1
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Bourgeois Y, Warren BH, Augiron S. The burden of anthropogenic changes and mutation load in a critically endangered harrier from the Reunion biodiversity hotspot, Circus maillardi. Mol Ecol 2024; 33:e17300. [PMID: 38372440 DOI: 10.1111/mec.17300] [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: 08/09/2022] [Revised: 01/18/2024] [Accepted: 01/30/2024] [Indexed: 02/20/2024]
Abstract
Anthropogenic impact is causing the decline of a large proportion of species worldwide and reduces their genetic diversity. Island species typically have smaller ranges than continental species. As a consequence, island species are particularly liable to undergo population bottlenecks, giving rise to conservation challenges such as inbreeding and unmasking of deleterious genetic load. Such challenges call for more detailed assessments of the genetic make-up of threatened island populations. The Mascarene islands (Indian Ocean) present many prime examples, being unusual in having been pristine until first human arrival ~400 years ago, following which anthropogenic pressure was unusually intense. A threatened harrier (Circus maillardi) endemic to the westernmost island of the archipelago is a good example of the challenges faced by species that have declined to small population size following intense anthropogenic pressure. In this study, we use an extensive set of population genomic tools to quantify variation at near-neutral and coding loci, in order to test the historical impact of human activity on this species, and evaluate the species' (mal)adaptive potential. We observed low but significant genetic differentiation between populations on the West and North-East sides of the island, echoing observations in other endemic species. Inbreeding was significant, with a substantial fraction of samples being first or second-degree relatives. Historical effective population sizes have declined from ~3000 to 300 individuals in the past 1000 years, with a more recent drop ~100 years ago consistent with human activity. Based on our simulations and comparisons with a close relative (Circus melanoleucos), this demographic history may have allowed purging of the most deleterious variants but is unlikely to have allowed the purging of mildly deleterious variants. Our study shows how using relatively affordable methods can reveal the massive impact that human activity may have on the genetic diversity and adaptive potential of island populations, and calls for urgent action to closely monitor the reproductive success of such endemic populations, in association with genetic studies.
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Affiliation(s)
- Yann Bourgeois
- DIADE, University of Montpellier, CIRAD, IRD, Montpellier, France
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France
| | - Steve Augiron
- Société d'Études Ornithologiques de La Réunion, Saint-André, France
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2
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Gabrielli M, Leroy T, Salmona J, Nabholz B, Milá B, Thébaud C. Demographic responses of oceanic island birds to local and regional ecological disruptions revealed by whole-genome sequencing. Mol Ecol 2024; 33:e17243. [PMID: 38108507 DOI: 10.1111/mec.17243] [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: 09/06/2023] [Revised: 11/26/2023] [Accepted: 11/30/2023] [Indexed: 12/19/2023]
Abstract
Disentangling the effects of ecological disruptions operating at different spatial and temporal scales in shaping past species' demography is particularly important in the current context of rapid environmental changes driven by both local and regional factors. We argue that volcanic oceanic islands provide useful settings to study the influence of past ecological disruptions operating at local and regional scales on population demographic histories. We investigate potential drivers of past population dynamics for three closely related species of passerine birds from two volcanic oceanic islands, Reunion and Mauritius (Mascarene archipelago), with distinct volcanic history. Using ABC and PSMC inferences from complete genomes, we reconstructed the demographic history of the Reunion Grey White-eye (Zosterops borbonicus (Pennant, 1781)), the Reunion Olive White-eye (Z. olivaceus (Linnaeus, 1766)) and the Mauritius Grey White-eye (Z. mauritianus (Gmelin, 1789)) and searched for possible causes underlying similarities or differences between species living on the same or different islands. Both demographic inferences strongly support ancient and long-term expansions in all species. They also reveal different trajectories between species inhabiting different islands, but consistent demographic trajectories in species or populations from the same island. Species from Reunion appear to have experienced synchronous reductions in population size during the Last Glacial Maximum, a trend not seen in the Mauritian species. Overall, this study suggests that local events may have played a role in shaping population trajectories of these island species. It also highlights the potential of our conceptual framework to disentangle the effects of local and regional drivers on past species' demography and long-term population processes.
