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Dietz L, Mayer C, Stolle E, Eberle J, Misof B, Podsiadlowski L, Niehuis O, Ahrens D. Metazoa-level USCOs as markers in species delimitation and classification. Mol Ecol Resour 2024; 24:e13921. [PMID: 38146909 DOI: 10.1111/1755-0998.13921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/06/2023] [Accepted: 12/13/2023] [Indexed: 12/27/2023]
Abstract
Metazoa-level universal single-copy orthologs (mzl-USCOs) are universally applicable markers for DNA taxonomy in animals that can replace or supplement single-gene barcodes. Previously, mzl-USCOs from target enrichment data were shown to reliably distinguish species. Here, we tested whether USCOs are an evenly distributed, representative sample of a given metazoan genome and therefore able to cope with past hybridization events and incomplete lineage sorting. This is relevant for coalescent-based species delimitation approaches, which critically depend on the assumption that the investigated loci do not exhibit autocorrelation due to physical linkage. Based on 239 chromosome-level assembled genomes, we confirmed that mzl-USCOs are genetically unlinked for practical purposes and a representative sample of a genome in terms of reciprocal distances between USCOs on a chromosome and of distribution across chromosomes. We tested the suitability of mzl-USCOs extracted from genomes for species delimitation and phylogeny in four case studies: Anopheles mosquitos, Drosophila fruit flies, Heliconius butterflies and Darwin's finches. In almost all instances, USCOs allowed delineating species and yielded phylogenies that corresponded to those generated from whole genome data. Our phylogenetic analyses demonstrate that USCOs may complement single-gene DNA barcodes and provide more accurate taxonomic inferences. Combining USCOs from sources that used different versions of ortholog reference libraries to infer marker orthology may be challenging and, at times, impact taxonomic conclusions. However, we expect this problem to become less severe as the rapidly growing number of reference genomes provides a better representation of the number and diversity of organismal lineages.
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Affiliation(s)
- Lars Dietz
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Christoph Mayer
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Eckart Stolle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Jonas Eberle
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Paris-Lodron-University, Salzburg, Austria
| | - Bernhard Misof
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
- Rheinische Friedrich-Wilhelms-Universität Bonn, Bonn, Germany
| | - Lars Podsiadlowski
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
| | - Oliver Niehuis
- Abt. Evolutionsbiologie und Ökologie, Institut für Biologie I, Albert-Ludwigs-Universität Freiburg, Freiburg, Germany
| | - Dirk Ahrens
- Museum A. Koenig, Leibniz Institute for the Analysis of Biodiversity Change, Bonn, Germany
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2
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Vázquez-Miranda H, Zink RM, Pinto BJ. Comparative phylogenomic patterns in the Baja California avifauna, their conservation implications, and the stages in lineage divergence. Mol Phylogenet Evol 2022; 171:107466. [DOI: 10.1016/j.ympev.2022.107466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/22/2022] [Accepted: 03/01/2022] [Indexed: 10/18/2022]
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3
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Yardeni G, Viruel J, Paris M, Hess J, Groot Crego C, de La Harpe M, Rivera N, Barfuss MHJ, Till W, Guzmán-Jacob V, Krömer T, Lexer C, Paun O, Leroy T. Taxon-specific or universal? Using target capture to study the evolutionary history of rapid radiations. Mol Ecol Resour 2021; 22:927-945. [PMID: 34606683 PMCID: PMC9292372 DOI: 10.1111/1755-0998.13523] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/09/2021] [Accepted: 09/22/2021] [Indexed: 12/20/2022]
Abstract
Target capture has emerged as an important tool for phylogenetics and population genetics in nonmodel taxa. Whereas developing taxon‐specific capture probes requires sustained efforts, available universal kits may have a lower power to reconstruct relationships at shallow phylogenetic scales and within rapidly radiating clades. We present here a newly developed target capture set for Bromeliaceae, a large and ecologically diverse plant family with highly variable diversification rates. The set targets 1776 coding regions, including genes putatively involved in key innovations, with the aim to empower testing of a wide range of evolutionary hypotheses. We compare the relative power of this taxon‐specific set, Bromeliad1776, to the universal Angiosperms353 kit. The taxon‐specific set results in higher enrichment success across the entire family; however, the overall performance of both kits to reconstruct phylogenetic trees is relatively comparable, highlighting the vast potential of universal kits for resolving evolutionary relationships. For more detailed phylogenetic or population genetic analyses, for example the exploration of gene tree concordance, nucleotide diversity or population structure, the taxon‐specific capture set presents clear benefits. We discuss the potential lessons that this comparative study provides for future phylogenetic and population genetic investigations, in particular for the study of evolutionary radiations.
