61 results on '"Inger Greve Alsos"'
Search Results
2. LocoGSE, a sequence-based genome size estimator for plants
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Pierre Guenzi-Tiberi, Benjamin Istace, Inger Greve Alsos, The PhyloNorway Consortium, Eric Coissac, Sébastien Lavergne, The PhyloAlps Consortium, Jean-Marc Aury, France Denoeud, L.G. Alsos, M.K. Føreid Merkel, Y. Lammers, E. Coissac, C. Pouchon, A. Alberti, F. Denoeud, and P. Wincker
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genome size estimation ,genome size ,ploidy ,genome-skimming ,environmental DNA ,plant genomics ,Plant culture ,SB1-1110 - Abstract
Extensive research has focused on exploring the range of genome sizes in eukaryotes, with a particular emphasis on land plants, where significant variability has been observed. Accurate estimation of genome size is essential for various research purposes, but existing sequence-based methods have limitations, particularly for low-coverage datasets. In this study, we introduce LocoGSE, a novel genome size estimator designed specifically for low-coverage datasets generated by genome skimming approaches. LocoGSE relies on mapping the reads on single copy consensus proteins without the need for a reference genome assembly. We calibrated LocoGSE using 430 low-coverage Angiosperm genome skimming datasets and compared its performance against other estimators. Our results demonstrate that LocoGSE accurately predicts monoploid genome size even at very low depth of coverage (
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- 2024
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3. The drivers of plant community composition have shifted from external to internal processes over the past 20,000 years
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C. Patrick Doncaster, Mary E. Edwards, Charlotte L. Clarke, and Inger Greve Alsos
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Geology ,QE1-996.5 ,Environmental sciences ,GE1-350 - Abstract
Abstract Internal and external factors regulating the past composition of plant communities are difficult to identify in palaeo-vegetation records. Here, we develop an index of relative entropy of community assembly, which applies to changes in the composition of a community over time, measuring disorder in its assembly relative to disassembly. Historical periods of relatively ordered assembly (negative index values) are characteristic of a community undergoing endogenous self-organisation, in contrast to relatively disordered assembly (positive values) characterising periods of exogenous abiotic forcing. We quantified the relative entropy index for a 22,000-year time-series of tundra vegetation obtained in the Polar Urals, based on sedimentary DNA. We find it most positive during the Late Pleistocene characterized by persistent taxa, and most negative during the post-glacial Holocene characterized by more ephemeral floras. Changes in relative entropy coincide with changes in regional temperature as reconstructed from stable oxygen composition of an Arctic ice-core. Our results suggest that temperature strongly influenced community assembly in the Polar Urals until about 9000 years before present, after which endogenous community self-organization prevailed through to the present. We conclude that time-series of community composition can reveal changes in the balance between internal and external influences on taxonomic turnover and resulting diversity.
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- 2023
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4. Plant biodiversity assessment through soil eDNA reflects temporal and local diversity
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María Ariza, Bertrand Fouks, Quentin Mauvisseau, Rune Halvorsen, Inger Greve Alsos, and Hugo J. deBoer
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metabarcoding ,plant identification ,soil eDNA ,spatial scale ,temporal change ,vegetation assessments ,Ecology ,QH540-549.5 ,Evolution ,QH359-425 - Abstract
Abstract Several studies have shown the potential of eDNA‐based proxies for plant identification, but little is known about their spatial and temporal resolution. This limits its use for plant biodiversity assessments and monitoring of vegetation responses to environmental changes. Here we calibrate the temporal and spatial plant signals detected with soil eDNA surveys by comparing with a standard visual above‐ground vegetation survey. Our approach compares vegetation in an old‐growth boreal forest in southern Norway, surveyed in 100 permanent 1‐m2 plots seven times over a 30‐year period, with a single soil eDNA metabarcoding‐based survey from soil samples collected at the same 100 plots in the year of the last vegetation survey. On average, 60% and 10% of the vascular plants and bryophytes recorded across all vegetation surveys were detected by soil eDNA. Taxa detected by soil eDNA were more representative for the local taxa pool than for the specific plot, and corresponded to those surveyed over the 30‐year period although most closely matched the current taxa composition. Soil eDNA detected abundant taxa better than rare ones although both rare taxa and taxa unrecorded by the visual survey were detected. Our study highlights the potential of soil eDNA assessments for monitoring of vegetation responses over broad spatial and temporal scales. The method's ability to detect abundant taxa makes it suitable for assessment of vegetation composition in a specific area and for broad‐scale plant diversity assessments.
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- 2023
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5. High resolution ancient sedimentary DNA shows that alpine plant diversity is associated with human land use and climate change
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Sandra Garcés-Pastor, Eric Coissac, Sébastien Lavergne, Christoph Schwörer, Jean-Paul Theurillat, Peter D. Heintzman, Owen S. Wangensteen, Willy Tinner, Fabian Rey, Martina Heer, Astrid Rutzer, Kevin Walsh, Youri Lammers, Antony G. Brown, Tomasz Goslar, Dilli P. Rijal, Dirk N. Karger, Loïc Pellissier, The PhyloAlps Consortium, Oliver Heiri, and Inger Greve Alsos
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Science - Abstract
Here, the authors use sedimentary DNA, pollen, fungal spores, chironomids, and microcharcoal from an alpine lake core to reconstruct vegetation across 12,000 years. They find that vegetation responded to climate in the early Holocene, followed by a shift to human activity from 6000 years onward corresponding with an increase in deforestation and agropastoralism.
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- 2022
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6. Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet
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Physilia Ying Shi Chua, Youri Lammers, Emmanuel Menoni, Torbjørn Ekrem, Kristine Bohmann, Sanne Boessenkool, and Inger Greve Alsos
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ecology ,environmental DNA ,grouse ,herbivory ,high‐throughput sequencing ,Environmental sciences ,GE1-350 ,Microbial ecology ,QR100-130 - Abstract
Abstract Conservation strategies centered around species habitat protection rely on species’ dietary information. One species at the focal point of conservation efforts is the herbivorous grouse, the western capercaillie (Tetrao urogallus), which is an indicator species for forest biodiversity conservation. Non‐molecular means used to study their diet are time‐consuming and at low taxonomic resolution. This delays the implementation of conservation strategies including resource protection due to uncertainty about its diet. Thus, limited knowledge on diet is hampering conservation efforts. Here, we use non‐invasive environmental DNA (eDNA) metabarcoding on DNA extracted from faces to present the first large‐scale molecular dietary analysis of capercaillies. Facal samples were collected from seven populations located in Norway (Finnmark, Troms, Trøndelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n = 172). We detected 122 plant taxa belonging to 46 plant families of which 37.7% of the detected taxa could be identified at species level. The average dietary richness of each sample was 7 ± 5 SD taxa. The most frequently occurring plant groups with the highest relative read abundance (RRA) were trees and dwarf shrubs, in particular, Pinus and Vaccinium myrtillus, respectively. There was a difference in dietary composition (RRA) between samples collected from the different locations (adonis pseudo F5,86 = 11.01, r2 = 0.17, p = 0.001) and seasons (adonis pseudo F2,03 = 0.64, r2 = 0.01, p = 0.036). Dietary composition also differed between sexes at each location (adonis pseudo F1,47 = 2.77, r2 = 0.04, p = 0.024), although not significant for all data combined. In total, 35 taxa (36.8% of taxa recorded) were new capercaillie food items compared with existing knowledge from non‐molecular means. The non‐invasive molecular dietary analysis applied in this study provides new ecological information of capercaillies’ diet, improving our understanding of adequate habitat required for their conservation.
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- 2021
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7. Environmental palaeogenomic reconstruction of an Ice Age algal population
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Youri Lammers, Peter D. Heintzman, and Inger Greve Alsos
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Biology (General) ,QH301-705.5 - Abstract
Lammers et al. use sedimentary ancient DNA to reconstruct palaeogenomes of Nannochloropsis. This study demonstrates the value of sedaDNA for palaeogenomic reconstructions and population genomic analysis.
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- 2021
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8. Prevention of microbial species introductions to the Arctic: The efficacy of footwear disinfection measures on cruise ships
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Sabine B. Rumpf, Inger Greve Alsos, and Chris Ware
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Biology (General) ,QH301-705.5 - Abstract
Biosecurity measures are commonly used to prevent the introduction of non-native species to natural environments globally, yet the efficacy of practices is rarely tested under operational conditions. A voluntary biosecurity measure was trialled in the Norwegian high Arctic following concern that non-native species might be transferred to the region on the footwear of travellers. Passengers aboard an expedition cruise ship disinfected their footwear with the broad spectrum disinfectant Virkon S prior to and in-between landing at sites around the remote Svalbard archipelago. The authors evaluated the efficacy of simply stepping through a disinfectant foot bath, which is the most common practice of footwear disinfection aboard expedition cruise ships in the Arctic. This was compared to a more time consuming and little-used method involving drying disinfected footwear, as proposed by other studies. The two practices were evaluated by measuring microbial growth on paired footwear samples before and after disinfection under both conditions. Step-through disinfection did not substantially reduce microbial growth on the footwear. Allowing disinfected footwear to dry, however, reduced the microbial burden significantly to lower levels. Thus, the currently adopted procedures used aboard ships are ineffective at removing microbial burden and are only effective when footwear is given more time to dry than currently granted under operational conditions. These findings underscore results from empirical research performed elsewhere and suggest the need to better relay this information to practitioners. It is suggested that footwear should minimally be wiped dry after step-through disinfection as a reasonable compromise between biosecurity and practicability.
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- 2018
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9. Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden
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Laura Parducci, Inger Greve Alsos, Per Unneberg, Mikkel W. Pedersen, Lu Han, Youri Lammers, J. Sakari Salonen, Minna M. Väliranta, Tanja Slotte, and Barbara Wohlfarth
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environmental DNA ,ancient DNA ,shotgun sequencing (metagenomics) ,pollen ,macrofossils remains ,lake sediments ,Evolution ,QH359-425 ,Ecology ,QH540-549.5 - Abstract
The lake sediments of Hässeldala Port in south-east Sweden provide an archive of local and regional environmental conditions ~14.5–9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerød (14.1–12.7 ka BP), Younger Dryas (12.7–11.7 ka BP), and Preboreal (
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- 2019
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10. The Treasure Vault Can be Opened: Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
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Inger Greve Alsos, Sebastien Lavergne, Marie Kristine Føreid Merkel, Marti Boleda, Youri Lammers, Adriana Alberti, Charles Pouchon, France Denoeud, Iva Pitelkova, Mihai Pușcaș, Cristina Roquet, Bogdan-Iuliu Hurdu, Wilfried Thuiller, Niklaus E. Zimmermann, Peter M. Hollingsworth, and Eric Coissac
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alpine ,chloroplast DNA ,environmental DNA ,ITS ,matK ,nuclear ribosomal DNA ,Botany ,QK1-989 - Abstract
Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was > 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.
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- 2020
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11. Plant DNA metabarcoding of lake sediments: How does it represent the contemporary vegetation.
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Inger Greve Alsos, Youri Lammers, Nigel Giles Yoccoz, Tina Jørgensen, Per Sjögren, Ludovic Gielly, and Mary E Edwards
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Medicine ,Science - Abstract
Metabarcoding of lake sediments have been shown to reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17-49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records of 47 plant taxa in the 11 lakes, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and may therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation.
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- 2018
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12. Tetraploids do not form cushions: association of ploidy level, growth form and ecology in the High Arctic Saxifraga oppositifolia L. s. lat. (Saxifragaceae) in Svalbard
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Pernille Bronken Eidesen, Eike Müller, Christian Lettner, Inger Greve Alsos, Morgan Bender, Martin Kristiansen, Bart Peeters, Froukje Postma, and Koen Frans Verweij
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Autopolyploidy ,flow cytometry ,morphotypes ,habitat segregation ,purple saxifrage ,Environmental sciences ,GE1-350 ,Oceanography ,GC1-1581 - Abstract
Saxifraga oppositifolia L. is a common circumpolar plant species that displays considerable morphological and genetic variation throughout its range. It is mainly diploid, but tetraploids are reported from several regions. The growth form varies from prostate to cushion-shaped, and the plant thrives in wet snow beds as well as on dry ridges. This variation has triggered the curiosity of many researchers, but as yet, no one has explained the observed morphological variation using ecological and/or genetic factors. However, the ploidy level has rarely been taken into account. This is the first study that demonstrates a significant correlation between ploidy level, ecology and growth form in S. oppositifolia. We successfully analysed 193 individuals of S. oppositifolia from 15 locations in Svalbard to investigate possible relationships among growth forms (prostrate, intermediate and cushion), ecological factors (vegetation and soil characteristics) and ploidy level. Results from flow cytometry reported 106 diploids, eight triploids and 79 tetraploids. Tetraploids almost exclusively showed prostrate growth, while the diploids displayed all three growth forms, evidence that growth form is at least partly genetically determined. Our analyses of environmental and vegetation data in relation to ploidy level indicated overlapping niches, but the tetraploids showed a narrower niche, and one shifted towards more benign habitats characterized by higher pH, higher soil temperatures and higher cover of vascular plants. The latter may suggest that tetraploids are slightly better competitors, but less hardy. Thus, autopolyploidy in S. oppositifolia has expanded the ecological amplitude of this species complex.
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- 2013
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13. Colonization of the arctic archipelago Svalbard
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Inger Greve Alsos
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Ecology ,QH540-549.5 ,Microbial ecology ,QR100-130 - Published
- 2009
14. Pollen, macrofossils and sedaDNA reveal climate and land use impacts on Holocene mountain vegetation of the Lepontine Alps, Italy
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Lieveke van Vugt, Sandra Garcés-Pastor, Erika Gobet, Sarah Brechbühl, Antonietta Knetge, Youri Lammers, Katja Stengele, Inger Greve Alsos, Willy Tinner, and Christoph Schwörer
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Archeology ,Global and Planetary Change ,Geology ,580 Plants (Botany) ,Ecology, Evolution, Behavior and Systematics - Abstract
Both climate change and anthropogenic disturbance affect vegetation composition, but it is difficult to separate these drivers of vegetation change from one another. A better understanding of past vegetation dynamics is necessary to disentangle the influence of different forcing factors and assess future vegetation change. Here we present the first multi-proxy palaeoecological study combining sedimentary ancient DNA (sedaDNA), pollen, spores, stomata, charcoal and plant macrofossils from the Alps. We reconstructed the Holocene vegetation dynamics and fire history at Lago Inferiore del Sangiatto (1980 m asl), a small lake in the subalpine belt of the Ossola region, Italian Lepontine Alps. Afforestation in response to climate warming started at 10,700 cal yr BP with Larix decidua and tree Betula, which formed open forests together with Pinus cembra from 10,500 cal yr BP onwards. Human impact on the regional vegetation started at 5100 cal yr BP, resulting in expansions of Picea abies and Alnus viridis and the collapse of Abies alba. Species response models and ordination analysis show that livestock grazing and fire were major drivers of vegetation change at Lago Inferiore del Sangiatto during the late Holocene. Finally, increasing human impact during the Bronze (ca. 4200e2900 cal yr BP) and Iron Age (ca. 2900 e2000 cal yr BP) led to the formation of species-rich larch meadows and alpine pastures that are still dominant today. The palaeoecological data suggest that under projected climate change and land abandonment, the treeline ecotone will likely shift to higher altitudes, leading to important changes in species composition and increasing the risk of biodiversity loss.
