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4 results on '"Lara Puetz"'

1. An integrated morphological–molecular approach reveals new insights on the systematics of the octocoral

Author

Martin V. Sørensen, Sarah S.T. Mak, Angelo Poliseno, Emily Petroni, M. Thomas P. Gilbert, Lara Puetz, Álvaro Altuna, Catherine S. McFadden, and Pilar Ríos

Subjects
0106 biological sciences, 0301 basic medicine, Cnidaria, Systematics, Octocorallia, biology, Phylogenetic tree, Zoology, biology.organism_classification, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, 030104 developmental biology, Alcyonacea, 28S ribosomal RNA, Molecular phylogenetics, Taxonomy (biology), Ecology, Evolution, Behavior and Systematics
Abstract

Telestula humilis (Thomson, 1927) is a rare deep-sea stoloniferan octocoral distributed in the eastern Atlantic. Here we compared seven putative colonies of this species collected off Spain with the lectotype from the Oceanographic Museum of Monaco and found them to be identical morphologically. Phylogenetic analyses on both full mitogenomes and a concatenated alignment containing two mtDNA genes (mtMutS and Cox1) and nuclear 28S rRNA gene recovered Telestula humilis sister to Incrustatus and Inconstantia rather than to other species of Telestula. This therefore supports its taxonomic reassignment to Pseudotelestula gen. nov. as Pseudotelestula humilis comb. nov. The taxonomic reassignment is also supported by subtle differences observed between the morphology of the colony and the sclerome of Pseudotelestula humilis comb. nov. and the two sister genera. The occurrence of an intrusion tissue with sclerites in the basal part of the gastric cavity of the adult polyps is shared among Telestula and Pseudotelestula gen. nov. However, Pseudotelestula gen. nov. has sclerites arranged in a collaret and points below the tentacles, the sclerites of the calyx wall and the stolon are plump warty spindles, and the intrusion tissue has long sticks and spindles with cone-like spines.

Published
2021
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2. Dense sampling of bird diversity increases power of comparative genomics