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Affiliation(s)
- Maëva Gabrielli
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 (Université Paul Sabatier, CNRS, IRD), Toulouse, France
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Thibault Leroy
- GenPhySE, INRAE, INP, ENVT, Université de Toulouse, Castanet-Tolosan, France
| | - Jordi Salmona
- 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
| | - 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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3
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Cicero C, Mason NA, Oong Z, Title PO, Morales ME, Feldheim KA, Koo MS, Bowie RCK. Deep ecomorphological and genetic divergence in Steller's Jays ( Cyanocitta stelleri, Aves: Corvidae). Ecol Evol 2022; 12:e9517. [PMCID: PMC9712489 DOI: 10.1002/ece3.9517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 09/27/2022] [Accepted: 10/04/2022] [Indexed: 12/05/2022] Open
Abstract
The relationship between ecology and morphology is a cornerstone of evolutionary biology, and quantifying variation across environments can shed light on processes that give rise to biodiversity. Three morphotypes of the Steller's Jay (Cyanocitta stelleri) occupy different ecoregions in western North America, which vary in climate and landcover. These morphotypes (Coastal, Interior, Rocky Mountain) differ in size, plumage coloration, and head pattern. We sampled 1080 Steller's Jays from 68 populations (plus 11 outgroups) to address three main questions using data on morphology, plumage, genetics (mtDNA, microsatellites), and ecological niches: (1) How do phenotypic and genetic traits vary within and among populations, morphotypes, and ecoregions? (2) How do population‐level differences in Steller's Jays compare with other sister species pairs of North American birds? (3) What can we infer about the population history of Steller's Jays in relation to past climates, paleoecology, and niche evolution? We found substantial morphological, genetic, and ecological differentiation among morphotypes. The greatest genetic divergence separated Coastal and Interior morphotypes from the Rocky Mountain morphotype, which was associated with warmer, drier, and more open habitats. Microsatellites revealed additional structure between Coastal and Interior groups. The deep mtDNA split between Coastal/Interior and Rocky Mountain lineages of Steller's Jay (ND2 ~ 7.8%) is older than most North American avian sister species and dates to approximately 4.3 mya. Interior and Rocky Mountain morphotypes contact across a narrow zone with steep clines in traits and reduced gene flow. The distribution of the three morphotypes coincides with divergent varieties of ponderosa pine and Douglas fir. Species distribution models support multiple glacial refugia for Steller's Jays. Our integrative dataset combined with extensive geographic sampling provides compelling evidence for recognizing at least two species of Steller's Jay.
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Affiliation(s)
- Carla Cicero
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Nicholas A. Mason
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA,Museum of Natural Science and Department of Biological SciencesLouisiana State UniversityBaton RougeLouisianaUSA
| | - Zheng Oong
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA,Bell Museum of Natural History and Department of Ecology, Evolution and BehaviorUniversity of MinnesotaSaint PaulMinnesotaUSA
| | - Pascal O. Title
- Environmental Resilience InstituteIndiana UniversityBloomingtonIndianaUSA,Department of Ecology & EvolutionStony Brook UniversityStony BrookNew YorkUSA
| | - Melissa E. Morales
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Kevin A. Feldheim
- Pritzker Laboratory for Molecular Systematics and Evolution, Negaunee Integrative Research CenterField Museum of Natural HistoryChicagoIllinoisUSA
| | - Michelle S. Koo
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA
| | - Rauri C. K. Bowie
- Museum of Vertebrate ZoologyUniversity of CaliforniaBerkeleyCaliforniaUSA,Department of Integrative BiologyUniversity of CaliforniaBerkeleyCaliforniaUSA
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4
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Lele A, Garrod HM, Ferguson E, Azahara Prieto Gil C, Ellis M. Variation in avian morphology along a short tropical elevational gradient. Biotropica 2022. [DOI: 10.1111/btp.13110] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Abhimanyu Lele
- Committee on Evolutionary Biology University of Chicago Chicago Illinois USA
- Negaunee Integrative Research Center The Field Museum Chicago Illinois USA
- Third Millennium Alliance Quito Pichincha Ecuador
| | | | | | | | - Mike Ellis
- Third Millennium Alliance Quito Pichincha Ecuador
- Department of Ecology & Evolutionary Biology Tulane University Louisiana USA