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- 2022
15. sPlotOpen – An environmentally balanced, open‐access, global dataset of vegetation plots
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Ben Sparrow, V. B. Martynenko, Jonathan Lenoir, Eszter Ruprecht, Idoia Biurrun, Luzmila Arroyo, Borja Jiménez-Alfaro, Aníbal Pauchard, Roberto Venanzoni, Stephan M. Hennekens, Mohamed Z. Hatim, Cyrus Samimi, Arkadiusz Nowak, Gerhard E. Overbeck, Petr Sklenář, Renata Ćušterevska, Valentin Golub, Eduardo Vélez-Martin, Gwendolyn Peyre, Inger Greve Alsos, Ioannis Tsiripidis, Tarek Hattab, Andrey Yu. Korolyuk, Jutta Kapfer, Jörg Ewald, Donald M. Waller, Ute Jandt, Tetiana Dziuba, Marco Schmidt, Alvaro G. Gutiérrez, Thomas Wohlgemuth, Adrian Indreica, Zygmunt Kącki, Jürgen Dengler, Željko Škvorc, Dirk Nikolaus Karger, Panayotis Dimopoulos, Viktor Onyshchenko, Hanhuai Shan, John Janssen, Hua Feng Wang, Holger Kreft, Jérôme Munzinger, Brian J. Enquist, Frederic Lens, Wannes Hubau, Birgit Jedrzejek, Alexander Christian Vibrans, Miguel D. Mahecha, Emmanuel Garbolino, Sophie Gachet, Abel Monteagudo Mendoza, Josep Peñuelas, Melisa A. Giorgis, Svetlana Aćić, Débora Vanessa Lingner, Victor V. Chepinoga, Richard Field, Ladislav Mucina, Michele De Sanctis, Mohamed A. El-Sheikh, Isabelle Aubin, Hamid Gholizadeh, Fahmida Sultana, Fabio Attorre, Valerijus Rašomavičius, Cindy Q. Tang, Tomáš Černý, Gonzalo Rivas-Torres, Donald A. Walker, Alicia Teresa Rosario Acosta, Timothy J. Killeen, Francesco Maria Sabatini, Susan K. Wiser, Urban Šilc, Andraž Čarni, Florian Jansen, Valério D. Pillar, Jonas V. Müller, Aaron Pérez-Haase, Els De Bie, Antonio Galán-de-Mera, Zhiyao Tang, Anne D. Bjorkman, Sylvia Haider, Kiril Vassilev, Risto Virtanen, Henrik von Wehrden, Hjalmar S. Kühl, Manfred Finckh, Zvjezdana Stančić, Pavel Shirokikh, Elizabeth Kearsley, Petr Petřík, Yves Bergeron, Iva Apostolova, Emiliano Agrillo, Jozef Šibík, Norbert Jürgens, Marta Gaia Sperandii, Anna Kuzemko, Jens-Christian Svenning, Timothy J. S. Whitfeld, Michael Kessler, Bruno Hérault, John-Arvid Grytnes, Laura Casella, Tomáš Peterka, Miguel Alvarez, Tsipe Aavik, Gregory Richard Guerin, André Luis de Gasper, Corrado Marcenò, Luis Cayuela, Brody Sandel, Cyrille Violle, Jens Kattge, Guillermo Hinojos Mendoza, Anke Jentsch, Arindam Banerjee, Jesper Erenskjold Moeslund, Mohammed Abu Sayed Arfin Khan, Patrice de Ruffray, Milan Chytrý, S. M. Yamalov, Tatiana Lysenko, Meelis Pärtel, Viktoria Bondareva, Helge Bruelheide, John S. Rodwell, Jiri Dolezal, Oliver L. Phillips, Rasmus Revermann, Larisa Khanina, Erwin Bergmeier, Robert K. Peet, Jörg Brunet, Solvita Rūsiņa, Oliver Purschke, Gianmaria Bonari, Jürgen Homeier, Martin Zobel, János Csiky, Marijn Bauters, Jalil Noroozi, Karsten Wesche, Kim André Vanselow, Norbert Hölzel, Flavia Landucci, Farideh Fazayeli, Wolfgang Willner, Viktoria Wagner, Alireza Naqinezhad, Aurora Levesley, Vadim Prokhorov, Hongyan Liu, Ali Kavgaci, Rodolfo Vásquez Martínez, Franziska Schrodt, Attila Lengyel, Elise A. Arnst, Sabatini F.M., Lenoir J., Hattab T., Arnst E.A., Chytry M., Dengler J., De Ruffray P., Hennekens S.M., Jandt U., Jansen F., Jimenez-Alfaro B., Kattge J., Levesley A., Pillar V.D., Purschke O., Sandel B., Sultana F., Aavik T., Acic S., Acosta A.T.R., Agrillo E., Alvarez M., Apostolova I., Arfin Khan M.A.S., Arroyo L., Attorre F., Aubin I., Banerjee A., Bauters M., Bergeron Y., Bergmeier E., Biurrun I., Bjorkman A.D., Bonari G., Bondareva V., Brunet J., Carni A., Casella L., Cayuela L., Cerny T., Chepinoga V., Csiky J., Custerevska R., De Bie E., de Gasper A.L., De Sanctis M., Dimopoulos P., Dolezal J., Dziuba T., El-Sheikh M.A.E.-R.M., Enquist B., Ewald J., Fazayeli F., Field R., Finckh M., Gachet S., Galan-de-Mera A., Garbolino E., Gholizadeh H., Giorgis M., Golub V., Alsos I.G., Grytnes J.-A., Guerin G.R., Gutierrez A.G., Haider S., Hatim M.Z., Herault B., Hinojos Mendoza G., Holzel N., Homeier J., Hubau W., Indreica A., Janssen J.A.M., Jedrzejek B., Jentsch A., Jurgens N., Kacki Z., Kapfer J., Karger D.N., Kavgaci A., Kearsley E., Kessler M., Khanina L., Killeen T., Korolyuk A., Kreft H., Kuhl H.S., Kuzemko A., Landucci F., Lengyel A., Lens F., Lingner D.V., Liu H., Lysenko T., Mahecha M.D., Marceno C., Martynenko V., Moeslund J.E., Monteagudo Mendoza A., Mucina L., Muller J.V., Munzinger J., Naqinezhad A., Noroozi J., Nowak A., Onyshchenko V., Overbeck G.E., Partel M., Pauchard A., Peet R.K., Penuelas J., Perez-Haase A., Peterka T., Petrik P., Peyre G., Phillips O.L., Prokhorov V., Rasomavicius V., Revermann R., Rivas-Torres G., Rodwell J.S., Ruprecht E., Rusina S., Samimi C., Schmidt M., Schrodt F., Shan H., Shirokikh P., Sibik J., Silc U., Sklenar P., Skvorc Z., Sparrow B., Sperandii M.G., Stancic Z., Svenning J.-C., Tang Z., Tang C.Q., Tsiripidis I., Vanselow K.A., Vasquez Martinez R., Vassilev K., Velez-Martin E., Venanzoni R., Vibrans A.C., Violle C., Virtanen R., von Wehrden H., Wagner V., Walker D.A., Waller D.M., Wang H.-F., Wesche K., Whitfeld T.J.S., Willner W., Wiser S.K., Wohlgemuth T., Yamalov S., Zobel M., Bruelheide H., Sabatini, Fm, Lenoir, J, Hattab, T, Arnst, Ea, Chytry, M, Dengler, J, De Ruffray, P, Hennekens, Sm, Jandt, U, Jansen, F, Jimenez-Alfaro, B, Kattge, J, Levesley, A, Pillar, Vd, Purschke, O, Sandel, B, Sultana, F, Aavik, T, Acic, S, Acosta, Atr, Agrillo, E, Alvarez, M, Apostolova, I, Khan, Masa, Arroyo, L, Attorre, F, Aubin, I, Banerjee, A, Bauters, M, Bergeron, Y, Bergmeier, E, Biurrun, I, Bjorkman, Ad, Bonari, G, Bondareva, V, Brunet, J, Carni, A, Casella, L, Cayuela, L, Cerny, T, Chepinoga, V, Csiky, J, Custerevska, R, De Bie, E, de Gasper, Al, De Sanctis, M, Dimopoulos, P, Dolezal, J, Dziuba, T, El-Sheikh, Mam, Enquist, B, Ewald, J, Fazayeli, F, Field, R, Finckh, M, Gachet, S, Galan-de-Mera, A, Garbolino, E, Gholizadeh, H, Giorgis, M, Golub, V, Alsos, Ig, Grytnes, Ja, Guerin, Gr, Gutierrez, Ag, Haider, S, Hatim, Mz, Herault, B, Mendoza, Gh, Holzel, N, Homeier, J, Hubau, W, Indreica, A, Janssen, Jam, Jedrzejek, B, Jentsch, A, Jurgens, N, Kacki, Z, Kapfer, J, Karger, Dn, Kavgaci, A, Kearsley, E, Kessler, M, Khanina, L, Killeen, T, Korolyuk, A, Kreft, H, Kuhl, H, Kuzemko, A, Landucci, F, Lengyel, A, Lens, F, Lingner, Dv, Liu, Hy, Lysenko, T, Mahecha, Md, Marceno, C, Martynenko, V, Moeslund, Je, Mendoza, Am, Mucina, L, Muller, Jv, Munzinger, Jm, Naqinezhad, A, Noroozi, J, Nowak, A, Onyshchenko, V, Overbeck, Ge, Partel, M, Pauchard, A, Peet, Rk, Penuelas, J, Perez-Haase, A, Peterka, T, Petrik, P, Peyre, G, Phillips, Ol, Prokhorov, V, Rasomavicius, V, Revermann, R, Rivas-Torres, G, Rodwell, J, Ruprecht, E, Rusina, S, Samimi, C, Schmidt, M, Schrodt, F, Shan, Hh, Shirokikh, P, Sibik, J, Silc, U, Sklenar, P, Skvorc, Z, Sparrow, B, Sperandii, Mg, Stancic, Z, Svenning, Jc, Tang, Zy, Tang, Cq, Tsiripidis, I, Vanselow, Ka, Martinez, Rv, Vassilev, K, Velez-Martin, E, Venanzoni, R, Vibrans, Ac, Violle, C, Virtanen, R, von Wehrden, H, Wagner, V, Walker, Da, Waller, Dm, Wang, Hf, Wesche, K, Whitfeld, Tj, Willner, W, Wiser, Sk, Wohlgemuth, T, Yamalov, S, Zobel, M, Bruelheide, H, Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut méditerranéen de biodiversité et d'écologie marine et continentale (IMBE), Avignon Université (AU)-Aix Marseille Université (AMU)-Institut de recherche pour le développement [IRD] : UMR237-Centre National de la Recherche Scientifique (CNRS), Centre de recherche sur les Risques et les Crises (CRC), Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Botanique et Modélisation de l'Architecture des Plantes et des Végétations (UMR AMAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-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), 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)-Université de Montpellier (UM)-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 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), ANR-07-BDIV-0006,BIONEOCAL,L'endémisme en Nouvelle-Calédonie : étude phylogénétique et populationnelle des son émergence.(2007), ANR-07-BDIV-0008,INC,Incendies et biodiversité de écosystèmes en Nouvelle-Calédonie.(2007), ANR-07-BDIV-0010,ULTRABIO,Biodiversité et stratégies adaptatives végétales et microbiennes des écosystèmes ultramafiques en Nouvelle-Calédonie.(2007), European Project: 610028,EC:FP7:ERC,ERC-2013-SyG,IMBALANCE-P(2014), European Project: 291585,EC:FP7:ERC,ERC-2011-ADG_20110209,T-FORCES(2012), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), MINES ParisTech - École nationale supérieure des mines de Paris, 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), and 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)
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0106 biological sciences ,Biome ,Bos- en Landschapsecologie ,Biodiversity ,DIVERSITY ,FOREST VEGETATION ,01 natural sciences ,purl.org/becyt/ford/1 [https] ,Abundance (ecology) ,big data ,Vegetation type ,PHYTOSOCIOLOGICAL DATABASE ,parcelle ,Forest and Landscape Ecology ,functional traits ,vascular plants ,biodiversity ,biogeography ,database ,macroecology ,vegetation plots ,Macroecology ,[SDV.EE]Life Sciences [q-bio]/Ecology, environment ,Global and Planetary Change ,Ecology ,vascular plant ,Vegetation ,F70 - Taxonomie végétale et phytogéographie ,PE&RC ,Vegetation plot ,Geography ,580: Pflanzen (Botanik) ,Ecosystems Research ,Diffusion de l'information ,Plantenecologie en Natuurbeheer ,Vegetatie, Bos- en Landschapsecologie ,Biodiversité ,ARCHIVE ,Communauté végétale ,Evolution ,[SDE.MCG]Environmental Sciences/Global Changes ,Biogéographie ,GRASSLAND VEGETATION ,Plant Ecology and Nature Conservation ,[SDV.BID]Life Sciences [q-bio]/Biodiversity ,010603 evolutionary biology ,Behavior and Systematics ,Couverture végétale ,577: Ökologie ,PLANT ,purl.org/becyt/ford/1.6 [https] ,functional trait ,Biology ,Ecology, Evolution, Behavior and Systematics ,Vegetatie ,010604 marine biology & hydrobiology ,Impact sur l'environnement ,DRY GRASSLANDS ,Plant community ,15. Life on land ,Végétation ,WETLAND VEGETATION ,Earth and Environmental Sciences ,UNIVERSITY ,Physical geography ,Vegetation, Forest and Landscape Ecology ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,données ouvertes - Abstract
Datos disponibles en https://github.com/fmsabatini/sPlotOpen_Code, EU H2020 project BACI, Grant No. 640176 (...), Sabatini, F.M., Lenoir, J., Hattab, T., Arnst, E.A., Chytrý, M., Dengler, J., De Ruffray, P., Hennekens, S.M., Jandt, U., Jansen, F., Jiménez-Alfaro, B., Kattge, J., Levesley, A., Pillar, V.D., Purschke, O., Sandel, B., Sultana, F., Aavik, T., Aćić, S., Acosta, A.T.R., Agrillo, E., Alvarez, M., Apostolova, I., Arfin Khan, M.A.S., Arroyo, L., Attorre, F., Aubin, I., Banerjee, A., Bauters, M., Bergeron, Y., Bergmeier, E., Biurrun, I., Bjorkman, A.D., Bonari, G., Bondareva, V., Brunet, J., Čarni, A., Casella, L., Cayuela, L., Černý, T., Chepinoga, V., Csiky, J., Ćušterevska, R., De Bie, E., de Gasper, A.L., De Sanctis, M., Dimopoulos, P., Dolezal, J., Dziuba, T., El-Sheikh, M.A.E.-R.M., Enquist, B., Ewald, J., Fazayeli, F., Field, R., Finckh, M., Gachet, S., Galán-de-Mera, A., Garbolino, E., Gholizadeh, H., Giorgis, M., Golub, V., Alsos, I.G., Grytnes, J.-A., Guerin, G.R., Gutiérrez, A.G., Haider, S., Hatim, M.Z., Hérault, B., Hinojos Mendoza, G., Hölzel, N., Homeier, J., Hubau, W., Indreica, A., Janssen, J.A.M., Jedrzejek, B., Jentsch, A., Jürgens, N., Kącki, Z., Kapfer, J., Karger, D.N., Kavgacı, A., Kearsley, E., Kessler, M., Khanina, L., Killeen, T., Korolyuk, A., Kreft, H., Kühl, H.S., Kuzemko, A., Landucci, F., Lengyel, A., Lens, F., Lingner, D.V., Liu, H., Lysenko, T., Mahecha, M.D., Marcenò, C., Martynenko, V., Moeslund, J.E., Monteagudo Mendoza, A., Mucina, L., Müller, J.V., Munzinger, J., Naqinezhad, A., Noroozi, J., Nowak, A., Onyshchenko, V., Overbeck, G.E., Pärtel, M., Pauchard, A., Peet, R.K., Peñuelas, J., Pérez-Haase, A., Peterka, T., Petřík, P., Peyre, G., Phillips, O.L., Prokhorov, V., Rašomavičius, V., Revermann, R., Rivas-Torres, G., Rodwell, J.S., Ruprecht, E., Rūsiņa, S., Samimi, C., Schmidt, M., Schrodt, F., Shan, H., Shirokikh, P., Šibík, J., Šilc, U., Sklenář, P., Škvorc, Ž., Sparrow, B., Sperandii, M.G., Stančić, Z., Svenning, J.-C., Tang, Z., Tang, C.Q., Tsiripidis, I., Vanselow, K.A., Vásquez Martínez, R., Vassilev, K., Vélez-Martin, E., Venanzoni, R., Vibrans, A.C., Violle, C., Virtanen, R., von Wehrden, H., Wagner, V., Walker, D.A., Waller, D.M., Wang, H.-F., Wesche, K., Whitfeld, T.J.S., Willner, W., Wiser, S.K., Wohlgemuth, T., Yamalov, S., Zobel, M., Bruelheide, H.
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- 2021
16. Sedimentary ancient DNA shows terrestrial plant richness continuously increased over the Holocene in northern Fennoscandia
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Iva Pitelkova, Dilli Prasad Rijal, Tomasz Goslar, Youri Lammers, Nigel G. Yoccoz, Karin F. Helmens, Inger Greve Alsos, Francisco Javier Ancin Murguzur, Torbjørn Alm, Kari Anne Bråthen, Mary E. Edwards, Peter D. Heintzman, Antony G. Brown, Kelsey Lorberau, Jostein Bakke, J. Sakari Salonen, and Department of Geosciences and Geography
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0106 biological sciences ,1171 Geosciences ,010506 paleontology ,010504 meteorology & atmospheric sciences ,Climate Change ,ved/biology.organism_classification_rank.species ,Annan geovetenskap och miljövetenskap ,Climate change ,medicine.disease_cause ,010603 evolutionary biology ,01 natural sciences ,Nutrient ,Effects of global warming ,Pollen ,Terrestrial plant ,medicine ,Humans ,DNA, Ancient ,Research Articles ,Ecosystem ,Holocene ,1172 Environmental sciences ,VDP::Mathematics and natural science: 400 ,0105 earth and related environmental sciences ,Multidisciplinary ,Ecology ,ved/biology ,Plant Sciences ,SciAdv r-articles ,VDP::Matematikk og Naturvitenskap: 400 ,Plants ,15. Life on land ,Lakes ,Geography ,Ancient DNA ,13. Climate action ,Species richness ,Other Earth and Related Environmental Sciences ,Research Article - Abstract
SedaDNA reveals regional climate and bedrock nutrients as major drivers of terrestrial plant diversity in northern Fennoscandia., The effects of climate change on species richness are debated but can be informed by the past. Here, we generated a sedimentary ancient DNA dataset covering 10 lakes and applied novel methods for data harmonization. We assessed the impact of Holocene climate changes and nutrients on terrestrial plant richness in northern Fennoscandia. We find that richness increased steeply during the rapidly warming Early Holocene. In contrast to findings from most pollen studies, we show that richness continued to increase thereafter, although the climate was stable, with richness and the regional species pool only stabilizing during the past three millennia. Furthermore, overall increases in richness were greater in catchments with higher soil nutrient availability. We suggest that richness will increase with ongoing warming, especially at localities with high nutrient availability and assuming that human activity remains low in the region, although lags of millennia may be expected.