Author

Rencia van der Sluis, Nadine Thiele, Borja Milá, Araxi O. Urrutia, Josefin Stiller, Joel Cracraft, Zongji Wang, Qiye Li, Barney A. Schlinger, Guojie Zhang, Ana Tereza Ribeiro de Vasconcelos, Oliver A. Ryder, Rebecca B. Dikow, Thomas L. Parchman, Emily Cavill, John G. Blake, Libby C. Megna, Andrew G. Clark, Christopher C. Witt, Ángela M. Parody-Merino, Jason T. Weir, Wanjun Chen, Jason T. Howard, T. Brandt Ryder, Michael G. Campana, Jon Fjeldså, Robb T. Brumfield, M. Thomas P. Gilbert, Alexandre Aleixo, Gerald Borgia, Qi Fang, Phil F. Battley, Ellen D. Ketterson, Matthew I. M. Louder, Scott A. Taylor, Glaucia Del-Rio, Scott V. Edwards, Sergio Andreu-Sánchez, Fumin Lei, Irby J. Lovette, Neil J. Gemmell, Mikkel-Holger S. Sinding, Carole A. Parent, Huanming Yang, André E. R. Soares, David W. Burt, Guanliang Meng, André Corvelo, Nicolas Dussex, Jimmy A. McGuire, Kira E. Delmore, Marc P. Hoeppner, Julio Rozas, Ângela M. Ribeiro, Les Christidis, Haw Chuan Lim, Guillermo Friis, Guangji Chen, Martin Stervander, Mads F. Bertelsen, Siavash Mirarab, Biao Wang, Hanna Sigeman, Lara Puetz, Qi Zhou, Marta Riutort, Knud A. Jønsson, Christopher N. Balakrishnan, Alexander Suh, Edward L. Braun, Nicholas Costa Barroso Lima, Jeffrey M. DaCosta, Reed Bowman, Yang Liu, Kim Rutherford, Ashot Margaryan, Peter Njoroge, Beth Shapiro, Benedict Paten, Shaohong Feng, Adam M. Fudickar, Jacob González-Solís, Bent O. Petersen, Subir B. Shakya, Henrik Mouritsen, Glauco Camenisch, Maude W. Baldwin, Andrew Hart Reeve, Bruce C. Robertson, Morgan Wirthlin, Shannon J. Hackett, Chunxue Guo, Bengt Hansson, Peter G. Ryan, Miriam Liedvogel, Alain Vignal, Saul J. Cowen, Matthew J. Fuxjager, Robert C. Fleischer, Dustin J. Foote, Joel Armstrong, Joann Mudge, Nancy F. Chen, Santiago Claramunt, Joan Ferrer-Obiol, John W. Fitzpatrick, Leopold Eckhart, Mark E. Hauber, Michael Bunce, Carsten Rahbek, George Pacheco, Dieter Thomas Tietze, Gang Song, Jérôme Fuchs, John P. Dumbacher, Henriette van der Zwan, Love Dalén, Michael J. Braun, Lukas F. Keller, Yuan Deng, Jian Wang, Thomas Sicheritz-Pontén, Tamás Székely, Erich D. Jarvis, Alison Cloutier, David Haussler, Matthew D. Carling, Carina Visser, Paul B. Frandsen, Anna Tigano, Andre Franke, Suvi Ponnikas, Claudio V. Mello, Vicki L. Friesen, Timothy B. Sackton, Rute R. da Fonseca, Frederick H. Sheldon, Duo Xie, Brant C. Faircloth, Bette A. Loiselle, Gary R. Graves, Ian G. Jamieson, Mark Diekhans, Lainy B. Day, Peter A. Hosner, Murray P. Cox, Oliver Krone, Andrew E. Fidler, Peter Houde, Francisco Prosdocimi, Zoology, Chinese Academy of Sciences, Carlsberg Foundation, Velux Foundation, National Natural Science Foundation of China, Howard Hughes Medical Institute, National Institutes of Health (US), China National GeneBank, Kunming Institute of Zoology, Chinese Academy of Sciences [Beijing] (CAS), Beijing Genomics Institute [Shenzhen] (BGI), University of Copenhagen = Københavns Universitet (KU), University of California [Santa Cruz] (UCSC), University of California, Natural History Museum of Denmark, Faculty of Science [Copenhagen], University of Copenhagen = Københavns Universitet (KU)-University of Copenhagen = Københavns Universitet (KU), University of Chinese Academy of Sciences [Beijing] (UCAS), Louisiana State University (LSU), Museum of Natural Science, IT University of Copenhagen, AIMST University, Zhejiang University, University of Vienna [Vienna], Zhejiang University School of Medicine [China], Institute of Molecular Biology of the National Academy of Sciences of Armenia (IMB NAS RA), National Academy of Sciences of the Republic of Armenia [Yerevan] (NAS RA), Novogene, Duke University Medical Center, Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), United States Department of Health & Human Services, National Institutes of Health (NIH) - USA, NIH National Human Genome Research Institute (NHGRI) (U54 HG007990, T32 HG008345, R01 HG010053), NIH National Heart Lung & Blood Institute (NHLBI) (U01 HL137183), 25621572 - Van der Zwan, Henriëtte, and 21224919 - Van der Sluis, Rencia

Subjects
0106 biological sciences, GENES, PROTEINS, Tree of life, Genomics, Biology, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 010603 evolutionary biology, 01 natural sciences, Genome, Article, Evolutionary genetics, génomique, Evolutionsbiologi, 03 medical and health sciences, Phylogenetics, ACCELERATED EVOLUTION, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, REVEALS, genomics, Genetics, DIVERGENCE, Genomes, Genetik, Cladistic analysis, Selection (genetic algorithm), TREE, 030304 developmental biology, Comparative genomics, 0303 health sciences, Evolutionary Biology, Multidisciplinary, Phylogenetic tree, SEQUENCES, Human evolutionary genetics, Cladística, Biodiversity, DNA, 15. Life on land, échantillonnage, Sampling Methods, Biodiversitat, DUPLICATION, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Evolutionary biology, 1181 Ecology, evolutionary biology, PACKAGE
Abstract