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5
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Cheek RG, Forester BR, Salerno PE, Trumbo DR, Chen N, Sillett TS, Morrison SA, Ghalambor CK, Funk WC. Habitat-linked genetic variation supports microgeographic adaptive divergence in an island-endemic bird species. Mol Ecol 2022; 31:2830-2846. [PMID: 35315161 PMCID: PMC9325526 DOI: 10.1111/mec.16438] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 03/03/2022] [Accepted: 03/14/2022] [Indexed: 11/27/2022]
Abstract
We investigated the potential mechanisms driving habitat-linked genetic divergence within a bird species endemic to a single 250 km2 island. The island scrub-jay (Aphelocoma insularis) exhibits microgeographic divergence in bill morphology across pine-oak ecotones on Santa Cruz Island, California (USA) similar to adaptive differences described in mainland congeners over much larger geographic scales. To test whether individuals exhibit genetic differentiation related to habitat type and divergence in bill length, we genotyped over 3,000 single nucleotide polymorphisms (SNPs) in 123 adult island scrub-jay males from across Santa Cruz Island using restriction site-associated DNA sequencing (RADseq). Neutral landscape genomic analyses revealed that genome-wide genetic differentiation was primarily related to geographic distance and differences in habitat composition. We also found 168 putatively adaptive loci associated with habitat type using multivariate redundancy analysis (RDA) while controlling for spatial effects. Finally, two genome-wide association analyses revealed a polygenic basis to variation in bill length with multiple loci detected in or near genes known to affect bill morphology in other birds. Our findings support the hypothesis that divergent selection at microgeographic scales can cause adaptive divergence in the presence of ongoing gene flow.
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Affiliation(s)
- Rebecca G Cheek
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Brenna R Forester
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Patricia E Salerno
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Centro de Investigación de la Biodiversidad y Cambio Climático (BioCamb), Facultad de Ciencias de Medio Ambiente, Universidad Tecnológica Indoamérica, Quito, Ecuador
| | - Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Nancy Chen
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - T Scott Sillett
- Migratory Bird Center, Smithsonian's National Zoo and Conservation Biology Institute, Washington, DC, 20013, USA
| | | | - Cameron K Ghalambor
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), N-7491, Trondheim, Norway
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, Colorado, 80523, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, Colorado, 80523, USA
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6
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Martin CA, Armstrong C, Illera JC, Emerson BC, Richardson DS, Spurgin LG. Genomic variation, population history and within-archipelago adaptation between island bird populations. ROYAL SOCIETY OPEN SCIENCE 2021; 8:201146. [PMID: 33972847 PMCID: PMC8074581 DOI: 10.1098/rsos.201146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 01/11/2021] [Indexed: 05/13/2023]
Abstract
Oceanic island archipelagos provide excellent models to understand evolutionary processes. Colonization events and gene flow can interact with selection to shape genetic variation at different spatial scales. Landscape-scale variation in biotic and abiotic factors may drive fine-scale selection within islands, while long-term evolutionary processes may drive divergence between distantly related populations. Here, we examine patterns of population history and selection between recently diverged populations of the Berthelot's pipit (Anthus berthelotii), a passerine endemic to three North Atlantic archipelagos. First, we use demographic trees and f3 statistics to show that genome-wide divergence across the species range is largely shaped by colonization and bottlenecks, with evidence of very weak gene flow between populations. Then, using a genome scan approach, we identify signatures of divergent selection within archipelagos at single nucleotide polymorphisms (SNPs) in genes potentially associated with craniofacial development and DNA repair. We did not detect within-archipelago selection at the same SNPs as were detected previously at broader spatial scales between archipelagos, but did identify signatures of selection at loci associated with similar biological functions. These findings suggest that similar ecological factors may repeatedly drive selection between recently separated populations, as well as at broad spatial scales across varied landscapes.
