météorologie Dynamique (UMR 8539) (LMD), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-École polytechnique (X)-École des Ponts ParisTech (ENPC)-Centre National de la Recherche Scientifique (CNRS)-Département des Géosciences - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), School of Marine Sciences, University of Maine, Institute for Chemical Research, Kyoto University, Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Max Delbrück Centre for Molecular Medicine, Stazione Zoologica Anton Dohrn (SZN), Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J, HAL-UPMC, Gestionnaire, Department of Bio-engineering Sciences, Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Sorbonne Université (SU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Mines Nantes (Mines Nantes)-Université de Nantes (UN), Department of Ecology and Evolutionary Biology, Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Département des Géosciences - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-École des Ponts ParisTech (ENPC)-École polytechnique (X)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Kyoto University [Kyoto], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)
Subjects: 0301 basic medicine, Chlorophyll, Aquatic Organisms, 010504 meteorology & atmospheric sciences, Genes, Viral, General Science & Technology, Oceans and Seas, chemistry.chemical_element, Biology, [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, 01 natural sciences, Deep sea, Article, 03 medical and health sciences, Ecosystem, Seawater, Viral, 14. Life underwater, Photosynthesis, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 0105 earth and related environmental sciences, Total organic carbon, Marine biology, Synechococcus, Deep chlorophyll maximum, Multidisciplinary, Geography, Ecology, Tara Oceans coordinators, fungi, Bacterial, 15. Life on land, Plankton, Carbon, 030104 developmental biology, Oceanography, Genes, chemistry, 13. Climate action, Ocean color, Genes, Bacterial, Dinoflagellida, Expeditions
Abstract: Guidi, Lionel ... et al.-- 16 pages, 4 figures, supplementary information https://dx.doi.org/10.1038/nature16942 .-- This article is contribution number 34 of Tara Oceans, The biological carbon pump is the process by which CO 2 is transformed to organic carbon via photosynthesis, exported through sinking particles, and finally sequestered in the deep ocean. While the intensity of the pump correlates with plankton community composition, the underlying ecosystem structure driving the process remains largely uncharacterized. Here we use environmental and metagenomic data gathered during the Tara Oceans expedition to improve our understanding of carbon export in the oligotrophic ocean. We show that specific plankton communities, from the surface and deep chlorophyll maximum, correlate with carbon export at 150 m and highlight unexpected taxa such as Radiolaria and alveolate parasites, as well as Synechococcus and their phages, as lineages most strongly associated with carbon export in the subtropical, nutrient-depleted, oligotrophic ocean. Additionally, we show that the relative abundance of a few bacterial and viral genes can predict a significant fraction of the variability in carbon export in these regions, We thank the commitment of the following people and sponsors: CNRS (in particular Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, Fund for Scientific Research – Flanders, Rega Institute, KU Leuven, The French Ministry of Research, the French Government ‘Investissements d’Avenir’ programmes OCEANOMICS (ANR-11-BTBR-0008), FRANCE GENOMIQUE (ANR-10-INBS-09-08), MEMO LIFE (ANR-10-LABX-54), PSL* Research University (ANR-11-IDEX-0001-02), ANR (projects POSEIDON/ANR-09-BLAN-0348, PHYTBACK/ANR-2010-1709-01, PROMETHEUS/ANR-09-PCS-GENM-217, TARA-GIRUS/ANR-09-PCS-GENM-218, SAMOSA, ANR-13-ADAP-0010), European Union FP7 (MicroB3/No.287589, ERC Advanced Grant Award to C.B. (Diatomite: 294823), Gordon and Betty Moore Foundation grant (#3790 and #2631) and the UA Technology and Research Initiative Fund and the Water, Environmental, and Energy Solutions Initiative to M.B.S., the Italian Flagship Program RITMARE to D.I., the Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS to S.G.A., TANIT (CONES 2010-0036) from the Agència de Gestió d'Ajusts Universitaris i Reserca to S.G.A., JSPS KAKENHI grant number 26430184 to H.O., and FWO, BIO5, Biosphere 2 to M.B.S. We also thank the support and commitment of Agnès b. and Etienne Bourgois, the Veolia Environment Foundation, Region Bretagne, Lorient Agglomeration, World Courier, Illumina, the EDF Foundation, FRB, the Prince Albert II de Monaco Foundation, the Tara schooner and its captains and crew. We thank MERCATOR-CORIOLIS and ACRI-ST for providing daily satellite data during the expedition. We are also grateful to the French Ministry of Foreign Affairs for supporting the expedition and to the countries who graciously granted sampling permissions
Published: 2016

35. Managing marine disease emergencies in an era of rapid change

Author: Maya L. Groner, Ryan B. Carnegie, Sandy Wyllie-Echeverria, Jeffrey D. Shields, Melissa Garren, Crawford W. Revie, Ernesto Weil, Rachel T. Noble, Andrew P. Dobson, Frances M. D. Gulland, Jeffrey Maynard, Brett Froelich, C. Drew Harvell, Scott F. Heron, Carolyn S. Friedman, Raphaël Vanderstichel, Rachel Breyta, Centre for Veterinary Epidemiological Research, University of Prince Edward Island, Department of Ecology & Evolutionary Biology, University of California, Laboratoire d'Excellence CORAIL (LabEX CORAIL), Institut de Recherche pour le Développement (IRD)-Université des Antilles et de la Guyane (UAG)-École des hautes études en sciences sociales (EHESS)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de La Réunion (UR)-Université de la Polynésie Française (UPF)-Université de la Nouvelle-Calédonie (UNC)-Institut d'écologie et environnement-Université des Antilles (UA), Centre de recherches insulaires et observatoire de l'environnement (CRIOBE), Université de Perpignan Via Domitia (UPVD)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), School of Aquatic and Fishery Sciences, University of Washington [Seattle], Virginia Institute of Marine Science (VIMS), Department of Ecology and Evolutionary Biology [Princeton], Princeton University, Institute of Marine Sciences, University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), Department of Science and Environmental Policy [Monterey Bay], California State University [Monterey Bay] (CSUMB), The Marine Mammal Center, Coral Reef Watch, NOAA Center for Satellite Applications and Research (STAR), NOAA National Environmental Satellite, Data, and Information Service (NESDIS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA)-NOAA National Environmental Satellite, Data, and Information Service (NESDIS), National Oceanic and Atmospheric Administration (NOAA)-National Oceanic and Atmospheric Administration (NOAA), Marine Geophysical Laboratory, James Cook University (JCU), Department of Marine Sciences, University of Puerto Rico (UPR), Center for Marine and Environmental Studies (CMES), University of the Virgin Islands (UVI), Friday Harbor Laboratories, Department of Ecology and Evolutionary Biology, and Cornell University [New York]
Subjects: 0106 biological sciences, 0301 basic medicine, Conservation of Natural Resources, adaptive management, marine disease, response plan, Disease, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, environmental law, Animals, 14. Life underwater, Resilience (network), [SDV.EE]Life Sciences [q-bio]/Ecology, environment, Disease surveillance, Transmission (medicine), business.industry, 010604 marine biology & hydrobiology, Environmental resource management, Articles, impact mitigation, Environmental law, Adaptive management, 030104 developmental biology, 13. Climate action, Mollusca, Host-Pathogen Interactions, Disease risk, surveillance, Emergencies, General Agricultural and Biological Sciences, business, Impact mitigation, Environmental Monitoring
Abstract: International audience; Infectious marine diseases can decimate populations and are increasing among some taxa due to global change and our increasing reliance on marine environments. Marine diseases become emergencies when significant ecological, economic or social impacts occur. We can prepare for and manage these emergencies through improved surveillance, and the development and iterative refinement of approaches to mitigate disease and its impacts. Improving surveillance requires fast, accurate diagnoses, forecasting disease risk and real-time monitoring of disease-promoting environmental conditions. Diversifying impact mitigation involves increasing host resilience to disease, reducing pathogen abundance and managing environmental factors that facilitate disease. Disease surveillance and mitigation can be adaptive if informed by research advances and catalysed by communication among observers, researchers and decision-makers using information-sharing platforms. Recent increases in the awareness of the threats posed by marine diseases may lead to policy frameworks that facilitate the responses and management that marine disease emergencies require.
Published: 2016