Whole-genome sequencing projects are increasingly populating the tree of life and characterizing biodiversity1–4. Sparse taxon sampling has previously been proposed to confound phylogenetic inference5, and captures only a fraction of the genomic diversity. Here we report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analysing 363 genomes from 92.4% of bird families—including 267 newly sequenced genomes produced for phase II of the Bird 10,000 Genomes (B10K) Project. We use this comparative genome dataset in combination with a pipeline that leverages a reference-free whole-genome alignment to identify orthologous regions in greater numbers than has previously been possible and to recognize genomic novelties in particular bird lineages. The densely sampled alignment provides a single-base-pair map of selection, has more than doubled the fraction of bases that are confidently predicted to be under conservation and reveals extensive patterns of weak selection in predominantly non-coding DNA. Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics. We anticipate that this genomic resource will offer new perspectives on evolutionary processes in cross-species comparative analyses and assist in efforts to conserve species., A dataset of the genomes of 363 species from the Bird 10,000 Genomes Project shows increased power to detect shared and lineage-specific variation, demonstrating the importance of phylogenetically diverse taxon sampling in whole-genome sequencing.

Published
2020
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3. A giant squid (Architeuthis dux) off Reunion Island, western Indian Ocean: the greatest giant ever?

Author

Sébastien Jaquemet, Lara Puetz, Evgeny V. Romanov, ARDA CAP RUN, Ecologie marine tropicale dans les Océans Pacifique et Indien (ENTROPIE [Réunion]), Centre National de la Recherche Scientifique (CNRS)-Université de La Réunion (UR)-Institut de Recherche pour le Développement (IRD), and University of Copenhagen = Københavns Universitet (KU)

Subjects
0106 biological sciences, Dorsum, distribution records, 010604 marine biology & hydrobiology, dorsal mantle length, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Aquatic Science, Biology, 010603 evolutionary biology, 01 natural sciences, Architeuthis dux, Cephalopod habitat, total length, Indian ocean, Oceanography, Beak, Comparable size, 14. Life underwater, Mantle (mollusc), Predator, lower rostral length
Abstract

A freshly dead individual of the giant squidArchiteuthis dux, presumably mutilated by a predator of bigger or comparable size, is reported from the south-western Indian Ocean in proximity to Reunion Island. The species was identified from body and beak morphology and validated genetically. The dorsal mantle length (DML) estimated from beak measurements (lower rostral length, LRL) varied between 2153 and 3060 mm depending on the allometric equation used. TheArchiteuthis duxindividual described here is the biggest giant squid ever reported for the region.

Published
2018
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4. 31° South: The physiology of adaptation to arid conditions in a passerine bird

Author

Nicholas B. Pattinson, Rute R. da Fonseca, M. Thomas P. Gilbert, Yuan Deng, Guojie Zhang, Lara Puetz, Ben Smit, Love Dalén, and Ângela M. Ribeiro

Subjects
0106 biological sciences, 0301 basic medicine, Genotype, Biodiversity, Physiology, Biology, 010603 evolutionary biology, 01 natural sciences, Energy homeostasis, Intraspecific competition, 03 medical and health sciences, South Africa, Genetics, Animals, Microbiome, Passeriformes, Ecology, Evolution, Behavior and Systematics, Genetic Association Studies, Natural selection, Mechanism (biology), Arid, Adaptation, Physiological, Gastrointestinal Microbiome, 030104 developmental biology, Genetics, Population, Phenotype, Gene-Environment Interaction, Basal Metabolism, Adaptation, Desert Climate
Abstract

Arid environments provide ideal ground for investigating the mechanisms of adaptive evolution. High temperatures and low water availability are relentless stressors for many endotherms, including birds; yet birds persist in deserts. While physiological adaptation probably involves metabolic phenotypes, the underlying mechanisms (plasticity, genetics) are largely uncharacterized. To explore this, we took an intraspecific approach that focused on a species that is resident over a mesic to arid gradient, the Karoo scrub-robin (Cercotrichas coryphaeus). Specifically, we integrated environmental (climatic and primary productivity), physiological (metabolic rates: a measure of energy expenditure), genotypic (genetic variation underlying the machinery of energy production) and microbiome (involved in processing food from where energy is retrieved) data, to infer the mechanism of physiological adaptation. We that found the variation in energetic physiology phenotypes and gut microbiome composition are associated with environmental features as well as with variation in genes underlying energy metabolic pathways. Specifically, we identified a small list of candidate adaptive genes, some of them with known ties to relevant physiology phenotypes. Together our results suggest that selective pressures on energetic physiology mediated by genes related to energy homeostasis and possibly microbiota composition may facilitate adaptation to local conditions and provide an explanation to the high avian intraspecific divergence observed in harsh environments.

Published
2018

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