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Affiliation(s)
- Claudia A. Martin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Claire Armstrong
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
| | - Juan Carlos Illera
- Oviedo University, Campus of Mieres, Research Unit of Biodiversity (UO-CSIC-PA), Research Building, 5th floor, c/Gonzalo Gutiérrez Quirós, s/n, 33600 Mieres, Asturias, Spain
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), C/Astrofísico Francisco Sánchez 3, 38206 La Laguna, Tenerife, Canary Islands, Spain
| | - David S. Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Lewis G. Spurgin
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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7
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Bourgeois YXC, Bertrand JAM, Delahaie B, Holota H, Thébaud C, Milá B. Differential divergence in autosomes and sex chromosomes is associated with intra-island diversification at a very small spatial scale in a songbird lineage. Mol Ecol 2020; 29:1137-1153. [PMID: 32107807 DOI: 10.1111/mec.15396] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 02/12/2020] [Accepted: 02/20/2020] [Indexed: 12/16/2022]
Abstract
Recently diverged taxa showing marked phenotypic and ecological diversity provide optimal systems to understand the genetic processes underlying speciation. We used genome-wide markers to investigate the diversification of the Reunion grey white-eye (Zosterops borbonicus) on the small volcanic island of Reunion (Mascarene archipelago), where this species complex exhibits four geographical forms that are parapatrically distributed across the island and differ strikingly in plumage colour. One form restricted to the highlands is separated by a steep ecological gradient from three distinct lowland forms which meet at narrow hybrid zones that are not associated with environmental variables. Analyses of genomic variation based on single nucleotide polymorphism data from genotyping-by-sequencing and pooled RAD-seq approaches show that signatures of selection associated with elevation can be found at multiple regions across the genome, whereas most loci associated with the lowland forms are located on the Z sex chromosome. We identified TYRP1, a Z-linked colour gene, as a likely candidate locus underlying colour variation among lowland forms. Tests of demographic models revealed that highland and lowland forms diverged in the presence of gene flow, and divergence has progressed as gene flow was restricted by selection at loci across the genome. This system holds promise for investigating how adaptation and reproductive isolation shape the genomic landscape of divergence at multiple stages of the speciation process.
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Affiliation(s)
- Yann X C Bourgeois
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK.,Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Joris A M Bertrand
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Laboratoire Génome & Développement des Plantes, UMR 5096, Université de Perpignan Via Domitia, Perpignan, France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France.,Department of Plant Sciences, University of Cambridge, Cambridge, UK
| | - Hélène Holota
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier, Toulouse, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
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8
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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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9
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Chambers EA, Hillis DM. The Multispecies Coalescent Over-Splits Species in the Case of Geographically Widespread Taxa. Syst Biol 2020; 69:184-193. [PMID: 31180508 DOI: 10.1093/sysbio/syz042] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 11/14/2022] Open
Abstract
Many recent species delimitation studies rely exclusively on limited analyses of genetic data analyzed under the multispecies coalescent (MSC) model, and results from these studies often are regarded as conclusive support for taxonomic changes. However, most MSC-based species delimitation methods have well-known and often unmet assumptions. Uncritical application of these genetic-based approaches (without due consideration of sampling design, the effects of a priori group designations, isolation by distance, cytoplasmic-nuclear mismatch, and population structure) can lead to over-splitting of species. Here, we argue that in many common biological scenarios, researchers must be particularly cautious regarding these limitations, especially in cases of well-studied, geographically variable, and parapatrically distributed species complexes. We consider these points with respect to a historically controversial species group, the American milksnakes (Lampropeltis triangulum complex), using genetic data from a recent analysis (Ruane et al. 2014). We show that over-reliance on the program Bayesian Phylogenetics and Phylogeography, without adequate consideration of its assumptions and of sampling limitations, resulted in over-splitting of species in this study. Several of the hypothesized species of milksnakes instead appear to represent arbitrary slices of continuous geographic clines. We conclude that the best available evidence supports three, rather than seven, species within this complex. More generally, we recommend that coalescent-based species delimitation studies incorporate thorough analyses of geographic variation and carefully examine putative contact zones among delimited species before making taxonomic changes.