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- 2021
17. Environmental palaeogenomic reconstruction of an Ice Age algal population
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Peter D. Heintzman, Inger Greve Alsos, and Youri Lammers
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0106 biological sciences ,Geologic Sediments ,Chloroplasts ,Population genetics ,QH301-705.5 ,Population ,Medicine (miscellaneous) ,Biology ,Polymorphism, Single Nucleotide ,010603 evolutionary biology ,01 natural sciences ,Genome ,Article ,General Biochemistry, Genetics and Molecular Biology ,Haplogroup ,03 medical and health sciences ,DNA, Algal ,Algae ,Microalgae ,Ice age ,DNA, Ancient ,Biology (General) ,education ,Phylogeny ,030304 developmental biology ,VDP::Mathematics and natural science: 400 ,0303 health sciences ,education.field_of_study ,Fossils ,Haplotype ,Paleontology ,Palaeoecology ,Last Glacial Maximum ,VDP::Matematikk og Naturvitenskap: 400 ,biology.organism_classification ,Computational biology and bioinformatics ,Taxon ,Ancient DNA ,Haplotypes ,Evolutionary biology ,Genome, Mitochondrial ,Metagenomics ,General Agricultural and Biological Sciences - Abstract
Palaeogenomics has greatly increased our knowledge of past evolutionary and ecological change, but has been restricted to the study of species that preserve either as or within fossils. Here we show the potential of shotgun metagenomics to reveal population genomic information for a taxon that does not preserve in the body fossil record, the algae Nannochloropsis. We shotgun sequenced two lake sediment samples dated to the Last Glacial Maximum and reconstructed full chloroplast and mitochondrial genomes to explore within-lake population genomic variation. This revealed two major haplogroups for each organellar genome, which could be assigned to known varieties of N. limnetica, although we show that at least three haplotypes were present using our minimum haplotype diversity estimation method. These approaches demonstrate the utility of lake sedimentary ancient DNA (sedaDNA) for population genomic analysis, thereby opening the door to environmental palaeogenomics, which will unlock the full potential of sedaDNA., Lammers et al. use sedimentary ancient DNA to reconstruct palaeogenomes of Nannochloropsis. This study demonstrates the value of sedaDNA for palaeogenomic reconstructions and population genomic analysis.
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- 2021
18. Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations
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Ulrike Herzschuh, Inger Greve Alsos, Marco J. L. Coolen, Marie-Eve Monchamp, Stefan Bertilsson, Daniel Ariztegui, Antony G. Brown, Laura S. Epp, Sarah E. Crump, Aurèle Vuillemin, Mikkel Winther Pedersen, Rebecca E. Garner, Irene Gregory-Eaves, David A. Walsh, Simon Belle, Kevin Nota, Youri Lammers, Kurt H. Kjær, Liv Heinecke, Camille Thomas, Fredrik Olajos, Joanna Gauthier, Göran Englund, Liisi Talas, Isabelle Domaizon, Joanne E. Littlefair, Charlotte Clarke, Eric Capo, Anan Ibrahim, Eske Willerslev, Didier Debroas, Johan Rydberg, Y. L. Wang, Fabien Arnaud, Trisha L. Spanbauer, Peter D. Heintzman, Pierre Taberlet, Gentile Francesco Ficetola, Dilli Prasad Rijal, Charline Giguet-Covex, Richard Bindler, Laura Parducci, Alexandra Rouillard, Kathleen R. Stoof-Leichsenring, Veljo Kisand, Heike Zimmermann, Christian Bigler, Anne van Woerkom, William D. Orsi, Erwan Messager, Umeå University, Environnements, Dynamiques et Territoires de Montagne (EDYTEM), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS), The Arctic University of Norway [Tromsø, Norway] (UiT), University of Copenhagen = Københavns Universitet (UCPH), Uppsala University, Department of Earth & Environmental Sciences, Ludwig-Maximilians-Universität München, 80331 Munich, GeoBio-CenterLMU, Université de Genève = University of Geneva (UNIGE), Swedish University of Agricultural Sciences (SLU), School of Geography and Environmental Science, University of Southampton, Southampton SO17 1BJ, Institute of Arctic Alpine Research [University of Colorado Boulder] (INSTAAR), University of Colorado [Boulder], Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Department of Environmental Science and Policy [Milano], Università degli Studi di Milano = University of Milan (UNIMI), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), Department of Biology [Concordia], Concordia University [Montreal], Groupe de recherche interuniversitaire en limnologie et en environnement aquatique - GRIL (Montréal, Canada), Université de Montréal (UdeM), Department of Biology [McGill University], McGill University = Université McGill [Montréal, Canada], ALFRED WEGENER INSTITUTE HELMHOLTZ CENTRE FOR POLAR AND MARINE RESEARCH POTSDAM DEU, 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), Institute of Mathematics, University of Potsdam = Universität Potsdam, Institute for Environmental Sciences and Geography, University of Potsdam, Department of Biology, University of Konstanz, Konstanz, Germany, University of Tartu, School of Biological and Chemical Sciences, Queen Mary University of London, London, UK., Department of Environmental Sciences and Lake Erie Center, University of Toledo, Toledo, OH 43606, University of Cambridge [UK] (CAM), Western Australia Organic and Isotope Geochemistry Centre, School of Earth and Planetary Sciences, the Institute for Geoscience Research (TIGeR), Curtin University, Bentley 6102, Limnological Institute, Department of Biology, University of Konstanz, 78464 Konstanz, Centre Alpin de Recherche sur les Réseaux Trophiques et Ecosystèmes Limniques (CARRTEL), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Environmental Biology, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Roma, Italy, Knut & Alice Wallenberg Foundation2016.0083Swedish Research Council for Sustainable Development FormasFR-2016/0005Research Council of NorwayEuropean Commission250963/F20German Research Foundation (DFG)OR 417/1-1VU 94/1-1E, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Ecology and Environmental Science, Umeå University, Environnements, Dynamiques et Territoires de la Montagne (EDYTEM), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Department of Geosciences, UiT the Arctic University of Norway, 9019 Tromsø, Section for Geogenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Department of Ecology and Genetics, the Evolutionary Biology Centre, Uppsala University, 752 36 Uppsala, The Arctic University Museum of Norway, UiT the Arctic University of Norway, 9010 Tromsø, Department of Earth Sciences, University of Geneva, University of Geneva [Switzerland], Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 75007 Uppsala, Institute of Arctic and Alpine Research (INSTAAR), Università degli Studi di Milano [Milano] (UNIMI), Department of Biology, Concordia University, Montréal, Department of Biology, McGill University, Montreal, Canada, University of Potsdam, Institute of Technology, University of Tartu, 50090 Tartu, Department of Zoology, University of Cambridge, Cambridge, United Kingdom, Willerslev, Eske [0000-0002-7081-6748], and Apollo - University of Cambridge Repository
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0106 biological sciences ,Earth science ,[SDV]Life Sciences [q-bio] ,Biodiversity ,lake sediments ,Sedimentary DNA ,lcsh:GN281-289 ,Oceanografi, hydrologi och vattenresurser ,Aquatic biota ,01 natural sciences ,Paleolimnology ,paleoecology ,Oceanography, Hydrology and Water Resources ,sedimentary ancient DNA ,Earth and Planetary Sciences (miscellaneous) ,ddc:550 ,lcsh:QE640-699 ,biodiversity ,0303 health sciences ,paleolimnology ,Paleogenetics ,Lake sediments ,VDP::Mathematics and natural science: 400::Geosciences: 450::Stratigraphy and paleontology: 461 ,[SDE]Environmental Sciences ,lcsh:Human evolution ,ancient DNA ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Sedimentologi: 456 ,sedimentary DNA ,paleogenetics ,paleogenomics ,metabarcoding ,metagenomics ,010603 evolutionary biology ,03 medical and health sciences ,lcsh:Stratigraphy ,VDP::Mathematics and natural science: 400::Geosciences: 450::Sedimentology: 456 ,ddc:570 ,030304 developmental biology ,Earth-Surface Processes ,Sedimentary ancient DNA ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Stratigrafi og paleontologi: 461 ,Geokemi ,Ancient DNA ,Geochemistry ,Paleogenomics ,Metagenomics ,Paleoecology ,Metabarcoding ,Environmental science ,Sedimentary rock - Abstract
International audience; The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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- 2021
19. Late Quaternary dynamics of Arctic biota from ancient environmental genomics
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Inger Greve Alsos, David Bravo Nogues, Adriana Alberti, Jialu Cao, Youri Lammers, Thorfinn Sand Korneliussen, Yubin Zhang, Alexandra Rouillard, Eske Willerslev, Antonio Fernandez-Guerra, John Inge Svendsen, Jeffrey T. Rasic, David W. Beilman, Patrick Wincker, Per Möller, Fernando Racimo, Christoph Dockter, Alexei Tikhonov, Marie Kristine Føreid Merkel, Anna Cherezova, Julie Esdale, Lasse Vinner, Daniel Money, Duane G. Froese, Bianca De Sanctis, Anthony Ruter, Hannah L. Owens, Hugh McColl, Richard Durbin, Galina Gusarova, David J. Meltzer, Neil R. Edwards, James Haile, Nicolaj K. Larsen, Yingchun Xing, Kurt H. Kjær, Jan Mangerud, Mary E. Edwards, Kristian K. Kjeldsen, Mikkel Winther Pedersen, Birgitte Skadhauge, Carsten Rahbek, Grigory Fedorov, Eric Coissac, Ludovic Orlando, Anders A. Bjørk, Y. L. Wang, Philip B. Holden, Ana Prohaska, Wang, Yucheng [0000-0002-7838-226X], Pedersen, Mikkel Winther [0000-0002-7291-8887], Alsos, Inger Greve [0000-0002-8610-1085], Prohaska, Ana [0000-0001-5459-6186], Rouillard, Alexandra [0000-0001-5778-6620], Alberti, Adriana [0000-0003-3372-9423], Denoeud, France [0000-0001-8819-7634], Money, Daniel [0000-0001-5151-3648], McColl, Hugh [0000-0002-7568-4270], Cherezova, Anna A. [0000-0002-6199-8164], Haile, James [0000-0002-8521-8337], Orlando, Ludovic [0000-0003-3936-1850], Beilman, David W. [0000-0002-2625-6747], Dockter, Christoph [0000-0001-5923-3667], Kjeldsen, Kristian K. [0000-0002-8557-5131], Mangerud, Jan [0000-0003-4793-7557], Rasic, Jeffrey T. [0000-0002-3549-6590], Skadhauge, Birgitte [0000-0001-7317-4376], Wincker, Patrick [0000-0001-7562-3454], Zhang, Yubin [0000-0003-4920-3100], Froese, Duane G. [0000-0003-1032-5944], Holden, Philip B. [0000-0002-2369-0062], Edwards, Neil R. [0000-0001-6045-8804], Durbin, Richard [0000-0002-9130-1006], Meltzer, David J. [0000-0001-8084-9802], Willerslev, Eske [0000-0002-7081-6748], Apollo - University of Cambridge Repository, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), 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)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE), Cherezova, Anna A [0000-0002-6199-8164], Beilman, David W [0000-0002-2625-6747], Kjeldsen, Kristian K [0000-0002-8557-5131], Rasic, Jeffrey T [0000-0002-3549-6590], Froese, Duane G [0000-0003-1032-5944], Holden, Philip B [0000-0002-2369-0062], Edwards, Neil R [0000-0001-6045-8804], Meltzer, David J [0000-0001-8084-9802], Apollo-University Of Cambridge Repository, University of Copenhagen = Københavns Universitet (UCPH)-University of Copenhagen = Københavns Universitet (UCPH), and 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)
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Geologic Sediments ,010504 meteorology & atmospheric sciences ,Woolly mammoth ,Rain ,[SDV]Life Sciences [q-bio] ,Greenland ,Population Dynamics ,Datasets as Topic ,Permafrost ,01 natural sciences ,631/158/2463 ,631/158/2462 ,Mammoths ,631/208/212/2142 ,Woolly rhinoceros ,Megafauna ,Databases, Genetic ,38/23 ,History, Ancient ,Phylogeny ,0303 health sciences ,education.field_of_study ,Multidisciplinary ,biology ,Arctic Regions ,Ecology ,Climate-change ecology ,631/208/514/2254 ,704/158/2165 ,article ,Palaeoecology ,Biota ,Vegetation ,Plants ,Grassland ,Mitochondria ,Geography ,[SDE]Environmental Sciences ,Climate Change ,Population ,45/22 ,Extinction, Biological ,03 medical and health sciences ,Spatio-Temporal Analysis ,VDP::Mathematics and natural science: 400::Zoology and botany: 480 ,Animals ,Humans ,Herbivory ,14. Life underwater ,DNA, Ancient ,education ,Perissodactyla ,030304 developmental biology ,0105 earth and related environmental sciences ,Mammoth ,15. Life on land ,biology.organism_classification ,DNA, Environmental ,Siberia ,Lakes ,Haplotypes ,Arctic ,13. Climate action ,Wetlands ,Ecological networks ,Next-generation sequencing ,Metagenomics ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 - Abstract
Acknowledgements: Acknowledgements: We thank D. H. Mann for his detailed and constructive comments; and T. Ager, J. Austin, T. B. Brand, A. Cooper, S. Funder, M. T. P. Gilbert, T. Jørgensen, N. J. Korsgaard, S. Liu, M. Meldgaard, P. V. S. Olsen, M. L. Siggaard-Andersen, J. Stenderup, S. A. Woodroffe and staff at the GeoGenetics Sequencing Core and National Park Service-Western Arctic National Parklands for help and support. E.W. and D.J.M. thank the staff at St. John’s College, Cambridge, for providing a stimulating environment for scientific discussion of the project. E.W. thanks Illumina for collaboration. The Lundbeck Foundation GeoGenetics Centre is supported by the Carlsberg Foundation (CF18-0024), the Lundbeck Foundation (R302-2018-2155), the Novo Nordisk Foundation (NNF18SA0035006), the Wellcome Trust (UNS69906) and GRF EXC CRS Chair (44113220)—Cluster of Excellence. The PhyloNorway plant genome database is part of the Norwegian Barcode of Life Network (https://www.norbol.org) funded by the Research Council of Norway (226134/F50), the Norwegian Biodiversity Information Centre (14-14, 70184209) and The Arctic University Museum of Norway. Metabarcoding sequencing was funded by the Central Public-Interest Scientific Institution Basal Research Fund, CAFS (2017B001 and 2020A001). B.D.S. is supported by the Wellcome Trust programme in Mathematical Genomics and Medicine (WT220023); F.R. by a Villum Fonden Young Investigator award (no. 00025300); D.J.M. by the Quest Archaeological Research Fund; P.M. by the Swedish Research Council (VR); R.D. by the Wellcome Trust (WT207492); and A.R. by a Marie Skłodowska-Curie Actions Individual Fellowship (MSCA-IF, 703542) and the Research Council of Norway (KLIMAFORSK, 294929). L.O. has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (no. 681605); I.G.A. and Y.L. from the ERC under the European Union’s Horizon 2020 research and innovation programme (no. 819192). J.I.S. and J.M. are supported by the Research Council of Norway. P.B.H. and N.R.E. acknowledge NERC funding (grant NE/P015093/1). D.W.B. was supported by a Marie Skłodowska-Curie Actions Incoming International Fellowship (MCIIF-40974). T.S.K. is funded by a Carlsberg Foundation Young Researcher Fellowship (CF19-0712)., During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.