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Affiliation(s)
- Gil Yardeni
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | | | - Margot Paris
- Unit of Ecology & Evolution, Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Jaqueline Hess
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Department of Soil Ecology, Helmholtz Centre for Environmental Research, UFZ, Halle (Saale), Germany
| | - Clara Groot Crego
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria.,Vienna Graduate School of Population Genetics, Vienna, Austria
| | - Marylaure de La Harpe
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Norma Rivera
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Michael H J Barfuss
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Walter Till
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Valeria Guzmán-Jacob
- Biodiversity, Macroecology and Biogeography, University of Goettingen, Göttingen, Germany
| | - Thorsten Krömer
- Centro de Investigaciones Tropicales, Universidad Veracruzana, Xalapa, Mexico
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Ovidiu Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Thibault Leroy
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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4
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Zink RM. Considering the use of the terms strain and adaptation in prion research. Heliyon 2021; 7:e06801. [PMID: 33898853 PMCID: PMC8060586 DOI: 10.1016/j.heliyon.2021.e06801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/08/2021] [Accepted: 04/11/2021] [Indexed: 12/20/2022] Open
Abstract
Evolutionary biologists and disease biologists use the terms strain and adaptation in Chronic Wasting Disease (CWD) research in different ways. In evolutionary biology, a strain is a nascent genetic lineage that can be described by a genealogy, and a phylogenetic nomenclature constructed to reflect that genealogy. Prion strains are described as showing distinct host range, clinical presentation, disease progression, and neuropathological and PrP biochemical profiles, and lack information that would permit phylogenetic reconstruction of their history. Prion strains are alternative protein conformations, sometimes derived from the same genotype. I suggest referring to prion strains as ecotypes, because the variant phenotypic conformations ("strains") are a function of the interaction between PRNP amino acid genotype and the host environment. In the case of CWD, a prion ecotype in white-tailed deer would be described by its genotype and the host in which it occurs, such as the H95 + ecotype. However, an evolutionary nomenclature is difficult because not all individuals with the same PRNP genotype show signs of CWD, therefore creating a nomenclature reflecting and one-to-one relationship between PRNP genealogy and CWD presence is difficult. Furthermore, very little information exists on the phylogenetic distribution of CWD ecotypes in wild deer populations. Adaptation has a clear meaning in evolutionary biology, the differential survival and reproduction of individual genotypes. If a new prion ecotype arises in a particular host and kills more hosts or kills at an earlier age, it is the antithesis of the evolutionary definition of adaptation. However, prion strains might be transmitted across generations epigenetically, but whether this represents adaptation depends on the fitness consequences of the strain. Protein phenotypes of PRNP that cause transmissible spongiform encephalopathies (TSEs), and CWD, are maladaptive and would not be propagated genetically or epigenetically via a process consistent with an evolutionary view of adaptation. I suggest terming the process of prion strain origination "phenotypic transformation", and only adaptation if evidence shows they are not maladaptive and persist over evolutionary time periods (e.g., thousands of generations) and across distinct species boundaries (via inheritance). Thus, prion biologists use strain and adaptation, historically evolutionary terms, in quite different ways.