36. Stochastic dynamics for adaptation and evolution of microorganisms

Author: Billiard, Sylvain, Collet, Pierre, Ferrière, Régis, Méléard, Sylvie, Tran, Viet Chi, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre de Physique Théorique [Palaiseau] (CPHT), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Department of Ecology and Evolutionary Biology, University of Arizona, Eco-évolution mathématique - IBENS, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Mathématiques Appliquées (CMAP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Paul Painlevé - UMR 8524 (LPP), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Chair ``Modélisation Mathématique et Biodiversité' of Veolia Environnement-Ecole Polytechnique-Museum National d'Histoire Naturelle-Fondation X., ANR-11-LABX-0007,CEMPI,Centre Européen pour les Mathématiques, la Physique et leurs Interactions(2011), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology [University of Arizona], École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Laboratoire Paul Painlevé (LPP), and V. Mehrmann and M. Skutella eds.
Subjects: [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 010102 general mathematics, Probability (math.PR), stochastic individual-based models, Populations and Evolution (q-bio.PE), interactions, 01 natural sciences, canonical equation, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], 010104 statistics & probability, bacterial conjugation, fixation probability, adaptive dynamics, large population approximation, trait substitution sequence, FOS: Biological sciences, FOS: Mathematics, horizontal gene transfer, Quantitative Biology::Populations and Evolution, 0101 mathematics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Quantitative Biology - Populations and Evolution, 92D25, 92D15, 92D30, 60J80, 60K35, 60F99, Mathematics - Probability
Abstract: International audience; We present a model for the dynamics of a population of bacteria with a continuum of traits, who compete for resources and exchange horizontally (transfer) an otherwise vertically inherited trait with possible mutations. Competition influences individual demographics, affecting population size, which feeds back on the dynamics of transfer. We consider a stochastic individual-based pure jump process taking values in the space of point measures, and whose jump events describe the individual reproduction, transfer and death mechanisms. In a large population scale, the stochastic process is proved to converge to the solution of a nonlinear integro-differential equation. When there are only two different traits and no mutation, this equation reduces to a non-standard two-dimensional dynamical system. We show how crucial the forms of the transfer rates are for the long-term behavior of its solutions. We describe the dynamics of invasion and fixation when one of the two traits is initially rare, and compute the invasion probabilities. Then, we study the process under the assumption of rare mutations. We prove that the stochastic process at the mutation time scale converges to a jump process which describes the successive invasions of successful mutants. We show that the horizontal transfer can have a major impact on the distribution of the successive mutational fixations, leading to dramatically different behaviors, from expected evolution scenarios to evolutionary suicide. Simulations are given to illustrate these phenomena.
Published: 2016
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37. Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses

Author: Simon Roux, Patrick Wincker, Marc Picheral, Alexander Loy, Silvia G. Acinas, Stephane Pesant, Bonnie T. Poulos, Julie Poulain, Jennifer R. Brum, Elena Lara, Shinichi Sunagawa, Sarah Searson, Adriana Alberti, Corinne Cruaud, Stefanie Kandels-Lewis, Peer Bork, Carlos M. Duarte, Dolors Vaqué, Josep M. Gasol, Natalie Solonenko, Céline Dimier, Bas E. Dutilh, Melissa B. Duhaime, Mathew B. Sullivan, Ohio State University [Columbus] (OSU), Universidade Federal do Rio de Janeiro (UFRJ), Theoretical Biology & Bioinformatics [Utrecht], University Medical Center [Utrecht], Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Structural and Computational Biology [Heidelberg], European Molecular Biology Laboratory [Heidelberg] (EMBL), Department of Ecology and Evolutionary Biology, University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, University of Vienna [Vienna], Austrian Polar Research Institute, Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Istituto di Scienze Marine [Venezia] (ISMAR-CNR), Istituto di Science Marine (ISMAR ), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR)-National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), Institut de Génomique d'Evry (IG), Université Paris-Saclay-Institut de Biologie François JACOB (JACOB), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Data Publisher for Earth and Environmental Science (PANGAEA), University of Bremen, Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), King Abdullah University of Science and Technology (KAUST), Max Delbrück Centre for Molecular Medicine, Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Department of Civil, Environmental and Geodetic Engineering [Columbus], Consiglio Nazionale delle Ricerche (CNR)-Consiglio Nazionale delle Ricerche (CNR), Institut de Biologie François JACOB (JACOB), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay, Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), National Science Foundation (US), Gordon and Betty Moore Foundation, Ministére de l'Education Nationale de la Recherche et de la Technologie (France), Agence Nationale de la Recherche (France), Ecosystem Genomics Institute (US), Netherlands Organization for Scientific Research, Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Brasil), Austrian Science Fund, HAL-UPMC, Gestionnaire, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)
Subjects: 0301 basic medicine, Water microbiology, Genes, Viral, Mesopelagic zone, viruses, Datasets as Topic, Geographic Mapping, [SDU.STU.OC] Sciences of the Universe [physics]/Earth Sciences/Oceanography, Genome, Tumours of the digestive tract Radboud Institute for Molecular Life Sciences [Radboudumc 14], Trophic level, [SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Marine biology, education.field_of_study, Multidisciplinary, Ecology, Nitrogen Cycle, 3. Good health, Viruses, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Expeditions, Oceans and Seas, 030106 microbiology, Population, Coronacrisis-Taverne, Phage biology, Genome, Viral, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Biology, 03 medical and health sciences, SIGNAL-TRANSDUCTION PROTEINS, DE-NOVO ASSEMBLER, MICROBIAL COMMUNITIES, PHYLOGENETIC TREES, GENOME SEQUENCES, INTERACTIVE TREE, SULFUR OXIDATION, MARINE VIRUSES, PHAGE, BACTERIOPHAGE, Seawater, Ecosystem, Human virome, 14. Life underwater, education, Microbial biooceanography, [SDU.STU.OC]Sciences of the Universe [physics]/Earth Sciences/Oceanography, 15. Life on land, 030104 developmental biology, 13. Climate action, Metagenomics, DNA, Viral, Metagenome, Sulfur, [SDV.BID] Life Sciences [q-bio]/Biodiversity
Abstract: Roux, Simon ... et al.-- 5 pages, 3 figures, supporting information https://dx.doi.org/10.1038/nature19366, Ocean microbes drive biogeochemical cycling on a global scale1. However, this cycling is constrained by viruses that affect community composition, metabolic activity, and evolutionary trajectories2, 3. Owing to challenges with the sampling and cultivation of viruses, genome-level viral diversity remains poorly described and grossly understudied, with less than 1% of observed surface-ocean viruses known4. Here we assemble complete genomes and large genomic fragments from both surface- and deep-ocean viruses sampled during the Tara Oceans and Malaspina research expeditions5, 6, and analyse the resulting ‘global ocean virome’ dataset to present a global map of abundant, double-stranded DNA viruses complete with genomic and ecological contexts. A total of 15,222 epipelagic and mesopelagic viral populations were identified, comprising 867 viral clusters (defined as approximately genus-level groups7, 8). This roughly triples the number of known ocean viral populations4 and doubles the number of candidate bacterial and archaeal virus genera8, providing a near-complete sampling of epipelagic communities at both the population and viral-cluster level. We found that 38 of the 867 viral clusters were locally or globally abundant, together accounting for nearly half of the viral populations in any global ocean virome sample. While two-thirds of these clusters represent newly described viruses lacking any cultivated representative, most could be computationally linked to dominant, ecologically relevant microbial hosts. Moreover, we identified 243 viral-encoded auxiliary metabolic genes, of which only 95 were previously known. Deeper analyses of four of these auxiliary metabolic genes (dsrC, soxYZ, P-II (also known as glnB) and amoC) revealed that abundant viruses may directly manipulate sulfur and nitrogen cycling throughout the epipelagic ocean. This viral catalog and functional analyses provide a necessary foundation for the meaningful integration of viruses into ecosystem models where they act as key players in nutrient cycling and trophic networks, This viral research was funded by a National Science Foundation grant (1536989) and Gordon and Betty Moore Foundation grants (3790, 2631) to M.B.S., and the French Ministry of Research and Government through the ‘Investissements d’Avenir’ program OCEANOMICS (ANR-11-BTBR-0008) and France Genomique (ANR-10-INBS-09-08). Virus researchers were partially supported by the Water, Environmental and Energy Solutions Initiative and the Ecosystem Genomics Institute (S.R.), the Netherlands Organization for Scientific Research Vidi grant 864.14.004 and CAPES/BRASIL (B.E.D.), and the Austrian Science Fund (project P25111-B22, A.L.)
Published: 2016