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- 2021
20. Rapid climate changes during the Lateglacial and the early Holocene as seen from plant community dynamics in the Polar Urals, Russia
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Charlotte Clarke, Aage Paus, Haflidi Haflidason, Maren S. Johansen, Jo Brendryen, Anne E. Bjune, Inger Greve Alsos, Jan Mangerud, Mary E. Edwards, John Inge Svendsen, and Carl Regnéll
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Paleontology ,Climate change ,Plant community ,medicine.disease_cause ,Arts and Humanities (miscellaneous) ,Pollen ,Earth and Planetary Sciences (miscellaneous) ,medicine ,VDP::Mathematics and natural science: 400::Zoology and botany: 480 ,Polar ,Physical geography ,Holocene ,Geology ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 - Abstract
A detailed, well-dated record of pollen and sedimentary ancient DNA (sedaDNA) for the period 15 000–9500 cal a bp describes changes at Lake Bolshoye Shchuchye in the Polar Ural Mountains, located far east of the classical Lateglacial sites in western Europe. Arctic tundra rapidly changed to lusher vegetation, possibly including both dwarf (Betula nana) and tree birch (B. pubescens), dated in our record to take place 14 565 cal a bp, coincident with the onset of the Bølling in western Europe; this was paralleled by increased summer temperatures. A striking feature is an early decline in Betula pollen and sedaDNA reads 300 years before the onset of the Younger Dryas (YD) in western Europe. Given the solid site chronology, this could indicate that the YD cooling started in Siberia and propagated westwards, or that the vegetation reacted to the inter-Allerød cooling at 13 100 cal a bp and did not recover during the late Allerød. During the YD, increases in steppe taxa such as Artemisia and Chenopodiaceae suggest drier conditions. At the onset of the Holocene, the vegetation around the lake reacted fast to the warmer conditions, as seen in the increase of arboreal taxa, especially Betula, and a decrease in herbs such as Artemisia and Cyperaceae. publishedVersion
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- 2021
21. Ancient DNA, Lipid Biomarkers and Palaeoecological Evidence Reveals Construction and Life on early Medieval Lake Settlements
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Ludovic Gielly, Nicki J. Whitehouse, Gentile Francesco Ficetola, Andrew C. G. Henderson, Peter G. Langdon, K. Head, Antony G. Brown, Phil Barratt, Finbar McCormick, Inger Greve Alsos, Graeme Cavers, Kimberley Davies, E. Murray, Thierry Fonville, Duncan Pirrie, M. van Hardenbroek, Helen Mackay, and Anne Crone
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0301 basic medicine ,010506 paleontology ,Celtic languages ,Science ,Wetland ,01 natural sciences ,Article ,03 medical and health sciences ,Human settlement ,Limnology ,Animals ,Humans ,DNA, Ancient ,0105 earth and related environmental sciences ,geography ,Minerals ,Multidisciplinary ,geography.geographical_feature_category ,Ecology ,Biological techniques ,Radiometric Dating ,food and beverages ,Excavation ,Archaeology ,Lipids ,History, Medieval ,United Kingdom ,Food resources ,Environmental social sciences ,Lakes ,030104 developmental biology ,Ancient DNA ,Medicine ,Lipid biomarkers ,Ireland ,Biomarkers ,Chronology - Abstract
Direct evidence of ancient human occupation is typically established through archaeological excavation. Excavations are costly and destructive, and practically impossible in some lake and wetland environments. We present here an alternative approach, providing direct evidence from lake sediments using DNA metabarcoding, steroid lipid biomarkers (bile acids) and from traditional environmental analyses. Applied to an early Medieval Celtic settlement in Ireland (a crannog) this approach provides a site chronology and direct evidence of human occupation, crops, animal farming and on-site slaughtering. This is the first independently-dated, continuous molecular archive of human activity from an archeological site, demonstrating a link between animal husbandry, food resources, island use. These sites are under threat but are impossible to preserve in-situ so this approach can be used, with or without excavation, to produce a robust and full site chronology and provide direct evidence of occupation, the use of plants and animals, and activities such as butchery.
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- 2021
22. Ancient sedimentary DNA shows rapid post-glacial colonisation of Iceland followed by relatively stable vegetation until the Norse settlement (Landnám) AD 870
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Skafti Brynjólfsson, Anders Schomacker, Wesley R. Farnsworth, Emma M. Bender, Sigrún Dögg Eddudóttir, Sofia E. Kjellman, Inger Greve Alsos, Youri Lammers, Egill Erlendsson, Guðrún Gísladóttir, Esther Ruth Guðmundsdóttir, Alexandra Rouillard, Ívar Örn Benediktsson, and Marie Kristine Føreid Merkel
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010506 paleontology ,Archeology ,010504 meteorology & atmospheric sciences ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Vegetation history: 495 ,01 natural sciences ,Island ,VDP::Mathematics and natural science: 400::Geosciences: 450::Sedimentology: 456 ,14. Life underwater ,Glacial period ,Ecology, Evolution, Behavior and Systematics ,Holocene ,0105 earth and related environmental sciences ,Ekologi ,Global and Planetary Change ,Ancient DNA ,Ecology ,Geology ,Colonisation ,Vegetation ,15. Life on land ,Miljövetenskap ,Lake sediments ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Vegetasjonshistorie: 495 ,Geography ,Arctic ,Vegetation history ,13. Climate action ,Metabarcoding ,Biological dispersal ,Species richness ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Sedimentologi: 456 ,Environmental Sciences - Abstract
Understanding patterns of colonisation is important for explaining both the distribution of single species and anticipating how ecosystems may respond to global warming. Insular flora may be especially vulnerable because oceans represent severe dispersal barriers. Here we analyse two lake sediment cores from Iceland for ancient sedimentary DNA to infer patterns of colonisation and Holocene vegetation development. Our cores from lakes Torfdalsvatn and Nykurvatn span the last c. 12,000 cal yr BP and c. 8600 cal yr BP, respectively. With near-centennial resolution, we identified a total of 191 plant taxa, with 152 taxa identified in the sedimentary record of Torfdalsvatn and 172 plant taxa in the sedimentary record of Nykurvatn. The terrestrial vegetation at Torfdalsvatn was initially dominated by bryophytes, arctic herbs such as Saxifraga spp. and grasses. Around 10,100 cal yr BP, a massive immigration of new taxa was observed, and shrubs and dwarf shrubs became common whereas aquatic macrophytes became dominant. At Nykurvatn, the dominant taxa were all present in the earliest samples; shrubs and dwarf shrubs were more abundant at this site than at Torfdalsvatn. There was an overall steep increase both in the local accumulated richness and regional species pool until 8000 cal yr BP, by which time ¾ of all taxa identified had arrived. The period 4500-1000 cal yr BP witnessed the appearance of a a small number of bryophytes, graminoids and forbs that were not recorded in earlier samples. The last millennium, after human settlement of the island (Landnám), is characterised by a sudden disappearance of Juniperus communis, but also reappearance of some high arctic forbs and dwarf shrubs. Notable immigration during the Holocene coincides with periods of increased incidence of sea ice, and we hypothesise that this may have acted as a dispersal vector. Thus, although ongoing climate change might provide a suitable habitat in Iceland for a large range of species only found in the neighbouring regions today, the reduction of sea ice may in fact limit the natural colonisation of new plant species.
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- 2021
23. Molecular dietary analyses of western capercaillies (Tetrao urogallus) reveal a diverse diet
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Youri Lammers, Emmanuel Menoni, Inger Greve Alsos, Kristine Bohmann, Sanne Boessenkool, Physilia Ying Shi Chua, and Torbjørn Ekrem
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0106 biological sciences ,Adonis ,Zoology ,Grouse ,010603 evolutionary biology ,01 natural sciences ,Microbial ecology ,03 medical and health sciences ,Abundance (ecology) ,Genetics ,GE1-350 ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,VDP::Mathematics and natural science: 400 ,2. Zero hunger ,0303 health sciences ,Herbivore ,Ecology ,biology ,herbivory ,QR100-130 ,high‐throughput sequencing ,high-throughput sequencing ,Vegetation ,VDP::Matematikk og Naturvitenskap: 400 ,15. Life on land ,biology.organism_classification ,environmental DNA ,Environmental sciences ,Habitat ,grouse ,Species richness ,Tetrao urogallus ,ecology - Abstract
Conservation strategies centred around species habitat protection rely on species’ dietary information. One species at the focal point of conservation efforts is the herbivorous grouse, the western capercaillie (Tetrao urogallus). Traditional microhistological analysis of crop contents or faeces and/or direct observations are time-consuming and at low taxonomic resolution. Thus, limited knowledge on diet is hampering conservation efforts. Here we use non-invasive environmental DNA (eDNA) metabarcoding on DNA extracted from faeces to present the first large-scale molecular dietary analysis of capercaillies. Faecal samples were collected from seven populations located in Norway (Finnmark, Troms, Trøndelag, Innlandet) and France (Vosges, Jura, Pyrenees) (n=172). We detected 122 plant taxa belonging to 46 plant families of which 37.7% of the detected taxa could be identified at species level. The average dietary richness of each sample was 7 ± 5 SD taxa. The most frequently occurring plant groups with the highest relative read abundance (RRA) were trees and dwarf shrubs, in particular, Pinus and Vaccinium myrtillus, respectively. There was a difference in dietary composition (RRA) between samples collected from the different locations (adonis F5,86= 11.01, p 2,03= 0.64, p 1,47 = 2.77, p
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- 2021
24. A 24,000-year ancient DNA and pollen record from the Polar Urals reveals temporal dynamics of arctic and boreal plant communities
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Ludovic Gielly, Aage Paus, Charlotte Clarke, John Inge Svendsen, Anne E. Bjune, Carl Regnéll, Paul D.M. Hughes, Inger Greve Alsos, Mary E. Edwards, Jan Mangerud, and Haflidi Haflidason
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010506 paleontology ,Archeology ,Global and Planetary Change ,Carex ,VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470::Molekylærbiologi: 473 ,010504 meteorology & atmospheric sciences ,biology ,Ecology ,VDP::Mathematics and natural science: 400::Basic biosciences: 470::Molecular biology: 473 ,Geology ,Plant community ,biology.organism_classification ,medicine.disease_cause ,01 natural sciences ,VDP::Humanities: 000 ,Tundra ,VDP::Humaniora: 000 ,Boreal ,Pollen ,medicine ,Dominance (ecology) ,Bryophyte ,Younger Dryas ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences - Abstract
A 24,000-year record of plant community dynamics, based on pollen and ancient DNA from the sediments (sedaDNA) of Lake Bolshoye Shchuchye in the Polar Ural Mountains, provides detailed information on the flora of the Last Glacial Maximum (LGM) and also changes in plant community composition and dominance. It greatly improves on incomplete records from short and fragmented stratigraphic sequences found in exposed sedimentary sections in the western Russian Arctic. In total, 162 plant taxa were detected by sedaDNA and 115 by pollen analysis. Several shifts in dominance between and within plant functional groups occurred over the studied period, but most taxa appear to have survived in situ. A diverse arctic-alpine herb flora characterised the interval ca. 24,000–17,000 cal years BP and persisted into the Holocene. Around 17,000 cal years BP, sedges (e.g. Carex) and bryophytes (e.g. Bryum, Aulacomnium) increased. The establishment of shrub-tundra communities of Dryas and Vaccinium sp., with potentially some Betula pubescens trees (influx ∼290 grains cm2 year−1), followed at ca. 15,000 cal years BP. Forest taxa such as Picea and ferns (e.g. Dryopteris fragrans, Gymnocarpium dryopteris) established near the lake from ca. 10,000 cal years BP, followed by the establishment of Larix trees from ca. 9000 cal years BP. Picea began to decline from ca. 7000 cal years BP. A complete withdrawal of forest tree taxa occurred by ca. 4000 cal years BP, presumably due to decreasing growing-season temperatures, allowing the expansion of dwarf-shrub tundra and a diverse herb community similar to the present-day vegetation mosaic. Contrary to some earlier comparative studies, sedaDNA and pollen from Lake Bolshoye Shchuchye showed high similarity in the timing of compositional changes and the occurrence of key plant taxa. The sedaDNA record revealed several features that the pollen stratigraphy and earlier palaeorecords in the region failed to detect; a sustained, long-term increase in floristic richness since the LGM until the early Holocene, turnover in grass and forb genera over the Pleistocene-Holocene transition, persistence of a diverse arctic-alpine flora over the late Quaternary, and a variable bryophyte flora through time. As pollen records are often limited by taxonomic resolution, differential productivity and dispersal, sedaDNA can provide improved estimates of floristic richness and is better able to distinguish between different plant assemblages. However, pollen remains superior at providing quantitative estimates of plant abundance changes and detecting several diverse groups (e.g. Poaceae, Cyperaceae, Asteraceae) which may be underreported in the sedaDNA. Joint use of the two proxies provided unprecedented floristic detail of past plant communities and helped to distinguish between long-distance transport of pollen and local presence, particularly for woody plant taxa.
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- 2020
25. Ancient plant DNA, macro- and microfossil studies of the lake sediments from the High Arctic lake Tenndammen, Svalbard
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Sandra Garces Pastor, Inger Greve Alsos, Anastasia Poliakova, Anders Schomacker, and Lena Håkansson
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Oceanography ,VDP::Mathematics and natural science: 400::Geosciences: 450 ,Arctic ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450 ,Macro ,Geology - Abstract
Ancient DNA metabarcoding applied together with the investigations of the plant macro-remains, pollen, spores and non-pollen palynomorphs (NPP), open new perspectives and give better taxonomical resolution, allowing to obtain more precise and specific data on the local environment conditions and their changes. So far, only three multiproxy studies that involve both molecular and palaeobotanical/palynological methods are available for the high Arctic archipelago Svalbard. We intend to contribute filling this gap. Therefore, a field trip to Svalbard was undertaken in September, 2019, and three sediment cores were retrieved from the Tenndammen lake (N 78°06.118; E 15°02.024, 7 m asl) which is a small and shallow water body (ca 2.5 m depth). The lake is located in the valley of Colesdalen, a well-known Svalbard’s biodiversity hot spots and a home for about seven to ten thermophilic plant species.To investigate the Holocene to modern vegetation history of this place, the 85cm core Te2019 was chosen, it was described for lithology, X-rayed, µXRF-scanned, line-scan photographed with high resolution and sampled for sedaDNA, pollen, spores and NPP studies as well as for studies on plant macrofossils. Ten 14C AMS dates were taken in order to establish an age-depth model. The DNA record contains around 100 taxa, most findings of those are supported by pollen studies (Asteraceae, Betula, Brassicaceae, Salix, Saxifraga, Vaccinium/Ericaceae) and by spores (Equisetum and Bryophyta). In addition, various fungi spores were identified. Investigations of plant macro-remains well support findings of the aquatic (i.e. Warnstorfia fluitans) and terrestrial mosses (e.g. Aulacomnium conf. turgidum, Bryum spp., Distichium capillaceum, Calliergon richardsonii, Scorpidium cossonii, Sphagnum spp., Rhizomnium spp.). Besides, fragments of Salix and Betula leaves and fruit parts, various leaf, stem tissues and flower fragments of Saxifraga species were found within the samples from the same depths with the correspondence to DNA records. Three DNA zones (SvDNA 1 – SvDNA3) and one subzone within the earliest zone (SvDNA-1a – SvDNA-1b) were established. Relations between DNA, pollen and macrofossil zones were studied. This study is performed within the “Future ArcTic Ecosystems” (FATE) research program: Initiative for investigation on drivers of diversity and future scenarios from ethnoecology, contemporary ecology and ancient DNA.
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- 2020
26. The Treasure Vault Can be Opened : Large-Scale Genome Skimming Works Well Using Herbarium and Silica Gel Dried Material
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Mihai Pușcaș, Sébastien Lavergne, Bogdan-Iuliu Hurdu, Martí Boleda, Niklaus E. Zimmermann, Inger Greve Alsos, Iva Pitelkova, Adriana Alberti, Peter M. Hollingsworth, Charles Pouchon, Cristina Roquet, Youri Lammers, Marie Kristine Føreid Merkel, Wilfried Thuiller, Eric Coissac, National Centre for Biosystematics [Oslo], Natural History Museum [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA), 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), Génomique métabolique (UMR 8030), 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), Institut Fédéral de Recherches sur la Forêt, la Neige et le Paysage (WSL), Institut Fédéral de Recherches [Suisse], Royal Botanic Garden [Edinburgh], UMR, Lab Ecol Alpine, 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), and Royal Botanic Garden Edinburgh
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0106 biological sciences ,0301 basic medicine ,[SDV]Life Sciences [q-bio] ,Plant Science ,rbcL ,01 natural sciences ,Genome ,DNA barcoding ,chemistry.chemical_compound ,chloroplast DNA ,lcsh:Botany ,Environmental DNA ,VDP::Mathematics and natural science: 400 ,Ecology ,biology ,Silica gel ,Nuclear ribosomal DNA ,Boraginaceae ,[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM] ,lcsh:QK1-989 ,Chloroplast DNA ,Rbcl ,Polar ,[SDV.BID]Life Sciences [q-bio]/Biodiversity ,Plant DNA barcode ,010603 evolutionary biology ,Article ,03 medical and health sciences ,matK ,Botany ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,polar ,Phylogenomic ,Ribosomal DNA ,Ecology, Evolution, Behavior and Systematics ,MatK ,phylogenomic ,alpine ,plant DNA barcode ,VDP::Matematikk og Naturvitenskap: 400 ,nuclear ribosomal DNA ,biology.organism_classification ,environmental DNA ,Alpine ,030104 developmental biology ,Herbarium ,chemistry ,ITS - Abstract
Genome skimming has the potential for generating large data sets for DNA barcoding and wider biodiversity genomic studies, particularly via the assembly and annotation of full chloroplast (cpDNA) and nuclear ribosomal DNA (nrDNA) sequences. We compare the success of genome skims of 2051 herbarium specimens from Norway/Polar regions with 4604 freshly collected, silica gel dried specimens mainly from the European Alps and the Carpathians. Overall, we were able to assemble the full chloroplast genome for 67% of the samples and the full nrDNA cluster for 86%. Average insert length, cover and full cpDNA and rDNA assembly were considerably higher for silica gel dried than herbarium-preserved material. However, complete plastid genomes were still assembled for 54% of herbarium samples compared to 70% of silica dried samples. Moreover, there was comparable recovery of coding genes from both tissue sources (121 for silica gel dried and 118 for herbarium material) and only minor differences in assembly success of standard barcodes between silica dried (89% ITS2, 96% matK and rbcL) and herbarium material (87% ITS2, 98% matK and rbcL). The success rate was >, 90% for all three markers in 1034 of 1036 genera in 160 families, and only Boraginaceae worked poorly, with 7 genera failing. Our study shows that large-scale genome skims are feasible and work well across most of the land plant families and genera we tested, independently of material type. It is therefore an efficient method for increasing the availability of plant biodiversity genomic data to support a multitude of downstream applications.