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Affiliation(s)
- Robert M. Zink
- School of Natural Resources, School of Biological Sciences, Nebraska State Museum, University of Nebraska-Lincoln, Lincoln, NE 68503, USA
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5
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Island songbirds as windows into evolution in small populations. Curr Biol 2021; 31:1303-1310.e4. [PMID: 33476557 DOI: 10.1016/j.cub.2020.12.040] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/12/2020] [Accepted: 12/23/2020] [Indexed: 11/20/2022]
Abstract
Due to their limited ranges and inherent isolation, island species have long been recognized as crucial systems for tackling a range of evolutionary questions, including in the early study of speciation.1,2 Such species have been less studied in the understanding of the evolutionary forces driving DNA sequence evolution. Island species usually have lower census population sizes (N) than continental species and, supposedly, lower effective population sizes (Ne). Given that both the rates of change caused by genetic drift and by selection are dependent upon Ne, island species are theoretically expected to exhibit (1) lower genetic diversity, (2) less effective natural selection against slightly deleterious mutations,3,4 and (3) a lower rate of adaptive evolution.5-8 Here, we have used a large set of newly sequenced and published whole-genome sequences of Passerida species (14 insular and 11 continental) to test these predictions. We confirm that island species exhibit lower census size and Ne, supporting the hypothesis that the smaller area available on islands constrains the upper bound of Ne. In the insular species, we find lower nucleotide diversity in coding regions, higher ratios of non-synonymous to synonymous polymorphisms, and lower adaptive substitution rates. Our results provide robust evidence that the lower Ne experienced by island species has affected both the ability of natural selection to efficiently remove weakly deleterious mutations and also the adaptive potential of island species, therefore providing considerable empirical support for the nearly neutral theory. We discuss the implications for both evolutionary and conservation biology.
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6
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Tobias JA, Ottenburghs J, Pigot AL. Avian Diversity: Speciation, Macroevolution, and Ecological Function. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2020. [DOI: 10.1146/annurev-ecolsys-110218-025023] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The origin, distribution, and function of biological diversity are fundamental themes of ecology and evolutionary biology. Research on birds has played a major role in the history and development of these ideas, yet progress was for many decades limited by a focus on patterns of current diversity, often restricted to particular clades or regions. Deeper insight is now emerging from a recent wave of integrative studies combining comprehensive phylogenetic, environmental, and functional trait data at unprecedented scales. We review these empirical advances and describe how they are reshaping our understanding of global patterns of bird diversity and the processes by which it arises, with implications for avian biogeography and functional ecology. Further expansion and integration of data sets may help to resolve longstanding debates about the evolutionary origins of biodiversity and offer a framework for understanding and predicting the response of ecosystems to environmental change.
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Affiliation(s)
- Joseph A. Tobias
- Department of Life Sciences, Imperial College London, Silwood Park, Ascot SL5 7PY, United Kingdom
| | - Jente Ottenburghs
- Department of Evolutionary Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Alex L. Pigot
- Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
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7
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Mays HL, Oehler DA, Morrison KW, Morales AE, Lycans A, Perdue J, Battley PF, Cherel Y, Chilvers BL, Crofts S, Demongin L, Fry WR, Hiscock J, Kusch A, Marin M, Poisbleau M, Quillfeldt P, Raya Rey A, Steinfurth A, Thompson DR, Weakley LA. Phylogeography, Population Structure, and Species Delimitation in Rockhopper Penguins (Eudyptes chrysocome and Eudyptes moseleyi). J Hered 2020; 110:801-817. [PMID: 31737899 DOI: 10.1093/jhered/esz051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 08/10/2019] [Indexed: 01/05/2023] Open
Abstract
Rockhopper penguins are delimited as 2 species, the northern rockhopper (Eudyptes moseleyi) and the southern rockhopper (Eudyptes chrysocome), with the latter comprising 2 subspecies, the western rockhopper (Eudyptes chrysocome chrysocome) and the eastern rockhopper (Eudyptes chrysocome filholi). We conducted a phylogeographic study using multilocus data from 114 individuals sampled across 12 colonies from the entire range of the northern/southern rockhopper complex to assess potential population structure, gene flow, and species limits. Bayesian and likelihood methods with nuclear and mitochondrial DNA, including model testing and heuristic approaches, support E. moseleyi and E. chrysocome as distinct species lineages with a divergence time of 0.97 Ma. However, these analyses also indicated the presence of gene flow between these species. Among southern rockhopper subspecies, we found evidence of significant gene flow and heuristic approaches to species delimitation based on the genealogical diversity index failed to delimit them as species. The best-supported population models for the southern rockhoppers were those where E. c. chrysocome and E. c. filholi were combined into a single lineage or 2 lineages with bidirectional gene flow. Additionally, we found that E. c. filholi has the highest effective population size while E. c. chrysocome showed similar effective population size to that of the endangered E. moseleyi. We suggest that the current taxonomic definitions within rockhopper penguins be upheld and that E. chrysocome populations, all found south of the subtropical front, should be treated as a single taxon with distinct management units for E. c. chrysocome and E. c. filholi.