38. Bark anatomy of Late Permian glossopterid trees from Antarctica

Author: Thomas N. Taylor, Edith L. Taylor, Anne-Laure Decombeix, Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Department of Ecology and Evolutionary Biology, University of Kansas [Lawrence] (KU), Department of Ecology and Evolutionary Biology, university of Kansas, Department of Ecology and Evolutionary Biology, University of Kansas, and Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD [France-Sud])
Subjects: 010506 paleontology, Paleozoic, Permian, Rhytidome, Glossopteridales, [SDE.BE.PAL]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.pal, Secondary phloem, Plant Science, 010502 geochemistry & geophysics, 01 natural sciences, complex mixtures, Secondary xylem, Paleontology, Botany, [SDE.BE.EVO]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.evo, Paleobotany, Cambium, 0105 earth and related environmental sciences, geography, geography.geographical_feature_category, biology, fungi, [SDE.BE.BIOD]Environmental Sciences/Biodiversity and Ecology/domain_sde.be.biod, Forestry, High latitude, Anatomy, 15. Life on land, biology.organism_classification, Ridge, visual_art, visual_art.visual_art_medium, Bark, Phloem, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Geology
Abstract: International audience; The Glossopteridales are an extinct group of seed plants that dominated Gondwanan floras during the Permian. Their remains are found across a wide range of habitats and paleolatitudes, and it is particularly interesting to understand the anatomical characteristics that might have enabled such an extensive distribution.Here, we document for the first time the bark anatomy of high-latitude glossopteridalean trees using peels and thin sections made from a Late Permian trunk from Skaar Ridge, Antarctica. The bark is 3 cm thick. The secondary phloem is composed of sieve cells, axial and ray parenchyma, and fibers arranged in discontinuous unicellular tangential layers. The outer bark is a rhytidome, with numerous alternating layers of periderm and non-conducting secondary phloem showing some proliferation of the axial parenchyma. Successive periderms mostly run parallel to the cambium, with some longitudinal undulation and rare connections between two periderms. A similar anatomy was observed in bark fragments found isolated in the matrix or closely associated with large glossopterid stems or roots.The anatomy of the Skaar Ridge specimens shows that Antarctic Glossopteridales had a relatively thick, probably stringy bark. The retention of a significant amount of insulating dead bark tissue on the trunk likely provided protection of the cambium, conducting secondary phloem, and potential latent buds against biotic and abiotic environmental hazards (fire, frost, scalding, insects, etc.) and may have contributed to the extensive paleolatitudinal distribution of the Glossopteridales during the Permian.
Published: 2016

39. The effect of competition and horizontal trait inheritance on invasion, fixation and polymorphism

Author: Pierre Collet, Régis Ferrière, Sylvain Billiard, Viet Chi Tran, Sylvie Méléard, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Centre de Physique Théorique [Palaiseau] (CPHT), Centre National de la Recherche Scientifique (CNRS)-École polytechnique (X), Department of Ecology and Evolutionary Biology, University of Arizona, Eco-évolution mathématique - IBENS, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Mathématiques Appliquées (CMAP), Université de Versailles Saint-Quentin-en-Yvelines (UVSQ)-École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Paul Painlevé - UMR 8524 (LPP), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, Chair 'Modélisation Mathématique et Biodiversité' of Veolia Environnement-Ecole Polytechnique-Museum National d'Histoire Naturelle-Fondation X, Pépinière Interdisciplinaire CNRS-PSL 'Eco-Evo-Devo', Partner University Fund, ANR-09-BLAN-0215,MANEGE,Modèles Aléatoires eN Ecologie, Génétique et Evolution(2009), ANR-11-LABX-0007,CEMPI,Centre Européen pour les Mathématiques, la Physique et leurs Interactions(2011), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology [University of Arizona], Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Paul Painlevé (LPP), and Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS)
Subjects: 0301 basic medicine, Time Factors, Population Dynamics, fixation probability, 92D25, 92D10, 60J80, 60J75, 60F05, education.field_of_study, Applied Mathematics, Population size, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], mobile genetic elements, General Medicine, Adaptation, Physiological, Fixation (population genetics), Phenotype, Modeling and Simulation, Horizontal gene transfer, Trait, horizontal gene transfer, General Agricultural and Biological Sciences, Algorithms, Mathematics - Probability, Statistics and Probability, Competitive Behavior, Demographics, Gene Transfer, Horizontal, Population, [MATH.MATH-DS]Mathematics [math]/Dynamical Systems [math.DS], Biology, General Biochemistry, Genetics and Molecular Biology, Evolution, Molecular, 03 medical and health sciences, plasmid, FOS: Mathematics, Animals, education, Quantitative Biology - Populations and Evolution, Evolutionary theory, Ecosystem, Probability, Population Density, Stochastic Processes, Polymorphism, Genetic, General Immunology and Microbiology, Models, Genetic, Probability (math.PR), Populations and Evolution (q-bio.PE), [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], bacterial conjugation, 030104 developmental biology, Genetics, Population, Evolutionary biology, FOS: Biological sciences, [SDV.SPEE]Life Sciences [q-bio]/Santé publique et épidémiologie, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, stochastic individual-based models and their limits, [SDV.EE.IEO]Life Sciences [q-bio]/Ecology, environment/Symbiosis
Abstract: Horizontal transfer (HT) of heritable information or `traits' (carried by genetic elements, endosymbionts, or culture) is widespread among living organisms. Yet current ecological and evolutionary theory addressing HT is limited. We present a modeling framework for the dynamics of two populations that compete for resources and exchange horizontally (transfer) an otherwise vertically inherited trait. Competition influences individual demographics, affecting population size, which feeds back on the dynamics of transfer. We capture this feedback with a stochastic individual-based model, from which we derive a deterministic approximation for large populations. The interaction between horizontal transfer and competition makes possible the stable (or bi-stable) polymorphic maintenance of deleterious traits (including costly plasmids). When transfer rates are of a general density-dependent form, transfer stochasticity contributes strongly to population fluctuations. For an initially rare trait, we describe the probabilistic dynamics of invasion and fixation. Acceleration of fixation by HT is faster when competition is weak in the resident population. Thus, HT can have a major impact on the distribution of mutational effects that are fixed, and our model provides a basis for a general theory of the influence of HT on eco-evolutionary dynamics and adaptation., 1 Electronic Supplementary Material
Published: 2015

40. Stochastic dynamics of adaptive trait and neutral marker driven by eco-evolutionary feedbacks

Author: Sylvain Billiard, Sylvie Méléard, Régis Ferrière, Viet Chi Tran, Génétique et évolution des populations végétales (GEPV), Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology, University of Arizona, Eco-évolution mathématique - IBENS, Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Mathématiques Appliquées - Ecole Polytechnique (CMAP), École polytechnique (X)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Paul Painlevé - UMR 8524 (LPP), Centre National de la Recherche Scientifique (CNRS)-Université de Lille, National Science Foundation Award EF-062363, Institut Universitaire de France, Chair 'Modélisation Mathématique et Biodiversité' of Veolia Environnement-Ecole Polytechnique-Museum National d'Histoire Naturelle-Fondation X, ANR MANEGE ANR-09-BLAN-0215, Labex CEMPI ANR-11-LABX-0007-01, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology [University of Arizona], École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Laboratoire Paul Painlevé (LPP), and Université de Lille-Centre National de la Recherche Scientifique (CNRS)
Subjects: Population Dynamics, Adaptation, Biological, 01 natural sciences, 010104 statistics & probability, selective sweeps, Econometrics, Feedback, Physiological, 0303 health sciences, education.field_of_study, Applied Mathematics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], hitchhiking, Biodiversity, 92D25, 60J80, 92D15, 60J75, Agricultural and Biological Sciences (miscellaneous), Substitution Fleming-Viot Process, limit theorems for multi-scale processes, Modeling and Simulation, Mutation (genetic algorithm), Trait, Mathematics - Probability, Genetic Markers, Population, neutral diversity, Biology, Evolution, Molecular, measure-valued individual-based model, 03 medical and health sciences, FOS: Mathematics, Computer Simulation, Selection, Genetic, 0101 mathematics, Quantitative Biology - Populations and Evolution, education, Ecosystem, Selection (genetic algorithm), 030304 developmental biology, Stochastic Processes, Models, Genetic, Probability (math.PR), Populations and Evolution (q-bio.PE), Mathematical Concepts, [MATH.MATH-PR]Mathematics [math]/Probability [math.PR], Genetic hitchhiking, Genetics, Population, Mutation-selection, adaptive dynamics, FOS: Biological sciences, Mutation, Adaptation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Selective sweep, Neutral theory of molecular evolution
Abstract: How the neutral diversity is affected by selection and adaptation is investigated in an eco-evolutionary framework. In our model, we study a finite population in continuous time, where each individual is characterized by a trait under selection and a completely linked neutral marker. Population dynamics are driven by births and deaths, mutations at birth, and competition between individuals. Trait values influence ecological processes (demographic events, competition), and competition generates selection on trait variation, thus closing the eco-evolutionary feedback loop. The demographic effects of the trait are also expected to influence the generation and maintenance of neutral variation. We consider a large population limit with rare mutation, under the assumption that the neutral marker mutates faster than the trait under selection. We prove the convergence of the stochastic individual-based process to a new measure-valued diffusive process with jumps that we call Substitution Fleming-Viot Process (SFVP). When restricted to the trait space this process is the Trait Substitution Sequence first introduced by Metz et al. (1996). During the invasion of a favorable mutation, a genetical bottleneck occurs and the marker associated with this favorable mutant is hitchhiked. By rigorously analysing the hitchhiking effect and how the neutral diversity is restored afterwards, we obtain the condition for a time-scale separation; under this condition, we show that the marker distribution is approximated by a Fleming-Viot distribution between two trait substitutions. We discuss the implications of the SFVP for our understanding of the dynamics of neutral variation under eco-evolutionary feedbacks and illustrate the main phenomena with simulations. Our results highlight the joint importance of mutations, ecological parameters, and trait values in the restoration of neutral diversity after a selective sweep., 29 pages
Published: 2015