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- 2020
27. A complete Holocene lake sediment ancient DNA record reveals long-standing high Arctic plant diversity hotspot in northern Svalbard
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Inger Greve Alsos, Peter D. Heintzman, Alexandra Rouillard, Anders Schomacker, Wesley R. Farnsworth, Linn H. Voldstad, Sofia E. Kjellman, Lena Håkansson, Pernille Bronken Eidesen, Jarðvísindastofnun (HÍ), Institute of Earth Sciences (UI), Verkfræði- og náttúruvísindasvið (HÍ), School of Engineering and Natural Sciences (UI), Háskóli Íslands, and University of Iceland
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SedaDNA ,ATLANTIC ,010506 paleontology ,Archeology ,LAND ,010504 meteorology & atmospheric sciences ,CONSERVATION ,Biodiversity ,01 natural sciences ,COLONIZATION ,Svalbard ,Vegetation dynamics ,Nýlífsöld ,Hotspot (geology) ,Eldvirkni ,Ecology, Evolution, Behavior and Systematics ,Holocene ,0105 earth and related environmental sciences ,VDP::Mathematics and natural science: 400 ,Global and Planetary Change ,biology ,Ancient DNA ,EDGEOYA ,Jarðlög ,AREA ,Biodiversity hotspot ,Geology ,VDP::Matematikk og Naturvitenskap: 400 ,biology.organism_classification ,Lake sediments ,SPITSBERGEN ,Geography ,Arctic ,NORWAY ,Metabarcoding ,Sedimentary rock ,Physical geography ,VEGETATION ,Empetrum nigrum ,GLACIAL HISTORY - Abstract
Publisher's version (útgefin grein), Arctic hotspots, local areas of high biodiversity, are potential key sites for conservation of Arctic biodiversity. However, there is a need for improved understanding of their long-term resilience. The Arctic hotspot of Ringhorndalen has the highest registered diversity of vascular plants in the Svalbard archipelago, including several remarkable and isolated plant populations located far north of their normal distribution range. Here we analyze a lake sediment core from Ringhorndalen for sedimentary ancient DNA (sedaDNA) and geochemical proxies to detect changes in local vegetation and climate. Half of the plant taxa appeared already before 10,600 cal. yr BP, indicating rapid colonization as the ice retreated. Thermophilous species had a reoccurring presence throughout the Holocene record, but stronger signal in the early than Late Holocene period. Thus, thermophilous Arctic plant species had broader distribution ranges during the Early Holocene thermal maximum c. 10,000 cal. yr BP than today. Most of these thermophilous species are currently not recorded in the catchment area of the studied lake, but occur locally in favourable areas further into the valley. For example, Empetrum nigrum was found in >40% of the sedaDNA samples, whereas its current distribution in Ringhorndalen is highly restricted and outside the catchment area of the lake. Our findings support the hypothesis of isolated relict populations in Ringhorndalen. The findings are also consistent with main Holocene climatic shifts in Svalbard identified by previous studies and indicate an early warm and species-rich postglacial period until c. 6500 cal. yr BP, followed by fluctuating cool and warm periods throughout the later Holocene., The core-samplingfield campaign, subsequent sub-sampling ofsediments and macrofossils, ITRAX-scans, and radiocarbon datingwere funded by the Svalbard Environmental Protection Fund(project 16/35 to WRF). Financial support for molecular analysisandfield work was provided by the Svalbard Environmental Pro-tection Fund (project 14/118 to PBE) and Jan Christensen’sendowment (to LHV). IGA and PDH acknowledge support from theResearch Council of Norway (Grant 250963:“ECOGEN”). We thankJohannes Sand Bolstad forfield assistance, Kari Klanderud forproject administration, the wider ECOGEN research group inTromsø, including Dilli Rijal for pooling and cleaning of the PCRproducts and Youri Lammers for helping with bioinformatic ana-lyses and reference libraries. Bioinformatic analyses were per-formed on the Abel Cluster, owned by the University of Oslo andUninett/Sigma2, and operated by the Department for ResearchComputing at USIT, the University of Oslo IT-department.http://www.hpc.uio.no/. We thank Marie-Louise Siggaard-Andersen forassistance with the ITRAX-scanning of the sediment core as well asDr. Skafti Brynj olfsson and Dr. Marc Macias-Fauria for collaborationin the field.
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- 2020
28. Ending the Cinderella Status of Terraces and Lynchets in Europe
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Daniel J. Fallu, Andreas Lang, Rosa-Maria Albert, Paolo Tarolli, Sara Cucchiaro, Kristof Van Oost, Pengzhi Zhao, Clive Waddington, Kevin Walsh, Tony Brown, Lisa Snape, Inger Greve Alsos, EGU - European Geoscience Union, and UCL - SST/ELI/ELIC - Earth & Climate
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terrace - Abstract
Terraces and lynchets are not only ubiquitous worldwide and within Europe but can provide increasingly important Ecosystem Services (ESs), which may be able to mitigate aspects of climate change. They are also probably a major cause of non-linearity between climate and erosion rates in agricultural systems as noted from alluvial and colluvial studies. In this paper we review the theoretical background of terraces and lynchets, present a modified classification, and show how new techniques are transforming the study of these widespread and often ancient anthropogenic landforms. Indeed the problems of dating terraces and also the time-consuming nature and costly surveys has held back the archaeological study of terraces until now. The applicable suite of techniques available now includes the creation of Digital Terrain Models (DTMs) from Structure from Motion (SfM) photogrammetry, Airborne and Terrestrial Laser Scanning (ALS-TLS); the use of OSL and pOSL, pXRF, FTIR, phytoliths, calcium oxalates from plants and potentially sedaDNA. Examples will be drawn from a recently started ERC project (TerrACE; ERC-2017-ADG: 787790, 2018-2023; https://www.terrace.no/) which is working at over 10 sites in Europe ranging from Norway to Greece.This paper explains the development of a new holistic approach to terrace archaeology driven by a modern conceptualisation of human-landscape relationships, and facilitated by new scientific developments. We explain the rationale for our choice of case study areas, for example, the range of bio-climatic zones. In addition, this multi-regional approach allows us to address contingent regional and local historical/socioeconomic processes; from demographic fluctuations to the development of specific forms of agricultural techniques. Examples of DTM creation, field analyses and selected results will be given from Martleburg in Belgium and sites in Italy. We will then move on to explain how this combination of a comprehensive suite of modern field and laboratory methods and an interpretive strategy informed by the environmental humanities will yield exciting and groundbreaking results.
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- 2020
29. Last Glacial Maximum environmental conditions at Andøya, northern Norway; evidence for a northern ice-edge ecological 'hotspot'
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Youri Lammers, Jostein Bakke, Aage Paus, Catherine Langdon, Tomasz Goslar, Ludovic Gielly, Per Sjögren, Mary E. Edwards, Melanie J. Leng, Inger Greve Alsos, Willem G.M. van der Bilt, Marie Kristine Føreid Merkel, Torbjørn Alm, and Antony G. Brown
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Vascular plant ,010506 paleontology ,Archeology ,010504 meteorology & atmospheric sciences ,medicine.disease_cause ,01 natural sciences ,Pollen ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450 ,medicine ,Glacial period ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,VDP::Mathematics and natural science: 400 ,Global and Planetary Change ,VDP::Mathematics and natural science: 400::Geosciences: 450 ,biology ,Macrofossil ,Geology ,Last Glacial Maximum ,VDP::Matematikk og Naturvitenskap: 400 ,15. Life on land ,biology.organism_classification ,Habitat ,Biological dispersal ,Sedimentary rock ,Physical geography - Abstract
Andøya on the NW coast of Norway is a key site for understanding the Last Glacial Maximum (LGM) in northern Europe. Controversy has arisen concerning the local conditions, especially about the timing and extent of local glacial cover, maximum July temperatures and whether pine and/or spruce could have grown there. We reviewed all existing data and add newly analysed ancient sedimentary DNA (sedaDNA), pollen, macrofossils, geochemistry and stable isotopes from three lake sediment cores from Øvre Æråsvatnet. A total of 23 new dates and age-depth modelling suggests the lake has been ice-free since GI2 (Pinus and Picea sedaDNA was found in all three cores but at such low frequencies that it could not be distinguished from background contamination. LGM samples have an exceptionally high organic matter content, with isotopic values indicating that carbon and nitrogen derive from a marine source. Along with finds of bones of the little auk (Alle alle), this indicates that the lake received guano from an adjacent bird colony.SedaDNA, pollen and macrofossil assemblages were dominated by Poaceae, Brassicaceae and Papaver, but scattered occurrence of species currently restricted to the Low Arctic Tundra Zone (July temperature of 8–9 °C) such as Apiaceae (sedaDNA, 8–9 °C), and Alchemilla alpina (macrofossil, 8–9 °C) were also recorded. The review of >14.7 cal ka BP data recorded 94 vascular plant taxa, of which 38% have a northern limit in Shrub Tundra or more southern vegetation zones. This unusual assemblage likely stems from a combination of proximity to ice-free water in summer, geographical isolation linked with stochastic long-distance dispersal events, and the presence of bird-fertilized habitats. The environmental reconstruction based on all records from the area does not preclude local growth of tree species, as the local climate combined with high nutrient input may have led to periodically suitable environmental ‘hotspot’ conditions.
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- 2020
30. Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden
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Inger Greve Alsos, Tanja Slotte, Youri Lammers, Per Unneberg, Barbara Wohlfarth, J. Sakari Salonen, Minna Väliranta, Laura Parducci, Lu Han, Mikkel Winther Pedersen, BioGeoClimate Modelling Lab, Department of Geosciences and Geography, Helsinki Institute of Sustainability Science (HELSUS), Environmental Change Research Unit (ECRU), and Ecosystems and Environment Research Programme
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0106 biological sciences ,0301 basic medicine ,1171 Geosciences ,shotgun sequencing (metagenomics) ,lake sediments ,lcsh:Evolution ,medicine.disease_cause ,VDP::Mathematics and natural science: 400::Geosciences: 450::Quaternary geology, glaciology: 465 ,010603 evolutionary biology ,01 natural sciences ,LAST TERMINATION ,EXTRACELLULAR DNA ,EVENTS ,macrofossils remains ,03 medical and health sciences ,Pollen ,lcsh:QH540-549.5 ,medicine ,HOLOCENE ,lcsh:QH359-425 ,Environmental DNA ,Geosciences, Multidisciplinary ,PLANT-COMMUNITIES ,RECORDS ,ancient DNA ,Ecology, Evolution, Behavior and Systematics ,Holocene ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Kvartærgeologi, glasiologi: 465 ,1172 Environmental sciences ,Ecology ,Macrofossil ,Plant community ,Vegetation ,15. Life on land ,Before Present ,environmental DNA ,Multidisciplinär geovetenskap ,READ ALIGNMENT ,030104 developmental biology ,Ancient DNA ,pollen ,SYNCHRONIZATION ,Physical geography ,VEGETATION ,lcsh:Ecology ,Geology - Abstract
Source at https://doi.org/10.3389/fevo.2019.00189. The lake sediments of Hässeldala Port in south-east Sweden provide an archive of local and regional environmental conditions ~14.5–9.5 ka BP (thousand years before present) and allow testing DNA sequencing techniques to reconstruct past vegetation changes. We combined shotgun sequencing with plant micro- and macrofossil analyses to investigate sediments dating to the Allerød (14.1–12.7 ka BP), Younger Dryas (12.7–11.7 ka BP), and Preboreal (
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- 2019
31. DNA metabarcoding—Need for robust experimental designs to draw sound ecological conclusions
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Inger Greve Alsos, Lucie Zinger, Gentile Francesco Ficetola, Aurélie Bonin, Frédéric Boyer, Marta De Barba, Simon N. Jarman, M. Thomas P. Gilbert, Ian A. Dickie, Leho Tedersoo, Anthony A. Chariton, Bruce E. Deagle, Philip Francis Thomsen, Johan Pansu, Alex J. Dumbrell, Ari Jumpponen, Håvard Kauserud, Holly M. Bik, Eske Willerslev, Pierre Taberlet, Luca Fumagalli, Simon Creer, Eric Coissac, Miklós Bálint, Jan Pawlowski, Ludovic Orlando, Noah Fierer, Laboratoire d'Ecologie Alpine (LECA ), Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, New York University [New York] (NYU), NYU System (NYU), Molecular Ecology and Fisheries Genetics Laboratory, School of Biological Sciences, Bangor University, Australian Antarctic Division (AAD), Australian Government, Department of the Environment and Energy, emlyon business school, Politecnico di Milano [Milan] (POLIMI), University of Copenhagen = Københavns Universitet (KU), Microbial Evolution Research Group (MERG), Department of Biology [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Section for GeoGenetics, Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU)-Faculty of Health and Medical Sciences, University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), Department of Genetics and Evolution, Université de Genève (UNIGE), University of Tartu, JP was supported by the Marie Skłodowska-Curie actions (TEAM-Coast project, MSCA-GF 750570), Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), Laboratoire des Sciences du Numérique de Nantes (LS2N), Université de Nantes - Faculté des Sciences et des Techniques, Université de Nantes (UN)-Université de Nantes (UN)-École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Robotique Et Vivant (ReV), and Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Université de Nantes - Faculté des Sciences et des Techniques
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0106 biological sciences ,replication ,Ecology (disciplines) ,[SDV]Life Sciences [q-bio] ,experimental controls ,Biology ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,chemistry.chemical_compound ,Dna genetics ,Replication (statistics) ,Genetics ,DNA Barcoding, Taxonomic ,data quality ,Environmental DNA ,Ecology, Evolution, Behavior and Systematics ,Sound (geography) ,ComputingMilieux_MISCELLANEOUS ,030304 developmental biology ,0303 health sciences ,geography ,geography.geographical_feature_category ,Ecology ,Biodiversity ,DNA ,environmental DNA ,chemistry ,Evolutionary biology ,[SDE]Environmental Sciences - Abstract
International audience
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- 2019
32. Metabarcoding lake sediments: taphonomy and representation of contemporary vegetation in environmental DNA (eDNA) records
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T Joergensen, Nigel G. Yoccoz, Ludovic Gielly, Inger Greve Alsos, Per Sjögren, Youri Lammers, and Mary E. Edwards
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Vascular plant ,biology ,Ecology ,Biodiversity ,Macrofossil ,biology.organism_classification ,Geography ,Deciduous ,Abundance (ecology) ,Aquatic plant ,medicine ,Environmental DNA ,medicine.symptom ,Vegetation (pathology) - Abstract
Metabarcoding of lake sediments may reveal current and past biodiversity, but little is known about the degree to which taxa growing in the vegetation are represented in environmental DNA (eDNA) records. We analysed composition of lake and catchment vegetation and vascular plant eDNA at 11 lakes in northern Norway. Out of 489 records of taxa growing within 2 m from the lake shore, 17-49% (mean 31%) of the identifiable taxa recorded were detected with eDNA. Of the 217 eDNA records, 73% and 12% matched taxa recorded in vegetation surveys within 2 m and up to about 50 m away from the lakeshore, respectively, whereas 16% were not recorded in the vegetation surveys of the same lake. The latter include taxa likely overlooked in the vegetation surveys or growing outside the survey area. The percentages detected were 61, 47, 25, and 15 for dominant, common, scattered, and rare taxa, respectively. Similar numbers for aquatic plants were 88, 88, 33 and 62%, respectively. Detection rate and taxonomic resolution varied among plant families and functional groups with good detection of e.g. Ericaceae, Roseaceae, deciduous trees, ferns, club mosses and aquatics. The representation of terrestrial taxa in eDNA depends on both their distance from the sampling site and their abundance and is sufficient for recording vegetation types. For aquatic vegetation, eDNA may be comparable with, or even superior to, in-lake vegetation surveys and therefore be used as an tool for biomonitoring. For reconstruction of terrestrial vegetation, technical improvements and more intensive sampling is needed to detect a higher proportion of rare taxa although DNA of some taxa may never reach the lake sediments due to taphonomical constrains. Nevertheless, eDNA performs similar to conventional methods of pollen and macrofossil analyses and may therefore be an important tool for reconstruction of past vegetation.