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Affiliation(s)
- Herman L Mays
- Department of Biological Sciences, Marshall University, Huntington, WV
| | - David A Oehler
- Wildlife Conservation Society, Bronx, NY.,Feather Link, Inc., Cincinnati, OH
| | | | - Ariadna E Morales
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY
| | - Alyssa Lycans
- Department of Biological Sciences, Marshall University, Huntington, WV
| | - Justin Perdue
- Department of Biological Sciences, Marshall University, Huntington, WV
| | - Phil F Battley
- School of Agriculture and Environment, Massey University, Palmerston North, New Zealand
| | - Yves Cherel
- Centre d'Etudes Biologiques de Chizé, UMR 7372 du CNRS-La Rochelle Université, Villiers-en-Bois, France
| | - B Louise Chilvers
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Sarah Crofts
- Falklands Conservation, Stanley, Falkland Islands
| | | | | | - Jo Hiscock
- Department of Conservation, Invercargill, New Zealand
| | - Alejandro Kusch
- Wildlife Conservation Society, Bronx, NY.,Feather Link, Inc., Cincinnati, OH
| | - Manuel Marin
- Feather Link, Inc., Cincinnati, OH.,Section of Ornithology, Natural History Museum of Los Angeles County, Los Angeles, CA
| | - Maud Poisbleau
- Department of Biology, Behavioural Ecology and Ecophysiology Group, University of Antwerp, Antwerp (Wilrijk), Belgium
| | - Petra Quillfeldt
- Department of Animal Ecology & Systematics, Justus Liebig University Giessen, Giessen, Germany
| | - Andrea Raya Rey
- National Scientific and Technical Research Council, Austral Center for Scientific Investigation, Ushuaia, Argentina.,Institute of Polar Science, National University of Tierra del Fuego, Ushuaia, Argentina.,Wildlife Conservation Society, Buenos Aires, Argentina
| | - Antje Steinfurth
- FitzPatrick Institute of African Ornithology, DST-NRF Centre of Excellence, University of Cape Town, Rondebosch, South Africa.,RSPB Centre for Conservation Science, Royal Society for the Protection of Birds, Cambridge, UK
| | - David R Thompson
- National Institute of Water and Atmospheric Research, Wellington, New Zealand
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8
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Bangs MR, Douglas MR, Chafin TK, Douglas ME. Gene flow and species delimitation in fishes of Western North America: Flannelmouth ( Catostomus latipinnis) and Bluehead sucker ( C. Pantosteus discobolus). Ecol Evol 2020; 10:6477-6493. [PMID: 32724527 PMCID: PMC7381754 DOI: 10.1002/ece3.6384] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 02/02/2023] Open
Abstract
The delimitation of species boundaries, particularly those obscured by reticulation, is a critical step in contemporary biodiversity assessment. It is especially relevant for conservation and management of indigenous fishes in western North America, represented herein by two species with dissimilar life histories codistributed in the highly modified Colorado River (i.e., flannelmouth sucker, Catostomus latipinnis; bluehead sucker, C. (Pantosteus) discobolus). To quantify phylogenomic patterns and examine proposed taxonomic revisions, we first employed double-digest restriction site-associated DNA sequencing (ddRAD), yielding 39,755 unlinked SNPs across 139 samples. These were subsequently evaluated with multiple analytical approaches and by contrasting life history data. Three phylogenetic methods and a Bayesian assignment test highlighted similar phylogenomic patterns in each, but with considerable difference in presumed times of divergence. Three lineages were detected in bluehead sucker, supporting elevation of C. (P.) virescens to species status and recognizing C. (P.) discobolus yarrowi (Zuni bluehead sucker) as a discrete entity. Admixture in the latter necessitated a reevaluation of its contemporary and historic distributions, underscoring how biodiversity identification can be confounded by complex evolutionary histories. In addition, we defined three separate flannelmouth sucker lineages as ESUs (evolutionarily significant units), given limited phenotypic and genetic differentiation, contemporary isolation, and lack of concordance (per the genealogical concordance component of the phylogenetic species concept). Introgression was diagnosed in both species, with the Little Colorado and Virgin rivers in particular. Our diagnostic methods, and the agreement of our SNPs with previous morphological, enzymatic, and mitochondrial work, allowed us to partition complex evolutionary histories into requisite components, such as isolation versus secondary contact.