41. Subspecific origin and haplotype diversity in the laboratory mouse

Author: Pierre Boursot, Priscilla K. Tucker, John P. Didion, Alex Hon Tsen Yu, Jaroslav Piálek, Franãois Bonhomme, Ryan J. Buus, Michael W. Nachman, Leonard McMillan, Catherine E. Welsh, Jeremy Wang, Timothy A. Bell, Gary A. Churchill, Hyuna Yang, Fernando Pardo-Manuel de Villena, The Jackson Laboratory [Bar Harbor] (JAX), Department of Computer Sciences, University of North Carolina at Chapel Hill (UNC), Department of Genetics, Lineberger Comprehensive Cancer Center (UNC Lineberger), University of North Carolina [Chapel Hill] (UNC), University of North Carolina System (UNC)-University of North Carolina System (UNC), Carolina Center for Genome Sciences, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Institute of Zoology, National Taiwan University [Taiwan] (NTU), Department of Ecology and Evolutionary Biology, University of Arizona, institute of vertebrate zoology, Czech Academy of Sciences [Prague] (CAS), University of Michigan [Ann Arbor], University of Michigan System-University of Michigan System, University of North Carolina System (UNC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), and Department of Ecology and Evolutionary Biology [University of Arizona]
Subjects: Genotype, Genetic Speciation, Molecular Sequence Data, Introgression, Mice, Inbred Strains, Subspecies, Biology, Polymorphism, Single Nucleotide, Identity by descent, Article, Mice, 03 medical and health sciences, 0302 clinical medicine, Species Specificity, Inbred strain, Genetics, Animals, Phylogeny, 030304 developmental biology, 0303 health sciences, Genetic diversity, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Phylogenetic tree, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Haplotype, Laboratory mouse, Chromosome Mapping, Genetic Variation, Chromosomes, Mammalian, Haplotypes, Evolutionary biology, 030217 neurology & neurosurgery
Abstract: Here we provide a genome-wide, high-resolution map of the phylogenetic origin of the genome of most extant laboratory mouse inbred strains. Our analysis is based on the genotypes of wild-caught mice from three subspecies of Mus musculus. We show that classical laboratory strains are derived from a few fancy mice with limited haplotype diversity. Their genomes are overwhelmingly Mus musculus domesticus in origin, and the remainder is mostly of Japanese origin. We generated genome-wide haplotype maps based on identity by descent from fancy mice and show that classical inbred strains have limited and non-randomly distributed genetic diversity. In contrast, wild-derived laboratory strains represent a broad sampling of diversity within M. musculus. Intersubspecific introgression is pervasive in these strains, and contamination by laboratory stocks has played a role in this process. The subspecific origin, haplotype diversity and identity by descent maps can be visualized using the Mouse Phylogeny Viewer (see URLs).
Published: 2011

42. Anatomy and affinities of permineralized gymnospermous trunks with preserved bark from the Middle Triassic of Antarctica

Author: Thomas N. Taylor, Edith L. Taylor, Anne-Laure Decombeix, Department of Ecology and Evolutionary Biology, University of Kansas, University of Kansas [Lawrence] (KU), and Department of Ecology and Evolutionary Biology, university of Kansas
Subjects: 0106 biological sciences, 010506 paleontology, biology, Paleontology, Plant anatomy, Anatomy, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, 15. Life on land, biology.organism_classification, Fremouw Formation, 010603 evolutionary biology, 01 natural sciences, Sclereid, Gymnosperm, Genus, visual_art, Botany, visual_art.visual_art_medium, Pith, Bark, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Ecology, Evolution, Behavior and Systematics, Dicroidium, 0105 earth and related environmental sciences
Abstract: International audience; Permineralized gymnosperm axes with pycnoxylic wood from the Middle Triassic Fremouw Formation of the Central Transantarctic Mountains, Antarctica, are assigned to the corystosperms (seed ferns) and conifers. Both groups have been previously described from this formation based on juvenile stems with attached leaf bases and decorticated trunks. Here we describe large axes with preserved bark from the Fremouw Peak permineralized peat locality. The specimens are characterized by a small parenchymatous pith with clusters of sclereids, a thick cylinder (> 10 cm) of pycnoxylic wood, and 1-2 cm of bark containing distinctive clusters of sclereids and a complex system of cortical vascular bundles. Comparison with axes previously described from the Middle Triassic of Antarctica shows that the new specimens are most similar to Kykloxylon, a corystosperm genus based on young stems bearing Dicroidium leaves, and with a portion of axis previously described as Rhexoxylon like. We suggest that both the new specimens and the Rhexoxylon-like axis represent proximal parts of a Dicroidium/Kykloxylon plant that possibly had a fluted trunk base, and we discuss the problem of delimiting features in corystosperm axes.
Published: 2010

43. Secondary Growth in Vertebraria Roots from the Late Permian of Antarctica: A Change in Developmental Timing

Author: Thomas N. Taylor, Edith L. Taylor, Anne-Laure Decombeix, Department of Ecology and Evolutionary Biology, University of Kansas, University of Kansas [Lawrence] (KU), and Department of Ecology and Evolutionary Biology, university of Kansas
Subjects: 010506 paleontology, Permian, biology, Secondary growth, fungi, Plant Science, Anatomy, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, 010502 geochemistry & geophysics, biology.organism_classification, 01 natural sciences, Developmental timing, Botany, Vascular cambium, Glossopteridales, Phloem, Cambium, [SDU.STU.PG]Sciences of the Universe [physics]/Earth Sciences/Paleontology, Ecology, Evolution, Behavior and Systematics, Vascular tissue, 0105 earth and related environmental sciences
Abstract: International audience; Permineralized Vertebraria roots from the late Permian of the Central Transantarctic Mountains, Antarctica, are investigated to understand the unusual vascular anatomy of the genus. The specimens range from ;1mm to several centimeters in diameter and illustrate all the stages of secondary growth. Our observations confirm previous hypotheses on the development of these roots and suggest that their unique anatomy is the result of a change in developmental timing. Vertebraria is characterized by a vascular cambium that remains discontinuous through several growth seasons, leading to the formation of lacunae alternating in cross section with wedges of secondary vascular tissues. The bifacial nature of the cambium is confirmed by the presence of well-developed secondary phloem composed of longitudinally elongated cells and uniseriate parenchymatous rays. In some of the largest specimens, a continuous vascular cylinder is formed by the differentiation of cambium from parenchymatous cells bordering the lacunae. The new specimens provide additional information on the secondary xylem anatomy and vascular connection to lateral roots.
Published: 2009