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Affiliation(s)
- E Anne Chambers
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
| | - David M Hillis
- Department of Integrative Biology and Biodiversity Center, The University of Texas at Austin, Austin, TX 78712, USA
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10
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Chavarria‐Pizarro T, Gomez JP, Ungvari‐Martin J, Bay R, Miyamoto MM, Kimball R. Strong phenotypic divergence in spite of low genetic structure in the endemic Mangrove Warbler subspecies ( Setophaga petechia xanthotera) of Costa Rica. Ecol Evol 2019; 9:13902-13918. [PMID: 31938490 PMCID: PMC6953683 DOI: 10.1002/ece3.5826] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 10/18/2019] [Indexed: 12/13/2022] Open
Abstract
Despite the enormous advances in genetics, links between phenotypes and genotypes have been made for only a few nonmodel organisms. However, such links can be essential to understand mechanisms of ecological speciation. The Costa Rican endemic Mangrove Warbler subspecies provides an excellent subject to study differentiation with gene flow, as it is distributed along a strong precipitation gradient on the Pacific coast with no strong geographic barriers to isolate populations. Mangrove Warbler populations could be subject to divergent selection driven by precipitation, which influences soil salinity levels, which in turn influences forest structure and food resources. We used single nucleotide polymorphisms (SNPs) and morphological traits to examine the balance between neutral genetic and phenotypic divergence to determine whether selection has acted on traits and genes with functions related to specific environmental variables. We present evidence showing: (a) associations between environmental variables and SNPs, identifying candidate genes related to bill morphology (BMP) and osmoregulation, (b) absence of population genetic structure in neutrally evolving markers, (c) divergence in bill size across the precipitation gradient, and (d) strong phenotypic differentiation (P ST) which largely exceeds neutral genetic differentiation (F ST) in bill size. Our results indicate an important role for salinity, forest structure, and resource availability in maintaining phenotypic divergence of Mangrove Warblers through natural selection. Our findings add to the growing body of literature identifying the processes involved in phenotypic differentiation along environmental gradients in the face of gene flow.
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Affiliation(s)
- Tania Chavarria‐Pizarro
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
- Department of BiologyLudwig Maximilian University of MunichMunichGermany
| | - Juan Pablo Gomez
- Department of BiologyUniversity of FloridaGainesvilleFLUSA
- Departamento de Química y BiologíaUniversidad del NorteBarranquillaColombia
| | | | - Rachael Bay
- Department of Evolution and EcologyUniversity of CaliforniaDavisCAUSA
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11
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Schlesselmann AV, Dussex N, Cooper J, Monks JM, O'Donnell CFJ, Robertson BC. Contrasting patterns of population structure at large and fine geographical scales in a migratory avian disturbance specialist of braided river ecosystems. DIVERS DISTRIB 2019. [DOI: 10.1111/ddi.12994] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Ann‐Kathrin V. Schlesselmann
- Manaaki Whenua Landcare Research Dunedin New Zealand
- Department of Zoology University of Otago Dunedin New Zealand
| | - Nicolas Dussex
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Jamie Cooper
- Department of Zoology University of Otago Dunedin New Zealand
| | - Joanne M. Monks
- Department of Conservation Biodiversity Group Dunedin New Zealand
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12
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Dubuc-Messier G, Caro SP, Perrier C, van Oers K, Réale D, Charmantier A. Gene flow does not prevent personality and morphological differentiation between two blue tit populations. J Evol Biol 2018; 31:1127-1137. [PMID: 29791058 DOI: 10.1111/jeb.13291] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 05/02/2018] [Accepted: 05/13/2018] [Indexed: 11/28/2022]
Abstract
Understanding the causes and consequences of population phenotypic divergence is a central goal in ecology and evolution. Phenotypic divergence among populations can result from genetic divergence, phenotypic plasticity or a combination of the two. However, few studies have deciphered these mechanisms for populations geographically close and connected by gene flow, especially in the case of personality traits. In this study, we used a common garden experiment to explore the genetic basis of the phenotypic divergence observed between two blue tit (Cyanistes caeruleus) populations inhabiting contrasting habitats separated by 25 km, for two personality traits (exploration speed and handling aggression), one physiological trait (heart rate during restraint) and two morphological traits (tarsus length and body mass). Blue tit nestlings were removed from their population and raised in a common garden for up to 5 years. We then compared adult phenotypes between the two populations, as well as trait-specific Qst and Fst . Our results revealed differences between populations similar to those found in the wild, suggesting a genetic divergence for all traits. Qst -Fst comparisons revealed that the trait divergences likely result from dissimilar selection patterns rather than from genetic drift. Our study is one of the first to report a Qst -Fst comparison for personality traits and adds to the growing body of evidence that population genetic divergence is possible at a small scale for a variety of traits including behavioural traits.