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- 2018
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33. Prevention of microbial species introductions to the Arctic: The efficacy of footwear disinfection measures on cruise ships
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Inger Greve Alsos, Sabine B. Rumpf, and Chris Ware
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0106 biological sciences ,Cruise ,Biosecurity ,Plant Science ,Aquatic Science ,Microbial contamination ,010603 evolutionary biology ,01 natural sciences ,Invasive species ,invasive species ,ddc:570 ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Plantegeografi: 496 ,microorganisms ,lcsh:QH301-705.5 ,disinfection ,Ecology, Evolution, Behavior and Systematics ,Ecology ,010604 marine biology & hydrobiology ,Ecological Modeling ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Plant geography: 496 ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Zoogeography: 486 ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Zoogeografi: 486 ,The arctic ,Fishery ,monitoring ,Geography ,lcsh:Biology (General) ,Insect Science ,tourism ,Animal Science and Zoology ,Tourism ,biosecurity - Abstract
Source at https://doi.org/10.3897/neobiota.37.22088. Biosecurity measures are commonly used to prevent the introduction of non-native species to natural environments globally, yet the efficacy of practices is rarely tested under operational conditions. A voluntary biosecurity measure was trialled in the Norwegian high Arctic following concern that non-native species might be transferred to the region on the footwear of travellers. Passengers aboard an expedition cruise ship disinfected their footwear with the broad spectrum disinfectant Virkon S prior to and in-between landing at sites around the remote Svalbard archipelago. The authors evaluated the efficacy of simply stepping through a disinfectant foot bath, which is the most common practice of footwear disinfection aboard expedition cruise ships in the Arctic. This was compared to a more time consuming and little-used method involving drying disinfected footwear, as proposed by other studies. The two practices were evaluated by measuring microbial growth on paired footwear samples before and after disinfection under both conditions. Step-through disinfection did not substantially reduce microbial growth on the footwear. Allowing disinfected footwear to dry, however, reduced the microbial burden significantly to lower levels. Thus, the currently adopted procedures used aboard ships are ineffective at removing microbial burden and are only effective when footwear is given more time to dry than currently granted under operational conditions. These findings underscore results from empirical research performed elsewhere and suggest the need to better relay this information to practitioners. It is suggested that footwear should minimally be wiped dry after step-through disinfection as a reasonable compromise between biosecurity and practicability.
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- 2018
34. Living on the edge: conservation genetics of seven thermophilous plant species in a high Arctic archipelago
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Inger Greve Alsos, Reidar Elven, Idunn Elisabeth Borgen Skjetne, Anne K. Brysting, and Siri Birkeland
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0106 biological sciences ,0301 basic medicine ,Conservation genetics ,Rare species ,Biodiversity ,islands ,Plant Science ,Kobresia simpliciuscula ,010603 evolutionary biology ,01 natural sciences ,Svalbard ,03 medical and health sciences ,Arctic ,Tofieldia pusilla ,VDP::Matematikk og Naturvitenskap: 400::Basale biofag: 470 ,edge populations ,Amplified fragment length polymorphism (AFLP) ,Genetic diversity ,biology ,Ecology ,biology.organism_classification ,regional red list ,VDP::Mathematics and natural science: 400::Basic biosciences: 470 ,030104 developmental biology ,Population bottleneck ,climate change ,conservation genetics ,geographic locations ,Research Article ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 - Abstract
Small and peripheral populations often contain low levels of genetic variation. This may limit their ability to adapt to environmental change, including climate warming. In a recent study published in AoB PLANTS, Birkeland, Skjetne and colleagues show that many rare and threatened plant species in the High Arctic archipelago Svalbard harbour low levels of genetic variation. Most of them are probably relicts from the early Holocene warmer period. They have likely experienced strong genetic founder/bottleneck effects due to climatic limitations. Even though temperatures now are rising, it is highly uncertain whether this will be beneficial for these warmth-demanding species., Small, isolated and/or peripheral populations are expected to harbour low levels of genetic variation and may therefore have reduced adaptability to environmental change, including climate warming. In the Arctic, global warming has already caused vegetation change across the region and is acting as a significant stressor on Arctic biodiversity. Many of the rare plants in the Arctic are relicts from early Holocene warm periods, but their ability to benefit from the current warming is dependent on the viability of their populations. We therefore examined Amplified Fragment Length Polymorphism (AFLP) data from regional red listed vascular plant species in the High Arctic archipelago of Svalbard and reference populations from the main distribution area of: (1) Botrychium lunaria, (2) Carex capillaris ssp. fuscidula, (3) Comastoma tenellum, (4) Kobresia simpliciuscula ssp. subholarctica, (5) Ranunculus wilanderi, (6) Sibbaldia procumbens and (7) Tofieldia pusilla. In addition, we gathered population size data in Svalbard. The Svalbard populations had low genetic diversity and distinctiveness and few or no private markers compared to populations outside the archipelago. This is similar to observations in other rare species in Svalbard and the genetic depletion may be due to an initial founder effect and/or a genetic bottleneck caused by late Holocene cooling. There seems to be limited gene flow from other areas and the Svalbard populations should therefore be considered as demographically independent management units. Overall, these management units have small and/or few populations and are therefore prone to stochastic events which may further increase vulnerability to inbreeding depression, loss of genetic variation, and reduced evolutionary potential. Our results support theory predicting lower levels of genetic diversity in small, isolated and/or peripheral populations and may be of importance for management of other rare plant species in the Arctic.
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- 2017
35. Ancient plant DNA in lake sediments
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Inger Greve Alsos, Yoshihisa Suyama, Keith Bennett, Jamie R. Wood, Laura Parducci, Mikkel Winther Pedersen, Gentile Francesco Ficetola, and University of St Andrews. Geography & Sustainable Development
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0301 basic medicine ,ancient plant DNA (aDNA) ,Taphonomy ,DNA, Plant ,Bioinformatics ,Physiology ,Sample point ,QH301 Biology ,T-NDAS ,lake sediments ,Plant Science ,high-throughput DNA sequencing ,Biology ,Geologic Sediments ,environmental DNA (eDNA) ,geologic sediments ,shotgun sequencing ,QH301 ,03 medical and health sciences ,Ancient plant DNA (aDNA) ,Abundance (ecology) ,G1 ,lakes ,DNA, Ancient ,Ecology ,taphonomy ,G Geography (General) ,bioinformatics ,High-throuput DNA sequencing ,Lake sediments ,Shotgun sequencing ,DNA plant ,High-Throughput DNA Sequencing ,030104 developmental biology ,Taxon ,Environmental DNA (eDNA) ,pollen ,metabarcoding ,Metabarcoding ,Pollen ,Taxonomic resolution ,fossils ,BDC - Abstract
This work was supported by the Swedish Research Council (grant no. 2013-D0568401), SciLifeLab Stockholm and the Carl Triggers’ Foundation (grant no. 14:371) to L.P., and the Research Council of Norway to I.G.A. (grant no. 213692/F20). Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras. Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. Lakes have larger catchment areas and recent studies have suggested that plant aDNA from lake sediments is a more powerful tool for palaeofloristic reconstruction. Furthermore, lakes can be found globally in nearly all environments, and are therefore not limited to perennially frozen areas. Here, we review the latest approaches and methods for the study of plant aDNA from lake sediments and discuss the progress made up to the present. We argue that aDNA analyses add new and additional perspectives for the study of ancient plant populations and, in time, will provide higher taxonomic resolution and more precise estimation of abundance. Despite this, key questions and challenges remain for such plant aDNA studies. Finally, we provide guidelines on technical issues, including lake selection, and we suggest directions for future research on plant aDNA studies in lake sediments. Postprint
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- 2017
36. Stay or go – how topographic complexity influences alpine plant population and community responses to climate change
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Jens-Christian Svenning, Hans Henrik Bruun, James D. M. Speed, Kari Anne Bråthen, Øystein H. Opedal, Ann Milbau, Bente J. Graae, Kristoffer Hylander, Hilary H. Birks, Kristine Bakke Westergaard, Inger Greve Alsos, Rasmus Ejrnæs, Kari Klanderud, Wolf L. Eiserhardt, Johan Ehrlén, H. John B. Birks, Vigdis Vandvik, W. Scott Armbruster, Jonathan Lenoir, University of Bergen (UiB), Dept Biol Sci, Ecoinformat & Biodivers Grp, Aarhus University [Aarhus], Stockholm University, Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), and Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS)
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0106 biological sciences ,010504 meteorology & atmospheric sciences ,[SDE.MCG]Environmental Sciences/Global Changes ,Population ,Niche ,Microclimate ,Climate change ,Plant Science ,[SDV.BID]Life Sciences [q-bio]/Biodiversity ,adaptation ,Refugia ,Biology ,010603 evolutionary biology ,01 natural sciences ,refugia ,VDP::Mathematics and natural science: 400::Zoology and botany: 480 ,Realized niche width ,Adaptation ,education ,dispersal ,resilience ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,Ecological niche ,[SDV.EE]Life Sciences [q-bio]/Ecology, environment ,education.field_of_study ,Community ,Resilience ,Ecology ,Dispersal ,15. Life on land ,niche ,13. Climate action ,Biological dispersal ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,microclimate ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480 - Abstract
Accepted manuscript version. Published version available at https://doi.org/10.1016/j.ppees.2017.09.008. Accepted manuscript version, licensed CC BY-NC-ND 4.0. In the face of climate change, populations have two survival options − they can remain in situ and tolerate the new climatic conditions (“stay”), or they can move to track their climatic niches (“go”). For sessile and small-stature organisms like alpine plants, staying requires broad climatic tolerances, realized niche shifts due to changing biotic interactions, acclimation through plasticity, or rapid genetic adaptation. Going, in contrast, requires good dispersal and colonization capacities. Neither the magnitude of climate change experienced locally nor the capacities required for staying/going in response to climate change are constant across landscapes, and both aspects may be strongly affected by local microclimatic variation associated with topographic complexity. We combine ideas from population and community ecology to discuss the effects of topographic complexity in the landscape on the immediate “stay” or “go” opportunities of local populations and communities, and on the selective pressures that may have shaped the stay or go capacities of the species occupying contrasting landscapes. We demonstrate, using example landscapes of different topographical complexity, how species’ thermal niches could be distributed across these landscapes, and how these, in turn, may affect many population and community ecological processes that are related to adaptation or dispersal. Focusing on treeless alpine or Arctic landscapes, where temperature is expected to be a strong determinant, our theorethical framework leads to the hypothesis that populations and communities of topographically complex (rough and patchy) landscapes should be both more resistant and more resilient to climate change than those of topographically simple (flat and homogeneous) landscapes. Our theorethical framework further points to how meta-community dynamics such as mass effects in topographically complex landscapes and extinction lags in simple landscapes, may mask and delay the long-term outcomes of these landscape differences under rapidly changing climates.
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- 2017
37. Giant invasive Heracleum persicum: Friend or foe of plant diversity?
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Dilli Prasad Rijal, Inger Greve Alsos, Torbjørn Alm, and Lennart Nilsen
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0106 biological sciences ,Ecology ,010604 marine biology & hydrobiology ,Biodiversity ,Species diversity ,Introduced species ,Plant community ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Plant geography: 496 ,Native plant ,Biology ,010603 evolutionary biology ,01 natural sciences ,Invasive species ,Species evenness ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Plantegeografi: 496 ,Species richness ,human activities ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation - Abstract
Source at https://dx.doi.org/10.1002%2Fece3.3055 The impact of invasion on diversity varies widely and remains elusive. Despite the con- siderable attempts to understand mechanisms of biological invasion, it is largely un- known whether some communities’ characteristics promote biological invasion, or whether some inherent characteristics of invaders enable them to invade other com- munities. Our aims were to assess the impact of one of the massive plant invaders of Scandinavia on vascular plant species diversity, disentangle attributes of invasible and noninvasible communities, and evaluate the relationship between invasibility and ge- netic diversity of a dominant invader. We studied 56 pairs of Heracleum persicum Desf. ex Fisch.- invaded and noninvaded plots from 12 locations in northern Norway. There was lower native cover, evenness, taxonomic diversity, native biomass, and species richness in the invaded plots than in the noninvaded plots. The invaded plots had nearly two native species fewer than the noninvaded plots on average. Within the in- vaded plots, cover of H. persicum had a strong negative effect on the native cover, evenness, and native biomass, and a positive association with the height of the native plants. Plant communities containing only native species appeared more invasible than those that included exotic species, particularly H. persicum . Genetic diversity of H. per - sicum was positively correlated with invasibility but not with community diversity. The invasion of a plant community by H. persicum exerts consistent negative pressure on vascular plant diversity. The lack of positive correlation between impacts and genetic diversity of H. persicum indicates that even a small founder population may cause high impact. We highlight community stability or saturation as an important determinant of invasibility. While the invasion by H. persicum may decrease susceptibility of a plant community to further invasion, it severely reduces the abundance of native species and makes them more vulnerable to competitive exclusion.
- Published
- 2017
38. Circumpolar Arctic vegetation: a hierarchic review and roadmap toward an internationally consistent approach to survey, archive and classify tundra plot data
- Author
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Donald A. Walker, William A. Gould, P. J. Webber, Martha K. Raynolds, Rolf A. Ims, Amy L. Breen, L.A. Druckenmiller, Fred J.A. Daniëls, Stephen S. Talbot, Jozef Šibík, Mary E. Edwards, Dorothee Ehrich, Howard E. Epstein, Inger Greve Alsos, Helga Bültmann, Uma S. Bhatt, Hans Meltofte, and Marcel Buchhorn
- Subjects
0106 biological sciences ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Systematisk zoologi: 487 ,010504 meteorology & atmospheric sciences ,Vegetation classification ,Biodiversity ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Systematisk botanikk: 493 ,Biology ,010603 evolutionary biology ,01 natural sciences ,medicine ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Marine biology: 497 ,Arctic vegetation ,0105 earth and related environmental sciences ,General Environmental Science ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Systematic botany: 493 ,Biomass (ecology) ,Renewable Energy, Sustainability and the Environment ,Public Health, Environmental and Occupational Health ,Circumpolar star ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Marinbiologi: 497 ,Tundra ,Arctic ,Physical geography ,medicine.symptom ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Systematic zoology: 487 ,Vegetation (pathology) - Abstract
Source: doi: 10.1088/1748-9326/11/5/055005 Satellite-derived remote-sensing products are providing a modern circumpolar perspective of Arctic vegetation and its changes, but this new view is dependent on a long heritage of ground-based observations in the Arctic. Several products of the Conservation of Arctic Flora and Fauna are key to our current understanding.Wereview aspects of the PanArctic Flora, the Circumpolar Arctic Vegetation Map, the Arctic Biodiversity Assessment, and the Arctic Vegetation Archive (AVA) as they relate to efforts to describe and map the vegetation, plant biomass, and biodiversity of the Arctic at circumpolar, regional, landscape and plot scales. Cornerstones for all these tools are ground-based plant-species and plant-community surveys. TheAVA is in progress and will store plot-based vegetation observations in a public-accessible database for vegetation classification, modeling, diversity studies, and other applications.Wepresent the current status of the Alaska Arctic Vegetation Archive (AVA-AK), as a regional example for the panarctic archive, and with a roadmap for a coordinated international approach to survey, archive and classify Arctic vegetation.Wenote the need for more consistent standards of plot-based observations, and make several recommendations to improve the linkage between plot-based observations biodiversity studies and satellite-based observations of Arctic vegetation.
- Published
- 2016
39. Past climate-driven range shifts and population genetic diversity in arctic plants
- Author
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Christian Brochmann, Nadir Alvarez, Peter Schönswetter, Miska Luoto, Mary S. Wisz, Christian Damgaard, Dorothee Ehrich, Kristine Bakke Westergaard, Patrice Descombes, Andreas Tribsch, Pernille Bronken Eidesen, Loïc Pellissier, Pascal Vittoz, Inger Greve Alsos, Niklaus E. Zimmermann, Signe Normand, and Antoine Guisan
- Subjects
0106 biological sciences ,Arctic plants ,Range (biology) ,Population ,Species distribution ,Biology ,migration ,010603 evolutionary biology ,01 natural sciences ,COLONIZATION ,Arctic vegetation ,education ,Ecology, Evolution, Behavior and Systematics ,Ecological niche ,education.field_of_study ,Genetic diversity ,Ecology ,Last Glacial Maximum ,REFUGIA ,climatic niche ,HIGH-MOUNTAIN PLANTS ,SPECIES DISTRIBUTION MODELS ,15. Life on land ,EVOLUTION ,SEED DISPERSAL ,Population bottleneck ,climate change ,EXTINCTION ,NORTHERN EURASIA ,13. Climate action ,DISTANCE ,Species richness ,ICE AGES ,010606 plant biology & botany - Abstract
Aim High intra specific genetic diversity is necessary for species adaptation to novel environments under climate change but species tracking suitable conditions are losing alleles through successive founder events during range shift. Here we investigated the relationship between range shift since the Last Glacial Maximum (LGM) and extant population genetic diversity across multiple plant species to understand variability in species responses. Location The circumpolar Arctic and northern temperate alpine ranges. Methods We estimated the climatic niches of 30 cold adapted plant species using range maps coupled with species distribution models and hindcasted species suitable areas to reconstructions of the mid Holocene and LGM climates. We computed the species specific migration distances from the species glacial refugia to their current distribution and correlated distances to extant genetic diversity in 1295 populations. Differential responses among species were related to life history traits. Results We found a negative association between inferred migration distances from refugia and genetic diversities in 25 species but only 11 had statistically significant negative slopes. The relationships between inferred distance and population genetic diversity were steeper for insect pollinated species than wind pollinated species but the difference among pollination system was marginally independent from phylogenetic autocorrelation. Main conclusion The relationships between inferred migration distances and genetic diversities in 11 species independent from current isolation indicate that past range shifts were associated with a genetic bottleneck effect with an average of 21 loss of genetic diversity per 1000 km-1. In contrast the absence of relationship in many species also indicates that the response is species specific and may be modulated by plant pollination strategies or result from more complex historical contingencies than those modelled here.