44. Globally invariant metabolism but density-diversity mismatch in springtails

Author: Anton M. Potapov, Carlos A. Guerra, Johan van den Hoogen, Anatoly Babenko, Bruno C. Bellini, Matty P. Berg, Steven L. Chown, Louis Deharveng, Ľubomír Kováč, Natalia A. Kuznetsova, Jean-François Ponge, Mikhail B. Potapov, David J. Russell, Douglas Alexandre, Juha M. Alatalo, Javier I. Arbea, Ipsa Bandyopadhyaya, Verónica Bernava, Stef Bokhorst, Thomas Bolger, Gabriela Castaño-Meneses, Matthieu Chauvat, Ting-Wen Chen, Mathilde Chomel, Aimee T. Classen, Jerome Cortet, Peter Čuchta, Ana Manuela de la Pedrosa, Susana S. D. Ferreira, Cristina Fiera, Juliane Filser, Oscar Franken, Saori Fujii, Essivi Gagnon Koudji, Meixiang Gao, Benoit Gendreau-Berthiaume, Diego F. Gomez-Pamies, Michelle Greve, I. Tanya Handa, Charlène Heiniger, Martin Holmstrup, Pablo Homet, Mari Ivask, Charlene Janion-Scheepers, Malte Jochum, Sophie Joimel, Bruna Claudia S. Jorge, Edite Jucevica, Olga Ferlian, Luís Carlos Iuñes de Oliveira Filho, Osmar Klauberg-Filho, Dilmar Baretta, Eveline J. Krab, Annely Kuu, Estevam C. A. de Lima, Dunmei Lin, Zoe Lindo, Amy Liu, Jing-Zhong Lu, María José Luciañez, Michael T. Marx, Matthew A. McCary, Maria A. Minor, Taizo Nakamori, Ilaria Negri, Raúl Ochoa-Hueso, José G. Palacios-Vargas, Melanie M. Pollierer, Pascal Querner, Natália Raschmanová, Muhammad Imtiaz Rashid, Laura J. Raymond-Léonard, Laurent Rousseau, Ruslan A. Saifutdinov, Sandrine Salmon, Emma J. Sayer, Nicole Scheunemann, Cornelia Scholz, Julia Seeber, Yulia B. Shveenkova, Sophya K. Stebaeva, Maria Sterzynska, Xin Sun, Winda I. Susanti, Anastasia A. Taskaeva, Madhav P. Thakur, Maria A. Tsiafouli, Matthew S. Turnbull, Mthokozisi N. Twala, Alexei V. Uvarov, Lisa A. Venier, Lina A. Widenfalk, Bruna R. Winck, Daniel Winkler, Donghui Wu, Zhijing Xie, Rui Yin, Douglas Zeppelini, Thomas W. Crowther, Nico Eisenhauer, Stefan Scheu, Johann-Friedrich Blumenbach Institut für Zoologie und Anthropologie, Georg-August-University = Georg-August-Universität Göttingen, A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences [Moscow] (RAS), German Centre for Integrative Biodiversity Research (iDiv), Institute of Biology, Leipzig University, Leipzig, Germany, Department of Environmental Systems Science [ETH Zürich] (D-USYS), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Department of Botany and Zoology, Biosciences Center, Federal University of Rio Grande do Norte (UFRGS), Systems Ecology, Department of Ecological Science, Vrije Universiteit, Amsterdam, The Netherlands, Community and Conservation Ecology Group [Groningen], Université de Groningen, Securing Antarctica’s Environmental Future, School of Biological Sciences, Monash University, Institut de Systématique, Evolution, Biodiversité (ISYEB ), Muséum national d'Histoire naturelle (MNHN)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Université des Antilles (UA), Department of Zoology, Institute of Biology and Ecology, Faculty of Science, Pavol Jozef Šafárik University in Košice, Košice, Slovakia, Institute of Biology and Chemistry, Moscow Pedagogical State University, Moscow, Russia, Mécanismes Adaptatifs et Evolution (MECADEV), Muséum national d'Histoire naturelle (MNHN)-Centre National de la Recherche Scientifique (CNRS), Department of Soil Zoology, Senckenberg Society for Nature Research, Görlitz, Germany, Department of Soil Science, Centre for Agriculture and Veterinary Science, Santa Catarina State University (UDUESC Lages), Lages, SC, Brazil (UDUESC), Environmental Science Center, Qatar University, Doha, Qatar, Department of Sciences, CEPA Camargo, Astillero, Spain, Visva Bharati University, Bengal, India, Administración de Parques Nacionales, San Antonio, Argentina, School of Biology and Environmental Science - University College of Dublin, University College Dublin [Dublin] (UCD), UCD Earth Institute, University College Dublin, Unidad Multidisciplinaria de Docencia e Investigación, Facultad de Ciencias, Campus Juriquilla, Universidad Nacional Autónoma de México, Querétaro, México, Etude et Compréhension de la biodiversité (ECODIV), Université de Rouen Normandie (UNIROUEN), Normandie Université (NU)-Normandie Université (NU), Institute of Entomology [České Budějovice] (BIOLOGY CENTRE CAS), Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), FiBL France, Department of Ecology and Evolutionary Biology, Museum of Zoology, The University of Michigan Research Museums Center, Ann Arbor, Michigan 48108-2228, USA, Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Montpellier, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Montpellier (UM), Departmento de Biología Zoología, Universidad Autónoma de Madrid, Madrid, Spain, Institute of Biology Bucharest, Romanian Academy, Department of General and Theoretical Ecology, University of Bremen, University of Bremen, Conservation Ecology, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, The Netherlands, Department of Coastal Systems, Royal Netherlands Institute for Sea Research, ‘t Horntje, the Netherlands, Forestry and Forest Products Research Institute (FFPRI), Université du Québec à Montréal = University of Québec in Montréal (UQAM), Ningbo University (NBU), Université du Québec en Outaouais (UQO), Universidad Nacional de Misiones, University of Pretoria [South Africa], Geneva School of Health Sciences, HES-SO University of Applied Sciences and Arts Western Switzerland (HEdS-Ge / HES-SO), Section of Terrestrial Ecology, Department of Ecoscience, Aarhus University, Aarhus, Denmark, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Tallinn University of Technology, Tartu College, Department of Biological Sciences, University of Cape Town, Cape Town, South Africa, Department of Entomology, Iziko Museums of South Africa, Cape Town, South Africa, Ecologie fonctionnelle et écotoxicologie des agroécosystèmes (ECOSYS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Universidade Federal do Rio Grande do Sul [Porto Alegre] (UFRGS), Institute of Biology, University of Latvia, Riga, Latvia, Department of Soil Science, Centre for Agriculture and Veterinary Science, Santa Catarina State University (UDESC-Lages), Lages, SC, Brazil, Department of Animal Science, Santa Catarina State University (UDESC Oeste), Chapecó, SC, Brazil, Department of Soil and Environment, Swedish University of Agricultural Sciences, Uppsala, Sweden, Climate Impacts Research Centre (CIRC), Umeå University, Estonian University of Life Sciences (EMU), Universidade Federal do Rio de Janeiro (UFRJ), Key Laboratory of the Three Gorges Reservoir Region’s Eco-Environment, Ministry of Education, Chongqing University, Chongqing, China, Department of Biology, University of Western Ontario, University of Western Ontario (UWO), Universidad Autónoma de Madrid (UAM), Johannes Gutenberg - Universität Mainz = Johannes Gutenberg University (JGU), Rice University [Houston], Wildlife and Ecology Group [New Zealand], Massey University, Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama, Japan, Department of Sustainable Crop Production (DI.PRO.VE.S.), Università Cattolica del Sacro Cuore, Piacenza, Italy, University of Cadiz, Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad Universitaria México, Natural History Museum [Vienna] (NHM), University of Natural Resources and Life Sciences, Department of Integrated Biology and Biodiversity Research, Institute of Zoology (BOKU), King Abdulaziz University, Department of Biological Sciences, Université du Québec à Montréal, Lancaster Environment Centre, Lancaster University, Smithsonian Tropical Research Institute, Senckenberg Museum of Natural History Görlitz, Senckenberg – Leibniz Institution for Biodiversity and Earth System Research - Senckenberg Gesellschaft für Naturforschung, Leibniz Association-Leibniz Association, Institute for Alpine Environment, Eurac Research, Ecology, University of Innsbruck, Leopold Franzens Universität Innsbruck - University of Innsbruck, State Nature Reserve 'Privolzhskaya Lesostep', Penza, Russia, Museum and Institute of Zoology, Polish Academy of Sciences, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China, Institute of Biology Komi Science Centre UB RAS, University of Bern, Aristotle University of Thessaloniki, Great Lakes Forestry Centre, Canadian Forest Service, Natural Resources Canada, Sault Ste. Marie, ON, Canada, Department of Ecology, Swedish University of Agricultural Sciences, Uppsala, Sweden, Greensway AB, Uppsala, Sweden, Institute of Wildlife Biology and Game Management, University of Natural Resources and Life Sciences, Institute of Wildlife Management and Wildlife Biology, University of Sopron, Sopron, Hungary, Key laboratory of Wetland Ecology and Environment, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China, Ministry of Education Key Laboratory of Vegetation Ecology, School of Life Sciences, Northeast Normal University, Changchun 130024, Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, School of Life Sciences, Northeast Normal University, Changchun 130024, Community Department, Helmholtz Center for Environmental Research, Halle, Germany, State University of Paraiba, Institute of Integrative Biology, Centre for Biodiversity and Sustainable Land-use [University of Göttingen] (CBL), Terrestrial Ecology (TE), Conservation Ecology Group, Govers group, Ecology & Evolution, Amsterdam Sustainability Institute, Systems Ecology, Animal Ecology, Muséum national d'Histoire naturelle (MNHN)-École Pratique des Hautes Études (EPHE), Université Paul-Valéry - Montpellier 3 (UPVM)-École Pratique des Hautes Études (EPHE), Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR (UREP), and VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDV]Life Sciences [q-bio], Soil Science, General Physics and Astronomy, 580 Plants (Botany), 000 Computer science, knowledge & systems, Markvetenskap, 590 Tiere (Zoologie), General Biochemistry, Genetics and Molecular Biology, Soil, terrestrial food web, SDG 13 - Climate Action, Humans, Animals, 000 Informatik, Wissen, Systeme, Macroecology, Arthropods, Tundra, Ecosystem, Ekologi, Multidisciplinary, Ecology, soil fertility, collembola, Biodiversity, General Chemistry, 580 Pflanzen (Botanik), Settore AGR/11 - ENTOMOLOGIA GENERALE E APPLICATA, [SDE]Environmental Sciences, 570 Life sciences, biology, 590 Animals (Zoology), 570 Biowissenschaften, Biologie
Abstract: Soil life supports the functioning and biodiversity of terrestrial ecosystems. Springtails (Collembola) are among the most abundant soil arthropods regulating soil fertility and flow of energy through above- and belowground food webs. However, the global distribution of springtail diversity and density, and how these relate to energy fluxes remains unknown. Here, using a global dataset representing 2470 sites, we estimate the total soil springtail biomass at 27.5 megatons carbon, which is threefold higher than wild terrestrial vertebrates, and record peak densities up to 2 million individuals per square meter in the tundra. Despite a 20-fold biomass difference between the tundra and the tropics, springtail energy use (community metabolism) remains similar across the latitudinal gradient, owing to the changes in temperature with latitude. Neither springtail density nor community metabolism is predicted by local species richness, which is high in the tropics, but comparably high in some temperate forests and even tundra. Changes in springtail activity may emerge from latitudinal gradients in temperature, predation and resource limitation in soil communities. Contrasting relationships of biomass, diversity and activity of springtail communities with temperature suggest that climate warming will alter fundamental soil biodiversity metrics in different directions, potentially restructuring terrestrial food webs and affecting soil functioning. The article is an outcome of the #GlobalCollembola community initiative that is voluntarily supported by researchers around the world. Data collection and analysis was supported by the Russian Science Foundation (19-74-00154 to A.P.) and by Deutsche Forschungsgemeinschaft (493345801 to A.P. and 192626868—SFB 990 to S.S.). We acknowledge support by the Open Access Publication Funds of the Göttingen University. The following funding bodies provided support for individual contributors: ARC SRIEAS Grant SR200100005 Securing Antarctica’s Environmental Future to S.L.C., Slovak Scientific Grant Agency VEGA 1/0438/22 to Ľ.K., RFBR 19-516-60002 to N.A.K., Carl Tryggers Stiftelse för Vetenskaplig Forskning and Qatar Petroleum to J.M.A., BIO 27 (2013-2014)-MAGyP and PICTO 2084 (2012)-ANPCyT to V.B., DAAD-19-10 and MSM200962001 to T.C., grant TE, PN-III-P1-1.1-TE-2019-0358 to C.F., NWO grant 821.01.015 to O.F., National Natural Sciences Foundation of China No 41471037 and 41871042 to M.G., BIO 27 (2013-2014), MAGyP; PICT 2084 (2012), FONCyT to D.F.G., NRF South African National Antarctic Programme grant 110734 to M.G., Natural Resources Canada (NRCan), EcoEnergy Innovation Initiative under the Office of Energy Research and Development, and the Natural Sciences and Engineering Research Council of Canada (NSERC) to I.T.H., L.A.V. and L.R., Independent Research Fund Denmark grant no. DFF-4002-00384 to M.H., Estonian Science Foundation G9145 to M.I., SA-France bilateral grant to C.J., SA (NRF)/Russia (RFBR) Joint Science and Technology Research Collaboration project no. 19-516-60002 (FRBR) and no. 118904 (NRF) to M.P. and C.J., European Research Council (ERC), European Union’s Horizon 2020 research and innovation programme (grant agreement no. 677232; to N.E.); iDiv, German Research Foundation (DFG–FZT 118, 202548816) to M.J. and N.E., French National Agency of Research (ANR) (JASSUR research project; ANR-12-VBDU-0011), «Ministère de l’Agriculture et de la Pêche» and «Ministère de l’Education Nationale de la Recherche et de la Technologie» (ACTA programme), «Ministère de l’Aménagement du Territoire et de l’Environnement» (Pnetox programme), EU-funded project, ECOGEN QLK5-CT-2002-01666 (www.ecogen.dk), “Agence de l’Environnement et de la Maîtrise de l'Énergie” (BIOINDICATEUR 2, BIOTECHNOSOL), ANDRA and GISFI (www.gisfi.fr) to S.J., GRR SER-BIODIV (Région Normandie, France) to MCha, ESF9258, B02 to A.K., Fundamental Research Funds for the Central Universities (grant no. 2018CDXYCH0014) to D.L., DFG 316045089 to J.L., Massey University Research Fund grant to M.A.M., DFG SCHE 376/38-2 to M.M.P., grant from the Austria Academy of Science: Heritage_2020-043_Modeling-Museum to P.Q., Slovak Scientific Grant Agency: VEGA Nos. 1/0441/03 and 1/3267/06 to N.R., Higher Education Commission of Pakistan to M.I.R., RSF 21-74-00126 to R.A.S., Austrian Federal Government and European Union (Rural Development 2014-2020) to J.S., АААА-А17-122040600025-2 to A.A.T., Brazilian Council for Scientific and Technological Development—CNPq (grant no. 152717/2016-1) to B.R.W., 309030/2018-8 to D.Z. and 305426/2018-4 to B.C.B., National Natural Science Foundation of China (31970434, 31772491) to N.N.G., Research and Innovation Support Foundation of Santa Catarina (FAPESC) (6.309/2011-6/FAPESC) and the CNPq (563251/2010-7/CNPq) to L.C.I.O.F., O.K.-F., the Latvian Council of Science Grants no. 90.108, 93.140, 96.0110, 01.0344 to E.J., CNPq for the Research Productivity Grant (305939/2018-1) to D.B., FPI-MICINN grant in the project INTERCAPA (CGL2014-56739-R) to P.H, the Natural Sciences and Engineering Research Council of Canada (NSERC) to Z.L., Ministry of Innovation and Technology of Hungary TKP2021-NKTA-43 to D.W. Authors are grateful to Penelope Greenslade for providing the literature on Australian Collembola communities. Authors are grateful to Frans Janssens for providing the global checklist of Collembola.
Published: 2023