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Affiliation(s)
- Gabrielle Dubuc-Messier
- Centre d'Écologie Fonctionnelle et Évolutive, Unité Mixte de Recherche CNRS 5175, Montpellier, France.,Département des sciences biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Samuel P Caro
- Centre d'Écologie Fonctionnelle et Évolutive, Unité Mixte de Recherche CNRS 5175, Montpellier, France.,Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Charles Perrier
- Centre d'Écologie Fonctionnelle et Évolutive, Unité Mixte de Recherche CNRS 5175, Montpellier, France
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Denis Réale
- Département des sciences biologiques, Université du Québec à Montréal, Montréal, QC, Canada
| | - Anne Charmantier
- Centre d'Écologie Fonctionnelle et Évolutive, Unité Mixte de Recherche CNRS 5175, Montpellier, France.,Département des sciences biologiques, Université du Québec à Montréal, Montréal, QC, Canada
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13
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Seeholzer GF, Brumfield RT. Isolation by distance, not incipient ecological speciation, explains genetic differentiation in an Andean songbird (Aves: Furnariidae:
Cranioleuca antisiensis,
Line‐cheeked Spinetail) despite near threefold body size change across an environmental gradient. Mol Ecol 2017; 27:279-296. [DOI: 10.1111/mec.14429] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 10/18/2017] [Accepted: 11/02/2017] [Indexed: 12/14/2022]
Affiliation(s)
- Glenn F. Seeholzer
- Museum of Natural Science and Department of Biological Sciences Louisiana State University Baton Rouge LA USA
| | - Robb T. Brumfield
- Museum of Natural Science and Department of Biological Sciences Louisiana State University Baton Rouge LA USA
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14
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Gadek CR, Newsome SD, Beckman EJ, Chavez AN, Galen SC, Bautista E, Witt CC. Why are tropical mountain passes “low” for some species? Genetic and stable-isotope tests for differentiation, migration and expansion in elevational generalist songbirds. J Anim Ecol 2017; 87:741-753. [DOI: 10.1111/1365-2656.12779] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/23/2017] [Indexed: 11/26/2022]
Affiliation(s)
- Chauncey R. Gadek
- Department of Biology; University of New Mexico; Albuquerque NM USA
- Museum of Southwestern Biology; University of New Mexico; Albuquerque NM USA
| | - Seth D. Newsome
- Department of Biology; University of New Mexico; Albuquerque NM USA
| | - Elizabeth J. Beckman
- Department of Biology; University of New Mexico; Albuquerque NM USA
- Museum of Southwestern Biology; University of New Mexico; Albuquerque NM USA
- Division of Biological Sciences; University of Montana; Missoula MT USA
| | - Andrea N. Chavez
- Department of Biology; University of New Mexico; Albuquerque NM USA
- Museum of Southwestern Biology; University of New Mexico; Albuquerque NM USA
- Bureau of Land Management; Rio Puerco District Office; Albuquerque NM USA
| | - Spencer C. Galen
- Sackler Institute for Comparative Genomics; American Museum of Natural History; New York NY USA
| | - Emil Bautista
- Centro de Ornitología y Biodiversidad (CORBIDI); Urbanización Huertos de San Antonio; Surco Lima Perú
| | - Christopher C. Witt
- Department of Biology; University of New Mexico; Albuquerque NM USA
- Museum of Southwestern Biology; University of New Mexico; Albuquerque NM USA
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15
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Delahaie B, Cornuault J, Masson C, Bertrand JAM, Bourgeois YXC, Milá B, Thébaud C. Narrow hybrid zones in spite of very low population differentiation in neutral markers in an island bird species complex. J Evol Biol 2017; 30:2132-2145. [DOI: 10.1111/jeb.13177] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 07/26/2017] [Accepted: 09/07/2017] [Indexed: 02/06/2023]