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- 2016
40. The role of sea ice for vascular plant dispersal in the Arctic
- Author
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Inger Greve Alsos, Marit-Solveig Seidenkrantz, Ole Bennike, Andreas Kirchhefer, Áslaug Geirsdóttir, and Dorothee Ehrich
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0106 biological sciences ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Ecology: 488 ,010504 meteorology & atmospheric sciences ,Driftwood ,Biology ,010603 evolutionary biology ,01 natural sciences ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Økologi: 488 ,Arctic ,Sea ice ,plant colonization ,Ice Cover ,Glacial period ,Arctic vegetation ,Arctic Biota ,Plant Dispersal ,Holocene ,0105 earth and related environmental sciences ,Islands ,geography ,plant dispersal ,geography.geographical_feature_category ,Ecology ,Arctic Regions ,driftwood ,Special Feature ,15. Life on land ,Agricultural and Biological Sciences (miscellaneous) ,Wood ,sea ice ,climate change ,Biological dispersal ,Embryophyta ,General Agricultural and Biological Sciences - Abstract
Published version. Source at http://dx.doi.org/10.1098/rsbl.2016.0264 Sea ice has been suggested to be an important factor for dispersal of vascular plants in the Arctic. To assess its role for postglacial colonization in the North Atlantic region, we compiled data on the first Late Glacial to Holocene occurrence of vascular plant species in East Greenland, Iceland, the Faroe Islands and Svalbard. For each record, we reconstructed likely past dispersal events using data on species distributions and genetics. We compared these data to sea-ice reconstructions to evaluate the potential role of sea ice in these past colonization events and finally evaluated these results using a compilation of driftwood records as an independent source of evidence that sea ice can disperse biological material. Our results show that sea ice was, in general, more prevalent along the most likely dispersal routes at times of assumed first colonization than along other possible routes. Also, driftwood is frequently dispersed in regions that have sea ice today. Thus, sea ice may act as an important dispersal agent. Melting sea ice may hamper future dispersal of Arctic plants and thereby cause more genetic differentiation. It may also limit the northwards expansion of competing boreal species, and hence favour the persistence of Arctic species.
- Published
- 2016
41. Disjunct populations of European vascular plant species keep the same climatic niches
- Author
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Safaa Wasof, Jonathan Lenoir, Per Arild Aarrestad, Inger Greve Alsos, Scott Armbruster, W., Gunnar Austrheim, Vegar Bakkestuen, Birks, H. John B., Kari Anne Brathen, Olivier Broennimann, Jörg Brunet, Hans Henrik Bruun, Carl Johan Dahlberg, Martin Diekmann, Stefan Dullinger, Mats Dynesius, Rasmus Erjnaes, Jean-Claude Gégout, Bente Jessen Graae, John-Arvid Grytnes, Antoine Guisan, Kristoffer Hylander, Jonsdottir, Ingibjörg S., Jutta Kapfer, Kari Klanderut, Miska Luoto, Ann Milbau, Mari Moora, Bettina Nygaard, Arvid Odland, Harald Pauli, Virve Ravolainen, Stefanie Reinhardt, Sylvi Marlen Sandvik, Fride Hoistad Schei, Speed, James D. M., Jens-Christian Svenning, Wilfried Thuiller, Liv Unn Tveraabak, Vigdis Vandvik, Liv Guri Velle, Risto Virtanen, Pascal Vittoz, Wolfgang Willner, Thomas Wohlgemuth, Zimmermann, Niklaus E., Martin Zobel, Guillaume Decocq, Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN), Université de Picardie Jules Verne (UPJV)-Centre National de la Recherche Scientifique (CNRS), National Centre for Biosystematics [Oslo], Natural History Museum [Oslo], University of Oslo (UiO)-University of Oslo (UiO), Department of Ecology & Evolution, Université de Lausanne (UNIL), Southern Swedish Forest Research Centre, Swedish University of Agricultural Sciences (SLU), University of Vienna [Vienna], Department of Ecology and Environmental Science, Umeå University, Laboratoire d'Etudes des Ressources Forêt-Bois (LERFoB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Biologie de la Conservation (LBC), University of Iceland [Reykjavik], Dept Bio, University of Tartu, Aarhus University [Aarhus], Laboratoire d'Ecologie Alpine (LECA), Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Université Joseph Fourier - Grenoble 1 (UJF)-Université Grenoble Alpes (UGA), Dept Biol, University of Oulu, Département d'écologie et évolution, Université de Lausanne (UNIL)-Université de Lausanne (UNIL), Vienna Institute for Nature Conservation and Analyses (VINCA), Swiss Federal Institute for Forest, Snow and Avalanche Research WSL, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology in Zürich [Zürich] (ETH Zürich), Institute of Botany and Ecology, UFR de pharmacie, Université de Picardie Jules Verne (UPJV), Ecologie et Dynamique des Systèmes Anthropisés - UMR CNRS 7058 (EDYSAN), Centre National de la Recherche Scientifique (CNRS)-Université de Picardie Jules Verne (UPJV), Norwegian Institute for Nature Research (NINA), University of Portsmouth, University of Alaska [Fairbanks] (UAF), Norwegian University of Science and Technology [Trondheim] (NTNU), Norwegian University of Science and Technology (NTNU), University of Bergen (UiB), The Arctic University of Norway (UiT), IT University of Copenhagen, Department of Ecology, Environment and Plant Sciences [Stockholm], Stockholm University, University of Bremen, Department of Ecology and Environmental Science [Umeå], AgroParisTech-Institut National de la Recherche Agronomique (INRA), Norwegian Univ Sci & Technol, N-7491 Trondheim, Norway, Norwegian Institute of Bioeconomy Research (NIBIO), Norwegian University of Life Sciences (NMBU), University of Helsinki, Telemark University College, Norwegian Polar Institute, University of Agder (UIA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Nesna University College, Norwegian Institute for Agricultural and Environmental Research (Bioforsk), Swiss Federal Institute for Forest, Snow and Landscape Research WSL, and Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich)
- Subjects
arctic plants ,Alpine plants ,climatic niche ,niche overlap ,species distribution modelling ,niche conservatism ,niche optimum ,distant populations ,niche width ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,Biology ,ComputingMilieux_MISCELLANEOUS ,disjunct distribution - Abstract
Aim Previous research on how climatic niches vary across species ranges has focused on a limited number of species, mostly invasive, and has not, to date, been very conclusive. Here we assess the degree of niche conservatism between distant populations of native alpine plant species that have been separated for thousands of years.LocationEuropean Alps and Fennoscandia. Methods Of the studied pool of 888 terrestrial vascular plant species occurring in both the Alps and Fennoscandia, we used two complementary approaches to test and quantify climatic-niche shifts for 31 species having strictly disjunct populations and 358 species having either a contiguous or a patchy distribution with distant populations. First, we used species distribution modelling to test for a region effect on each species' climatic niche. Second, we quantified niche overlap and shifts in niche width (i.e. ecological amplitude) and position (i.e. ecological optimum) within a bi-dimensional climatic space. Results Only one species (3%) of the 31 species with strictly disjunct populations and 58 species (16%) of the 358 species with distant populations showed a region effect on their climatic niche. Niche overlap was higher for species with strictly disjunct populations than for species with distant populations and highest for arctic–alpine species. Climatic niches were, on average, wider and located towards warmer and wetter conditions in the Alps. Main conclusion Climatic niches seem to be generally conserved between populations that are separated between the Alps and Fennoscandia and have probably been so for 10,000–15,000 years. Therefore, the basic assumption of species distribution models that a species' climatic niche is constant in space and time – at least on time scales 104 years or less – seems to be largely valid for arctic–alpine plants.
- Published
- 2015
42. Long-distance plant dispersal to North Atlantic islands:colonization routes and founder effect
- Author
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Christian Brochmann, Kristine Bakke Westergaard, Andreas Tribsch, Pernille Bronken Eidesen, Siri Birkeland, Peter Schönswetter, Inger Greve Alsos, Dorothee Ehrich, Reidar Elven, and Heidi Solstad
- Subjects
Insular biogeography ,islands ,Outcrossing ,Plant Science ,Biology ,SPECIAL ISSUE: Island Plant Biology—Celebrating Carlquist's Legacy ,Atlantic Islands ,species traits ,genetic diversity ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Plantegeografi: 496 ,Colonization ,Plant Dispersal ,Research Articles ,Amplified fragment length polymorphism (AFLP) ,dispersal vector ,Ecology ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Plant geography: 496 ,long-distance dispersal (LDD) ,postglacial ,founder effect ,Dispersal vector ,Mathematics and natural science: 400 [VDP] ,Biological dispersal ,Founder effect - Abstract
Our study provides new knowledge of two processes that are important for plant adaptation in a changing environment: 1) long-distance dispersal patterns, and 2) genetic founder effect on islands. Although the theoretical framework for the genetic founder effect on islands was proposed in 1973, we are the first to quantify it in relation to island size, dispersal distance, and plant traits. In addition, our genetic results are mainly coherent with post-glacial colonisation rather than in situ glacial survival, and should therefore bring a final end to the 140-year-long glacial survival-tabula rasa debate among northern biologists., Long-distance dispersal (LDD) processes influence the founder effect on islands. We use genetic data for 25 Atlantic species and similarities among regional floras to analyse colonization, and test whether the genetic founder effect on five islands is associated with dispersal distance, island size and species traits. Most species colonized postglacially via multiple dispersal events from several source regions situated 280 to >3000 km away, and often not from the closest ones. A strong founder effect was observed for insect-pollinated mixed maters, and it increased with dispersal distance and decreased with island size in accordance with the theory of island biogeography. Only a minor founder effect was observed for wind-pollinated outcrossing species. Colonization patterns were largely congruent, indicating that despite the importance of stochasticity, LDD is mainly determined by common factors, probably dispersal vectors. Our findings caution against a priori assuming a single, close source region in biogeographic analyses.
- Published
- 2015
43. Biological introduction risks from shipping in a warming Arctic
- Author
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Georgy A. Semenov, Darren J. Kriticos, Steffen M. Olsen, Inger Greve Alsos, Loïc Pellissier, Chris Ware, Sławomir Kwaśniewski, Mary S. Wisz, Jørgen Berge, and Anders Jelmert
- Subjects
0106 biological sciences ,Ballast ,zooplankton ,habitat suitability ,regeneration niche ,Climate change ,Biology ,010603 evolutionary biology ,01 natural sciences ,Invasive species ,Arctic ,Propagule ,shipping ,Regeneration (ecology) ,marine non-indigenous species ,ballast water exchange ,geography ,geography.geographical_feature_category ,Ecology ,010604 marine biology & hydrobiology ,Plankton ,invasion ,Fishery ,climate change ,Archipelago ,ecophysiological thresholds - Abstract
Several decades of research on invasive marine species have yielded a broad understanding of the nature of species invasion mechanisms and associated threats globally. However, this is not true of the Arctic, a region where ongoing climatic changes may promote species invasion. Here, we evaluated risks associated with non-indigenous propagule loads discharged with ships' ballast water to the high-Arctic archipelago, Svalbard, as a case study for the wider Arctic. We sampled and identified transferred propagules using traditional and DNA barcoding techniques. We then assessed the suitability of the Svalbard coast for non-indigenous species under contemporary and future climate scenarios using ecophysiological models based on critical temperature and salinity reproductive thresholds. Ships discharging ballast water in Svalbard carried high densities of zooplankton (mean 1522335 SE individuals m(-3)), predominately comprised of indigenous species. Ballast water exchange did not prevent non-indigenous species introduction. Non-indigenous coastal species were present in all except one of 16 ballast water samples (mean 14467 SE individuals m(-3)), despite five of the eight ships exchanging ballast water en route. Of a total of 73 taxa, 36 species including 23 non-indigenous species were identified. Of those 23, sufficient data permitted evaluation of the current and future colonization potential for eight widely known invaders. With the exception of one of these species, modelled suitability indicated that the coast of Svalbard is unsuitable presently; under the 2100 Representative Concentration Pathway (RCP) 85 climate scenario, however, modelled suitability will favour colonization for six species.Synthesis and applications. We show that current ballast water management practices do not prevent non-indigenous species from being transferred to the Arctic. Consequences of these shortcomings will be shipping-route dependent, but will likely magnify over time: our models indicate future conditions will favour the colonization of non-indigenous species Arctic-wide. Invasion threats will be greatest where shipping transfers organisms across biogeographic realms, and for these shipping routes ballast water treatment technologies may be required to prevent impacts. Our results also highlight critical gaps in our understanding of ballast water management efficacy and prioritization. Thereby, our study provides an agenda for research and policy development. We show that current ballast water management practices do not prevent non-indigenous species from being transferred to the Arctic. Consequences of these shortcomings will be shipping-route dependent, but will likely magnify over time: our models indicate future conditions will favour the colonization of non-indigenous species Arctic-wide. Invasion threats will be greatest where shipping transfers organisms across biogeographic realms, and for these shipping routes ballast water treatment technologies may be required to prevent impacts. Our results also highlight critical gaps in our understanding of ballast water management efficacy and prioritization. Thereby, our study provides an agenda for research and policy development.
- Published
- 2015
44. Reconstructing the invasion history of Heracleum persicum (Apiaceae) into Europe
- Author
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Inger Greve Alsos, Hans K. Stenøien, Dilli Prasad Rijal, Šárka Jahodová, and Torbjørn Alm
- Subjects
VDP::Mathematics and natural science: 400::Zoology and botany: 480::Ecology: 488 ,DNA, Plant ,Genotype ,Heracleum ,Zoology ,Linkage Disequilibrium ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Økologi: 488 ,Botany ,Genetics ,Cluster Analysis ,Ecology, Evolution, Behavior and Systematics ,Historical record ,biodiversity ,invasive alien species ,Apiaceae ,biology ,giant hogweeds ,population genetics ,Bayes Theorem ,Sequence Analysis, DNA ,biology.organism_classification ,Europe ,Genetics, Population ,Heracleum persicum ,Approximate Bayesian Computation ,genetic variation ,Introduced Species ,Microsatellite Repeats - Abstract
This is the submitted manuscript version. Published version can be found at http://doi.org/10.1111/mec.13411. Sparse, incomplete and inappropriate historical records of invasive species often hamper invasive species management interventions. Population genetic analyses of invaders might provide a suitable context for the identification of their source populations and possible introduction routes. Here, we describe the population genetics of Heracleum persicum Desf. ex Fisch and trace its route of introduction into Europe. Microsatellite markers revealed a significantly higher genetic diversity of H. persicum in its native range, and the loss of diversity in the introduced range may be attributed to a recent genetic bottleneck. Bayesian cluster analysis on regional levels identified three and two genetic clusters in the native and the introduced ranges, respectively. A global structure analysis revealed two worldwide distinct genetic groups: one primarily in Iran and Denmark, the other primarily in Norway. There were also varying degrees of admixture in England, Sweden, Finland and Latvia. Approximate Bayesian computation indicated two independent introductions of H. persicum from Iran to Europe: the first one in Denmark and the second one in England. Finland was subsequently colonized by English populations. In contrast to the contemporary hypothesis of English origin of Norwegian populations, we found Finland to be a more likely source for Norwegian populations, a scenario supported by higher estimated histor-ical migration from Finland to Norway. Genetic diversity per se is not a primary determinant of invasiveness in H. persicum. Our results indicate that, due to either pre-adaptations or rapid local adaptations, introduced populations may have acqu-ired invasiveness after subsequent introductions, once a suitable environment was encountered.
- Published
- 2015
45. Sedimentary ancient DNA from Lake Skartjørna, Svalbard: Assessing the resilience of arctic flora to Holocene climate change
- Author
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Per Sjögren, Marie K Føreid, Matthias Forwick, Antony G. Brown, Eric Coissac, Inger Greve Alsos, Mikkel Winther Pedersen, Mary E. Edwards, Jon Y. Landvik, Leif V Jakobsen, and Ludovic Gielly
- Subjects
0301 basic medicine ,Archeology ,Flora ,media_common.quotation_subject ,03 medical and health sciences ,Arctic ,Holocene climate change ,plant macrofossils ,ancient DNA ,VDP::Matematikk og Naturvitenskap: 400::Geofag: 450::Kvartærgeologi, glasiologi: 465 ,Earth-Surface Processes ,media_common ,Global and Planetary Change ,Ecology ,vegetation reconstruction ,Paleontology ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Vegetasjonshistorie: 495 ,climate change ,030104 developmental biology ,Ancient DNA ,Geography ,Oceanography ,Research council ,metabarcoding ,Sedimentary rock ,Psychological resilience - Abstract
Reconstructing past vegetation and species diversity from arctic lake sediments can be challenging because of low pollen and plant macrofossil concentrations. Information may be enhanced by metabarcoding of sedimentary ancient DNA ( sedaDNA). We developed a Holocene record from Lake Skartjørna, Svalbard, using sedaDNA, plant macrofossils and sediment properties, and compared it with published records. All but two genera of vascular plants identified as macrofossils in this or a previous study were identified with sedaDNA. Six additional vascular taxa were found, plus two algal and 12 bryophyte taxa, by sedaDNA analysis, which also detected more species per sample than macrofossil analysis. A shift from Salix polaris-dominated vegetation, with Koenigia islandica, Ranunculaceae and the relatively thermophilic species Arabis alpina and Betula, to Dryas octopetala-dominated vegetation ~6600–5500 cal. BP suggests a transition from moist conditions 1–2°C warmer than today to colder/drier conditions. This coincides with a decrease in runoff, inferred from core lithology, and an independent record of declining lacustrine productivity. This mid-Holocene change in terrestrial vegetation is broadly coincident with changes in records from marine sediments off the west coast of Svalbard. Over the Holocene sedaDNA records little floristic change, and it clearly shows species persisted near the lake during time intervals when they are not detected as macrofossils. The flora has shown resilience in the presence of a changing climate, and, if future warming is limited to 2°C or less, we might expect only minor floristic changes in this region. However, the Holocene record provides no analogues for greater warming.