45. Metagenomic characterization of viral communities in corals: mining biological signal from methodological noise

Author: Wood-Charlson, Elisha, Weynberg, Karen, Suttle, Curtis, Roux, Simon, van Oppen, Madeleine, Department of Ecology and Evolutionary Biology, University of Arizona, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), and Department of Ecology and Evolutionary Biology [University of Arizona]
Subjects: [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [STAT.OT]Statistics [stat]/Other Statistics [stat.ML], [SDV.MP.PRO]Life Sciences [q-bio]/Microbiology and Parasitology/Protistology, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2015

46. Diversity and comparative genomics of Microviridae in Sphagnum-dominated peatlands

Author: Quaiser, Achim, Dufresne, Alexis, Ballaud, Flore, Roux, Simon, Zivanovic, Yvan, Colombet, Jonathan, Sime-Ngando, Télesphore, Francez, Andre-Jean, Ecosystèmes, biodiversité, évolution [Rennes] (ECOBIO), Université de Rennes (UR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR), Université de Rennes (UR)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Centre National de la Recherche Scientifique (CNRS), Centre d'études d'océanographie et de biologie marine (CEOBM), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, Institut de génétique et microbiologie [Orsay] (IGM), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), INSU-CNRS EC2CO Program 'VIRTOU', grants from the university of Rennes/CNRS and OSUR, Centre National de la Recherche Scientifique (CNRS)-Observatoire des Sciences de l'Univers de Rennes (OSUR)-Institut Ecologie et Environnement (INEE), Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES), Department of Ecology and Evolutionary Biology, and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)
Subjects: viruses, virus diversity, ssDNAphage, virusecology, viralmetagenomics, Microbiology, virusdiversity, ssDNA phage, Aravirinae, Gokushovirinae, Microviridae, Stokavirinae, virus ecology, viral metagenomics, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Original Research
Abstract: Microviridae, a family of bacteria-infecting ssDNA viruses, is one of the still poorly characterized bacteriophage groups, even though it includes phage PhiX174, one of the main models in virology for genomic and capsid structure studies. Recent studies suggest that they are diverse and well represented in marine and freshwater virioplankton as well as in human microbiomes. However, their diversity, abundance, and ecological role are completely unknown in soil ecosystems. Here we present the comparative analysis of 17 completely assembled Microviridae genomes from 12 viromes of a Sphagnum-dominated peatland. Phylogenetic analysis of the conserved major capsid protein sequences revealed the affiliation to Gokushovirinae and Pichovirinae as well as to two newly defined subfamilies, the Aravirinae and Stokavirinae. Additionally, two new distinct prophages were identified in the genomes of Parabacteroides merdae and Parabacteroides distasonis representing a potential new subfamily of Microviridae. The differentiation of the subfamilies was confirmed by gene order and similarity analysis. Relative abundance analysis using the affiliation of the major capsid protein (VP1) revealed that Gokushovirinae, followed by Aravirinae, are the most abundant Microviridae in 11 out of 12 peat viromes. Sequences matching the Gokushovirinae and Aravirinae VP1 matching sequences, respectively, accounted for up to 4.19 and 0.65% of the total number of sequences in the corresponding virome, respectively. In this study we provide new genome information of Microviridae and pave the way toward quantitative estimations of Microviridae subfamilies.
Published: 2015