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Affiliation(s)
- Max R. Bangs
- Department of Biological SciencesFlorida State UniversityTallahasseeFLUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Tyler K. Chafin
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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9
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Gabrielli M, Nabholz B, Leroy T, Milá B, Thébaud C. Within-island diversification in a passerine bird. Proc Biol Sci 2020; 287:20192999. [PMID: 32183633 DOI: 10.1098/rspb.2019.2999] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The presence of congeneric taxa on the same island suggests the possibility of in situ divergence, but can also result from multiple colonizations of previously diverged lineages. Here, using genome-wide data from a large population sample, we test the hypothesis that intra-island divergence explains the occurrence of four geographical forms meeting at hybrid zones in the Reunion grey white-eye (Zosterops borbonicus), a species complex endemic to the small volcanic island of Reunion. Using population genomic and phylogenetic analyses, we reconstructed the population history of the different forms. We confirmed the monophyly of the complex and found that one of the lowland forms is paraphyletic and basal relative to others, a pattern highly consistent with in situ divergence. Our results suggest initial colonization of the island through the lowlands, followed by expansion into the highlands, which led to the evolution of a distinct geographical form, genetically and ecologically different from the lowland ones. Lowland forms seem to have experienced periods of geographical isolation, but they diverged from one another by sexual selection rather than niche change. Overall, low dispersal capabilities in this island bird combined with both geographical and ecological opportunities seem to explain how divergence occurred at such a small spatial scale.
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Affiliation(s)
- Maëva Gabrielli
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 (Université Paul Sabatier, CNRS, IRD), Toulouse, France
| | - Benoit Nabholz
- Institut des Sciences de l'Evolution de Montpellier, UMR 5554 (Université de Montpellier, CNRS, IRD, EPHE), Montpellier, France
| | - Thibault Leroy
- Institut des Sciences de l'Evolution de Montpellier, UMR 5554 (Université de Montpellier, CNRS, IRD, EPHE), Montpellier, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 (Université Paul Sabatier, CNRS, IRD), Toulouse, France
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10
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Brüniche‐Olsen A, Kellner KF, DeWoody JA. Island area, body size and demographic history shape genomic diversity in Darwin's finches and related tanagers. Mol Ecol 2019; 28:4914-4925. [PMID: 31597210 DOI: 10.1111/mec.15266] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 12/18/2022]
Affiliation(s)
- Anna Brüniche‐Olsen
- Department of Forestry & Natural Resources Purdue University West Lafayette IN USA
| | - Kenneth F. Kellner
- Camp Fire Program in Wildlife Conservation State University of New York College of Environmental Science and Forestry Syracuse NY USA
| | - J. Andrew DeWoody
- Department of Forestry & Natural Resources Purdue University West Lafayette IN USA
- Department of Biological Sciences Purdue University West Lafayette IN USA
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