- Published
- 2015
46. Genetic roadmap of the Arctic: plant dispersal highways, traffic barriers and capitals of diversity
- Author
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Christian Brochmann, Oliver Gilg, Pierre Taberlet, Inger Greve Alsos, Vegar Bakkestuen, Dorothee Ehrich, Pernille Bronken Eidesen, National Centre for Biosystematics, University of Oslo ( UiO ) -Natural History Museum, The University Centre in Svalbard ( UNIS ), Department of Biology, University of Tromsø ( UiT ), Norwegian Institute for Nature Research (NINA), Tromsø University Museum, Biogéosciences [Dijon] ( BGS ), Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Laboratoire d'Ecologie Alpine ( LECA ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Université Savoie Mont Blanc ( USMB [Université de Savoie] [Université de Chambéry] ) -Centre National de la Recherche Scientifique ( CNRS ), Funding provided by the Research Council of Norway (grants 150322/720 and 146515/420)., National Centre for Biosystematics [Oslo], Natural History Museum [Oslo], University of Oslo (UiO)-University of Oslo (UiO), The University Centre in Svalbard (UNIS), University of Tromsø (UiT), Biogéosciences [UMR 6282] [Dijon] (BGS), Centre National de la Recherche Scientifique (CNRS)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire d'Ecologie Alpine (LECA), Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry]), Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique (CNRS), and Université Joseph Fourier - Grenoble 1 (UJF)-Université Savoie Mont Blanc (USMB [Université de Savoie] [Université de Chambéry])-Centre National de la Recherche Scientifique (CNRS)
- Subjects
0106 biological sciences ,comparative phylogeography ,Physiology ,Greenland ,Plant Science ,01 natural sciences ,Gene flow ,refugia ,Arctic ,Refugium (population biology) ,genetic structure ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Plantegeografi: 496 ,Ice Cover ,Amplified Fragment Length Polymorphism Analysis ,Atlantic Ocean ,Phylogeny ,0303 health sciences ,plant dispersal ,Arctic Regions ,Ecology ,DNA, Chloroplast ,genetic diversity ,Plants ,Phylogeography ,[ SDV.GEN.GPO ] Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] ,Geography ,Interglacial ,Genetic structure ,geographic locations ,Gene Flow ,geographical information system (GIS) ,Pleistocene ,mplified fragment length polymorphisms (AFLP) ,[SDV.BID]Life Sciences [q-bio]/Biodiversity ,010603 evolutionary biology ,Beringia ,03 medical and health sciences ,Ecosystem ,030304 developmental biology ,[ SDV.BID ] Life Sciences [q-bio]/Biodiversity ,Genetic diversity ,[ SDE.BE ] Environmental Sciences/Biodiversity and Ecology ,Polymorphism, Genetic ,[SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE] ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Plant geography: 496 ,15. Life on land ,Siberia ,Haplotypes ,amplified fragment length polymorphisms (AFLP) ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology - Abstract
This is the peer reviewed version of the following article: Eidesen, P.B., Ehrich, D., Bakkestuen, V., Alsos, I.G., Gilg, O., Taberlet, P. & Brochmann, C. (2013). Genetic roadmap of the Arctic: plant dispersal highways, traffic barriers and capitals of diversity. New Phytologist, 200(3), 898-910. https://doi.org/10.1111/nph.12412, which has been published in final form at https://doi.org/10.1111/nph.12412. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. We provide the first comparative multispecies analysis of spatial genetic structure and diversity in the circumpolar Arctic using a common strategy for sampling and genetic analyses. We aimed to identify and explain potential general patterns of genetic discontinuity/connectivity and diversity, and to compare our findings with previously published hypotheses. We collected and analyzed 7707 samples of 17 widespread arctic–alpine plant species for amplified fragment length polymorphisms (AFLPs). Genetic structure, diversity and distinctiveness were analyzed for each species, and extrapolated to cover the geographic range of each species. The resulting maps were overlaid to produce metamaps. The Arctic and Atlantic Oceans, the Greenlandic ice cap, the Urals, and lowland areas between southern mountain ranges and the Arctic were the strongest barriers against gene flow. Diversity was highest in Beringia and gradually decreased into formerly glaciated areas. The highest degrees of distinctiveness were observed in Siberia. We conclude that large‐scale general patterns exist in the Arctic, shaped by the Pleistocene glaciations combined with long‐standing physical barriers against gene flow. Beringia served as both refugium and source for interglacial (re)colonization, whereas areas further west in Siberia served as refugia, but less as sources for (re)clonization.
- Published
- 2013
47. Tetraploids do not form cushions: association of ploidy level, growth form and ecology in the High Arctic Saxifraga oppositifolia L. s. lat. (Saxifragaceae) in Svalbard
- Author
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Christian Lettner, Pernille Bronken Eidesen, Inger Greve Alsos, Bart Peeters, Morgan Bender, Eike Müller, Martin Kristiansen, Froukje M. Postma, and Koen Frans Verweij
- Subjects
VDP::Mathematics and natural science: 400::Zoology and botany: 480::Ecology: 488 ,Autopolyploidy ,DYNAMICS ,Species complex ,flow cytometry ,morphotypes ,habitat segregation ,purple saxifrage ,Range (biology) ,Niche ,VEGETATION MAP ,Biology ,MOLECULAR ANALYSIS ,Oceanography ,FREQUENCY ,Saxifraga oppositifolia ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Økologi: 488 ,lcsh:Oceanography ,Botany ,Naturvetenskap ,Earth and Planetary Sciences (miscellaneous) ,Environmental Chemistry ,CARBONATE ,lcsh:GC1-1581 ,PLANT ,lcsh:Environmental sciences ,General Environmental Science ,lcsh:GE1-350 ,Ecological niche ,VDP::Mathematics and natural science: 400::Zoology and botany: 480::Plant physiology: 492 ,Ecology ,biology ,Saxifragaceae ,fungi ,food and beverages ,Vegetation ,biology.organism_classification ,VDP::Matematikk og Naturvitenskap: 400::Zoologiske og botaniske fag: 480::Plantefysiologi: 492 ,IGNITION ,Ploidy ,Natural Sciences ,SEDIMENTS - Abstract
Saxifraga oppositifolia L. is a common circumpolar plant species that displays considerable morphological and genetic variation throughout its range. It is mainly diploid, but tetraploids are reported from several regions. The growth form varies from prostate to cushion-shaped, and the plant thrives in wet snow beds as well as on dry ridges. This variation has triggered the curiosity of many researchers, but as yet, no one has explained the observed morphological variation using ecological and/or genetic factors. However, the ploidy level has rarely been taken into account. This is the first study that demonstrates a significant correlation between ploidy level, ecology and growth form in S. oppositifolia . We successfully analysed 193 individuals of S. oppositifolia from 15 locations in Svalbard to investigate possible relationships among growth forms (prostrate, intermediate and cushion), ecological factors (vegetation and soil characteristics) and ploidy level. Results from flow cytometry reported 106 diploids, eight triploids and 79 tetraploids. Tetraploids almost exclusively showed prostrate growth, while the diploids displayed all three growth forms, evidence that growth form is at least partly genetically determined. Our analyses of environmental and vegetation data in relation to ploidy level indicated overlapping niches, but the tetraploids showed a narrower niche, and one shifted towards more benign habitats characterized by higher pH, higher soil temperatures and higher cover of vascular plants. The latter may suggest that tetraploids are slightly better competitors, but less hardy. Thus, autopolyploidy in S. oppositifolia has expanded the ecological amplitude of this species complex. Keywords: Autopolyploidy; flow cytometry; morphotypes; habitat segregation; purple saxifrage (Published: 6 June 2013) To access the supplementary material for this article, please see Supplementary files in the column to the right (under Article Tools) Citation: Polar Research 2013, 32 , 20071, http://dx.doi.org/10.3402/polar.v32i0.20071
- Published
- 2013
48. Local temperatures inferred from plant communities suggest strong spatial buffering of climate warming across Northern Europe
- Author
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Guillaume Decocq, Inger Greve Alsos, Mats Dynesius, Per Arild Aarrestad, Liv Guri Velle, W. Scott Armbruster, Risto Virtanen, Liv Unn Tveraabak, Stefanie Reinhardt, Jens-Christian Svenning, John-Arvid Grytnes, Martin Diekmann, Hans Henrik Bruun, Arvid Odland, Miska Luoto, Gunnar Austrheim, Ann Milbau, James D. M. Speed, Fride Høistad Schei, Kari Klanderud, Jonathan Lenoir, Carl Johan Dahlberg, H. John B. Birks, Vigdis Vandvik, Rasmus Ejrnæs, Virve Ravolainen, Martin Zobel, Kari Anne Bråthen, Bente J. Graae, Mari Moora, Bettina Nygaard, Jörg Brunet, Sylvi M. Sandvik, Claes Bergendorff, and Kristoffer Hylander
- Subjects
0106 biological sciences ,010504 meteorology & atmospheric sciences ,Climate Change ,Climate change ,Metapopulation ,010603 evolutionary biology ,01 natural sciences ,Environmental Chemistry ,Plant Physiological Phenomena ,0105 earth and related environmental sciences ,General Environmental Science ,Global and Planetary Change ,Ecology ,Geography ,Global warming ,Temperature ,Plant community ,Biota ,15. Life on land ,Models, Theoretical ,Spatial heterogeneity ,Europe ,13. Climate action ,Climatology ,Spatial ecology ,Spatial extent - Abstract
Recent studies from mountainous areas of small spatial extent (2500 km(2) ) suggest that fine-grained thermal variability over tens or hundreds of metres exceeds much of the climate warming expected for the coming decades. Such variability in temperature provides buffering to mitigate climate-change impacts. Is this local spatial buffering restricted to topographically complex terrains? To answer this, we here study fine-grained thermal variability across a 2500-km wide latitudinal gradient in Northern Europe encompassing a large array of topographic complexities. We first combined plant community data, Ellenberg temperature indicator values, locally measured temperatures (LmT) and globally interpolated temperatures (GiT) in a modelling framework to infer biologically relevant temperature conditions from plant assemblages within1000-m(2) units (community-inferred temperatures: CiT). We then assessed: (1) CiT range (thermal variability) within 1-km(2) units; (2) the relationship between CiT range and topographically and geographically derived predictors at 1-km resolution; and (3) whether spatial turnover in CiT is greater than spatial turnover in GiT within 100-km(2) units. Ellenberg temperature indicator values in combination with plant assemblages explained 46-72% of variation in LmT and 92-96% of variation in GiT during the growing season (June, July, August). Growing-season CiT range within 1-km(2) units peaked at 60-65°N and increased with terrain roughness, averaging 1.97 °C (SD = 0.84 °C) and 2.68 °C (SD = 1.26 °C) within the flattest and roughest units respectively. Complex interactions between topography-related variables and latitude explained 35% of variation in growing-season CiT range when accounting for sampling effort and residual spatial autocorrelation. Spatial turnover in growing-season CiT within 100-km(2) units was, on average, 1.8 times greater (0.32 °C km(-1) ) than spatial turnover in growing-season GiT (0.18 °C km(-1) ). We conclude that thermal variability within 1-km(2) units strongly increases local spatial buffering of future climate warming across Northern Europe, even in the flattest terrains.
- Published
- 2013
49. No divergence in Cassiope tetragona: Persistence of growth response along a latitudinal temperature gradient and under multi-year experimental warming
- Author
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Jelte Rozema, Stef Weijers, Inger Greve Alsos, Rob Broekman, Pernille Bronken Eidesen, Maarten J.J.E. Loonen, Arctic and Antarctic studies, Systems Ecology, and Amsterdam Global Change Institute
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North Sweden ,Climate ,ved/biology.organism_classification_rank.species ,Growing season ,Plant Science ,Dendroclimatology ,high- to sub-arctic ,Atmospheric sciences ,Shrub ,Global Warming ,Cassiope tetragona ,TIBETAN PLATEAU ,odivergence problem' ,Svalbard ,RETROSPECTIVE ANALYSIS ,SDG 13 - Climate Action ,RECONSTRUCTION ,experimental warming ,growth variables ,Sweden ,CLIMATE SIGNALS ,biology ,ved/biology ,Ecology ,Arctic Regions ,Global warming ,Temperature ,Original Articles ,biology.organism_classification ,ALASKA ,SUMMER TEMPERATURE ,Tundra ,temperature reconstruction ,TUNDRA ,Plant Leaves ,Arctic ,Shoot ,Ericaceae ,Seasons ,VEGETATION ,ARCTIC DWARF-SHRUB ,DENDROCLIMATOLOGY ,Plant Shoots ,climate proxy - Abstract
The dwarf shrub Cassiope tetragona (Arctic bell-heather) is increasingly used for arctic climate reconstructions, the reliability of which depends on the existence of a linear climategrowth relationship. This relationship was examined over a high-arctic to sub-arctic temperature gradient and under multi-year artificial warming at a high-arctic site.Growth chronologies of annual shoot length, as well as total leaf length, number of leaves and average leaf length per year, were constructed for three sites. Cassiope tetragona was sampled near its cold tolerance limit at Ny-lesund, Svalbard, at its assumed climatic optimum in Endalen, Svalbard, and near its European southern limit at Abisko, Sweden. Together these sites represent the entire temperature gradient of this species. Leaf life span was also determined. Each growing season from 2004 to 2010, 17 open top chambers (OTCs) were placed near Ny-lesund, thus increasing the daily mean temperatures by 123C. At the end of the 2010 growing season, shoots were harvested from OTCs and control plots, and growth parameters were measured.All growth parameters, except average leaf length, exhibited a linear positive response (R-2 between 063 and 091) to mean July temperature over the temperature gradient. Average leaf life span was 14 years shorter in sub-arctic Sweden compared with arctic Svalbard. All growth parameters increased in response to the experimental warming; the leaf life span was, however, not significantly affected by OTC warming.The linear July temperaturegrowth relationships, as well as the 7 year effect of experimental warming, confirm that the growth parameters annual shoot length, total leaf length and number of leaves per year can reliably be used for monitoring and reconstructing temperature changes. Furthermore, reconstructing July temperature from these parameters is not hampered by divergence.
- Published
- 2012
50. Range shifts and global warming: ecological responses of Empetrum nigrum. to experimental warming at its northern (high Arctic) and southern (Atlantic) geographical range margin
- Author
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Inger Greve Alsos, Bert Buizer, Jaap van Rijckevorsel, Stef Weijers, Jelte Rozema, Peter M. van Bodegom, Maarten de Korte, Johan van Breda, Pernille Bronken Eidesen, Systems Ecology, and Amsterdam Global Change Institute
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0106 biological sciences ,Empetrum ,010504 meteorology & atmospheric sciences ,Growing season ,010603 evolutionary biology ,01 natural sciences ,SDG 13 - Climate Action ,Cassiope tetragona ,0105 earth and related environmental sciences ,General Environmental Science ,VDP::Mathematics and natural science: 400 ,biology ,Renewable Energy, Sustainability and the Environment ,Ecology ,Phenology ,Global warming ,Public Health, Environmental and Occupational Health ,food and beverages ,VDP::Matematikk og Naturvitenskap: 400 ,15. Life on land ,biology.organism_classification ,Tundra ,13. Climate action ,Plant cover ,Environmental science ,Empetrum nigrum - Abstract
Global change is expected to lead to range shifts of plant species. The ecological mechanisms underpinning these shifts are currently not well understood. Here, we compared ecological responses possibly underlying southern range contraction and northern range expansion of Empetrum nigrum, a key species in northern heathlands, which may be related to global change. We hypothesized a negative response to warming in the 'south' (i.e.the Netherlands) and a positive response at the northern range margin (the tundra on Svalbard). Open top chambers (OTCs) were used to simulate global warming. In the 'south', OTC warming caused enhanced shoot growth and growth rate, biomass increment, advanced phenology, larger and heavier berries of Empetrum, while its growing season was extended by 75 days. Under OTC warming co-occurring Calluna vulgaris also showed an increased growing season length (by 98 days) as well as increased shoot growth rate and biomass growth, plant cover and height. Still, we found no evidence for increased competitiveness relative to Empetrum. In the 'north', Empetrum responded with increased shoot and biomass growth, enhanced berry development and ripening to warming. These responses exceeded those of co-occurring Cassiope tetragona with the exception of its biomass response. The direct and indirect ecological responses found do not readily explain the observed northward retreat of Empetrum at the southern range margin. The direct ecological responses found at its northern range margin are, on the other hand, in line with the increased occurrences of this species on Svalbard. © 2012 IOP Publishing Ltd.
- Published
- 2012
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