47. Genomic characteristics and environmental distributions of the uncultivated Far-T4 phages

Author: Viviane Ravet, François Enault, Olivier Pereira, Simon Roux, Matthew B. Sullivan, Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Centre National de la Recherche Scientifique (CNRS), Department of Ecology and Evolutionary Biology, and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Centre National de la Recherche Scientifique (CNRS)-Université d'Auvergne - Clermont-Ferrand I (UdA)
Subjects: Genetics, Microbiology (medical), Viral metagenomics, Phylogenetic tree, freshwater ecology, lcsh:QR1-502, Sequence assembly, Biology, biology.organism_classification, Genome, Microbiology, 6. Clean water, lcsh:Microbiology, capsid proteins, viral genomes, T4 phages, Caudovirales, Metagenomics, [SDE]Environmental Sciences, Sequence space (evolution), [SDE.BE]Environmental Sciences/Biodiversity and Ecology, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Clade, Original Research
Abstract: International audience; Viral metagenomics (viromics) is a tremendous tool to reveal viral taxonomic and functional diversity across ecosystems ranging from the human gut to the world's oceans. As with microbes however, there appear vast swaths of "dark matter" yet to be documented for viruses, even among relatively well-studied viral types. Here, we use viromics to explore the "Far-T4 phages" sequence space, a neighbor clade from the well-studied T4-like phages that was first detected through PCR study in seawater and subsequently identified in freshwater lakes through 454-sequenced viromes. To advance the description of these viruses beyond this single marker gene, we explore Far-T4 genome fragments assembled from two deeply-sequenced freshwater viromes. Single gene phylogenetic trees confirm that the Far-T4 phages are divergent from the T4-like phages, genome fragments reveal largely collinear genome organizations, and both data led to the delineation of five Far-T4 clades. Three-dimensional models of major capsid proteins are consistent with a T4-like structure, and highlight a highly conserved core flanked by variable insertions. Finally, we contextualize these now better characterized Far-T4 phages by re-analyzing 196 previously published viromes. These suggest that Far-T4 are common in freshwater and seawater as only four of 82 aquatic viromes lacked Far-T4-like sequences. Variability in representation across the five newly identified clades suggests clade-specific niche differentiation may be occurring across the different biomes, though the underlying mechanism remains unidentified. While complete genome assembly from complex communities and the lack of host linkage information still bottleneck virus discovery through viromes, these findings exemplify the power of metagenomics approaches to assess the diversity, evolutionary history, and genomic characteristics of novel uncultivated phages.
Published: 2015

48. Open science resources for the discovery and analysis of Tara Oceans data

Author: Pesant, Stéphane, Not, Fabrice, Picheral, Marc, Kandels-Lewis, Stefanie, Le Bescot, Noan, Gorsky, Gabriel, Iudicone, Daniele, Karsenti, Eric, Speich, Sabrina, Troublé, Romain, Dimier, Céline, Searson, Sarah, Acinas, Silvia G., Bork, Peer, Boss, Emmanuel, Bowler, Chris, De Vargas, Colomban, Grimsley, Nigel, Hingamp, Pascal, Jaillon, Olivier, Karp-Boss, Lee, Krzic, Uros, Ogata, Hiroyuki, Raes, Jeroen, Reynaud, Emmanuel G., Sardet, Christian, Sieracki, Mike, Stemmann, Lars, Sullivan, Matthew B., Sunagawa, Shinichi, Weissenbach, Jean, Wincker, Patrick, Follows, Michael J, Center for Marine Environmental Sciences [Bremen] (MARUM), Universität Bremen, PANGAEA Consulting Engineers, Diversité et Interactions au sein du Plancton Océanique (DIPO), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'océanographie de Villefranche (LOV), Observatoire océanologique de Villefranche-sur-mer (OOVM), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), European Molecular Biology Laboratory [Heidelberg] (EMBL), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Stazione Zoologica Anton Dohrn (SZN), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physique des océans (LPO), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Tara Expéditions, Department of Marine Biology and Oceanography [Barcelone], Institute of Marine Sciences / Institut de Ciències del Mar [Barcelona] (ICM), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC)-Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), European Molecular Biology Laboratory [Grenoble] (EMBL), University of Maine, Department of Earth, Atmospheric and Planetary Sciences [MIT, Cambridge] (EAPS), Massachusetts Institute of Technology (MIT), Biologie intégrative des organismes marins (BIOM), Observatoire océanologique de Banyuls (OOB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Information génomique et structurale (IGS), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Génomique métabolique (UMR 8030), Genoscope - Centre national de séquençage [Evry] (GENOSCOPE), Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Kyoto University, Rega Institute - VIB Center for the Biology of Disease, Department of Microbiology and Immunology, Bioinformatics and (eco-)systems Biology Laboratory, Louvain, Belgique, Université Catholique de Louvain = Catholic University of Louvain (UCL), School of Biology & Environmental Science, University College Dublin [Dublin] (UCD), Laboratoire de Biologie du Développement de Villefranche sur mer (LBDV), Bigelow Laboratory for Ocean Sciences, Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, European Molecular Biology Laboratory, DVIPC, Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Department of Marine Biology and Oceanography, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Kyoto University [Kyoto], Department of Ecology and Evolutionary Biology, Research Foundation - Flanders, Stazione Zoologica Anton Dohrn, Università degli Studi di Milano-Bicocca, Agence Nationale de la Recherche (France), European Research Council, Ministerio de Ciencia e Innovación (España), Japan Society for the Promotion of Science, Veolia Foundation, Région Bretagne, World Courier, Illumina, Lorient Agglomération, Fondation EDF, Fondation Prince Albert II de Monaco, Centre National de Séquençage (France), Centre National de la Recherche Scientifique (France), Massachusetts Institute of Technology. Department of Earth, Atmospheric, and Planetary Sciences, Follows, Michael J, HAL-UPMC, Gestionnaire, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Raes, Jeroen, and Lorient Agglomération (France)
Subjects: [SDE] Environmental Sciences, Statistics and Probability, Open science, Data Descriptor, 010504 meteorology & atmospheric sciences, Oceans and Seas, [SDV]Life Sciences [q-bio], Context (language use), Library and Information Sciences, 01 natural sciences, Education, Environmental data, 03 medical and health sciences, Seawater, 14. Life underwater, Ecosystem, 030304 developmental biology, 0105 earth and related environmental sciences, 0303 health sciences, business.industry, Information Dissemination, Environmental resource management, Ecological genetics, Biodiversity, Plankton, Biooceanography, Computer Science Applications, [SDV] Life Sciences [q-bio], Oceanography, Geography, Ocean sciences, 13. Climate action, Viruses, [SDE]Environmental Sciences, Expeditions, Statistics, Probability and Uncertainty, business, Information Systems
Abstract: Pesant, Stéphane ... et. al.-- 16 pages, 5 figures, 2 tables.-- This article is contribution number 26 of the Tara Oceans Consortium, The Tara Oceans expedition (2009–2013) sampled contrasting ecosystems of the world oceans, collecting environmental data and plankton, from viruses to metazoans, for later analysis using modern sequencing and state-of-the-art imaging technologies. It surveyed 210 ecosystems in 20 biogeographic provinces, collecting over 35,000 samples of seawater and plankton. The interpretation of such an extensive collection of samples in their ecological context requires means to explore, assess and access raw and validated data sets. To address this challenge, the Tara Oceans Consortium offers open science resources, including the use of open access archives for nucleotides (ENA) and for environmental, biogeochemical, taxonomic and morphological data (PANGAEA), and the development of on line discovery tools and collaborative annotation tools for sequences and images. Here, we present an overview of Tara Oceans Data, and we provide detailed registries (data sets) of all campaigns (from port-to-port), stations and sampling events, We thank the commitment of the following people and sponsors who made this singular expedition possible: CNRS (in particular the Groupement de Recherche GDR3280), European Molecular Biology Laboratory (EMBL), Genoscope/CEA, Fund for Scientific Research—Flanders, VIB, Stazione Zoologica Anton Dohrn, UNIMIB, ANR (projects POSEIDON/ANR-09-BLAN-0348, BIOMARKS/ANR-08-BDVA- 003, PROMETHEUS/ANR-09-GENM-031, PROMETHEUS/ANR-09-PCS-GENM-217, TARAGIRUS/ANR-09-PCS-GENM-218, OCEANOMICS/ANR-11-BTBR-0008, FRANCE GENOMIQUE/ANR-10-INBS-09-08), EU FP7 (MicroB3/No.287589, IHMS/HEALTH-F4-2010-261376, MetaCardis/HEALTH-F4-2012-305312), ERC Advanced Grant Awards to CB (Diatomite: 294823) and PB (CancerBiome: 268985), Spanish Ministry of Science and Innovation grant CGL2011-26848/BOS MicroOcean PANGENOMICS to SGA, JSPS KAKENHI Grant Number 26430184 to HO, FWO, BIO5, Biosphere 2, agne`s b., the Veolia Environment Foundation, Region Bretagne, World Courier, Illumina, Cap L’Orient, the EDF Foundation EDF Diversiterre, FRB, the Prince Albert II de Monaco Foundation, Etienne Bourgois, the Tara schooner and its captain and crew. Tara Oceans would not exist without continuous support from 23 institutes (http://oceans.taraexpeditions.org)
Published: 2015

49. Testing models for the leaf economics spectrum with leaf and whole-plant traits in [i]Arabidopsis thaliana[/i]

Author: Benjamin Blonder, Brian J. Enquist, Bill Shipley, Cyrille Violle, Denis Vile, François Vasseur, Environmental Change Institute, University of Oxford, Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre d’Ecologie Fonctionnelle et Evolutive (CEFE), Université Paul-Valéry - Montpellier 3 (UPVM)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département de Biologie, Université de Sherbrooke (UdeS), Department of Ecology and Evolutionary Biology [University of Arizona], University of Arizona, Santa Fe Institute, European Project: 221060, University of Oxford [Oxford], Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université Paul-Valéry - Montpellier 3 (UM3), Sherbrooke University, Department of Ecology and Evolutionary Biology, Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Université Paul-Valéry - Montpellier 3 (UPVM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Université Paul-Valéry - Montpellier 3 (UM3)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)
Subjects: Venation network, genotype, [SDV]Life Sciences [q-bio], Arabidopsis, Vascular patterning, Plant Biology, Plant Science, structural equation modelling, vein density, Structural equation modeling, cytoplasm–cell wall partitioning, Inbred strain, Botany, Arabidopsis thaliana, modélisation structurelle, Leaf economics spectrum, assimilation du carbone, Plant traits, Research Articles, Ecotype, biology, leaf economics spectrum, venation network, arabidopsis thaliana, système vasculaire, biology.organism_classification, plateforme de phénotypage, nervure, Cytoplasm-cell wall partitioning, Structural equation modelling, Vein density, Trait, paroi cellulaire
Abstract: The LES is a global set of patterns that describes correlations between functional traits (e.g. carbon assimilation rate, lifespan) that determine terrestrial resource fluxes. Several classes of models have been proposed to explain the LES, but none have been extensively tested against each other with fine-scale data. Here we assemble a large set of genotypes of Arabidopsis thaliana that show variation in leaf functional traits. We show that no extant theory for the LES is supported, but that some leaf venation networks likely play a role in driving the pattern. Our study provides a roadmap for the measurements that could generate further insight into this fundamental ecological pattern., The leaf economics spectrum (LES) describes strong relationships between multiple functional leaf traits that determine resource fluxes in vascular plants. Five models have been proposed to explain these patterns: two based on patterns of structural allocation, two on venation networks and one on resource allocation to cell walls and cell contents. Here we test these models using data for leaf and whole-plant functional traits. We use structural equation modelling applied to multiple ecotypes, recombinant inbred lines, near isogenic lines and vascular patterning mutants of Arabidopsis thaliana that express LES trait variation. We show that a wide variation in multiple functional traits recapitulates the LES at the whole-plant scale. The Wright et al. (2004) model and the Blonder et al. (2013) venation network model cannot be rejected by data, while two simple models and the Shipley et al. (2006) allocation model are rejected. Venation networks remain a key hypothesis for the origin of the LES, but simpler explanations also cannot be ruled out.
Published: 2015

50. Leaf water potential measurements using the pressure chamber: Synthetic testing of assumptions towards best practices for precision and accuracy

Author: Celia M. Rodriguez‐Dominguez, Alicia Forner, Sebastia Martorell, Brendan Choat, Rosana Lopez, Jennifer M. R. Peters, Sebastian Pfautsch, Stefan Mayr, Madeline R. Carins‐Murphy, Scott A. M. McAdam, Freya Richardson, Antonio Diaz‐Espejo, Virginia Hernandez‐Santana, Paulo E. Menezes‐Silva, Jose M. Torres‐Ruiz, Timothy A. Batz, Lawren Sack, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Museo Nacional de Ciencias Naturales, Departamento de Biogeografía y Cambio Global, Laboratorio Internacional de Cambio Global (LINC-Global), Spanish National Research Council (CSIC), Université des îles Baléares (UIB), Western Sydney University, Departamento de Sistemas y Recursos Naturales, Escuela Técnica Superior de Ingeniería de Montes, Forestal y del Medio Natural, Universidad Politécnica de Madrid, Madrid, Hawkesbury Institute for the Environment [Richmond] (HIE), Institute of Botany [Innsbruck], Leopold Franzens Universität Innsbruck - University of Innsbruck, School of Biological Sciences [Hobart], University of Tasmania [Hobart, Australia] (UTAS), Purdue University [West Lafayette], Laboratoire de Physique et Physiologie Intégratives de l’Arbre en environnement Fluctuant (PIAF), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Perdue University, Department of Ecology and Evolutionary Biology (Faculty of Biology), University of Science-Vietnam National Universities, SKA South Africa751918-AgroPHYSAustrian Science Fund (FWF)P32203National Science Foundation (NSF)1457279, European Project: 624473,EC:FP7:PEOPLE,FP7-PEOPLE-2013-IOF,HYDROPIT(2015), European Commission, Austrian Research Promotion Agency, National Science Foundation (US), Rodríguez Domínguez, Celia M., Forner, Alicia, Choat, B., López, Rosana, Peters, J.M.R., Pfautsch, S., Carins Murphy, Madeline R., McAdam S.A.M., Richardson, Freya, Díaz-Espejo, Antonio, Hernández Santana, V., Menezes-Silva, Paulo E., Torres Ruiz, José Manuel, Sack, Lawren, Rodríguez Domínguez, Celia M. [0000-0003-2352-0829], Forner, Alicia [0000-0002-7123-6403], Choat, B.[0000-0002-9105-640X], López, Rosana [0000-0003-3553-9148], Peters, J.M.R. [0000-0003-4627-7788], Pfautsch, S. [0000-0002-4390-4195], Carins Murphy, Madeline R. [0000-0003-4370-9485], McAdam S.A.M. [0000-0002-9625-6750], Richardson, Freya [0000-0003-2460-3423], Díaz-Espejo, Antonio [0000-0002-4711-2494], Hernández Santana, V. [0000-0001-9018-8622], Menezes-Silva, Paulo E. [0000-0002-8122-3489], Torres Ruiz, José Manuel [0000-0003-1367-7056], and Sack, Lawren [0000-0002-7009-7202]
Subjects: Physiology, Water stress, Reproducibility of Results, Water, plant water relations, Plant water relations, pressure bomb, Plant Science, Leaf water potential, leaf water potential, Droughts, Plant Leaves, water stress, Pressure bombpressure chamber, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, plant water status, Plant water status, pressure chamber
Abstract: 25 páginas.- 8 figuras.- 2 tablas.- 66 referencias.- Additional supporting information can be found online in the Supporting Information section at the end of this article., eaf water potential (psi(leaf)), typically measured using the pressure chamber, is the most important metric of plant water status, providing high theoretical value and information content for multiple applications in quantifying critical physiological processes including drought responses. Pressure chamber measurements of psi(leaf) (psi(leafPC)) are most typical, yet, the practical complexity of the technique and of the underlying theory has led to ambiguous understanding of the conditions to optimize measurements. Consequently, specific techniques and precautions diversified across the global research community, raising questions of reliability and repeatability. Here, we surveyed specific methods of psi(leafPC) from multiple laboratories, and synthesized experiments testing common assumptions and practices in psi(leafPC) for diverse species: (i) the need for equilibration of previously transpiring leaves; (ii) leaf storage before measurement; (iii) the equilibration of psi(leaf) for leaves on bagged branches of a range of dehydration; (iv) the equilibration of psi(leaf) across the lamina for bagged leaves, and the accuracy of measuring leaves with artificially 'elongated petioles'; (v) the need in psi(leaf) measurements for bagging leaves and high humidity within the chamber; (vi) the need to avoid liquid water on leaf surfaces; (vii) the use of 'pulse' pressurization versus gradual pressurization; and (viii) variation among experimenters in psi(leafPC) determination. Based on our findings we provide a best practice protocol to maximise accuracy, and provide recommendations for ongoing species-specific tests of important assumptions in future studies., European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 751918-AgroPHYS; Marie Curie Fellowship (FP7-PEOPLE-2013-IOF-624473); Austrian research agency (FWF) project P32203; National Science Foundation (Grant IOS-#1457279)
Published: 2022

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