Affiliation(s)
- B. Delahaie
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
- Centre d'Ecologie Fonctionnelle et Evolutive; CNRS-UMR5175 CEFE; Montpellier France
| | - J. Cornuault
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - C. Masson
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - J. A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - Y. X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
| | - B. Milá
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
| | - C. Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); Toulouse France
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16
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Branch CL, Jahner JP, Kozlovsky DY, Parchman TL, Pravosudov VV. Absence of population structure across elevational gradients despite large phenotypic variation in mountain chickadees ( Poecile gambeli). ROYAL SOCIETY OPEN SCIENCE 2017; 4:170057. [PMID: 28405402 PMCID: PMC5383859 DOI: 10.1098/rsos.170057] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 02/16/2017] [Indexed: 06/07/2023]
Abstract
Montane habitats are characterized by predictably rapid heterogeneity along elevational gradients and are useful for investigating the consequences of environmental heterogeneity for local adaptation and population genetic structure. Food-caching mountain chickadees inhabit a continuous elevation gradient in the Sierra Nevada, and birds living at harsher, high elevations have better spatial memory ability and exhibit differences in male song structure and female mate preference compared to birds inhabiting milder, low elevations. While high elevation birds breed, on average, two weeks later than low elevation birds, the extent of gene flow between elevations is unknown. Despite phenotypic variation and indirect evidence for local adaptation, population genetic analyses based on 18 073 single nucleotide polymorphisms across three transects of high and low elevation populations provided no evidence for genetic differentiation. Analyses based on individual genotypes revealed no patterns of clustering, pairwise estimates of genetic differentiation (FST, Nei's D) were very low, and AMOVA revealed no evidence for genetic variation structured by transect or by low and high elevation sites within transects. In addition, we found no consistent evidence for strong parallel allele frequency divergence between low and high elevation sites within the three transects. Large elevation-related phenotypic variation may be maintained by strong selection despite gene flow and future work should focus on the mechanisms underlying such variation.
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17
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Bourgeois YXC, Delahaie B, Gautier M, Lhuillier E, Malé PJG, Bertrand JAM, Cornuault J, Wakamatsu K, Bouchez O, Mould C, Bruxaux J, Holota H, Milá B, Thébaud C. A novel locus on chromosome 1 underlies the evolution of a melanic plumage polymorphism in a wild songbird. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160805. [PMID: 28386436 PMCID: PMC5367300 DOI: 10.1098/rsos.160805] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Accepted: 01/12/2017] [Indexed: 06/07/2023]
Abstract
Understanding the mechanisms responsible for phenotypic diversification within and among species ultimately rests with linking naturally occurring mutations to functionally and ecologically significant traits. Colour polymorphisms are of great interest in this context because discrete colour patterns within a population are often controlled by just a few genes in a common environment. We investigated how and why phenotypic diversity arose and persists in the Zosterops borbonicus white-eye of Reunion (Mascarene archipelago), a colour polymorphic songbird in which all highland populations contain individuals belonging to either a brown or a grey plumage morph. Using extensive phenotypic and genomic data, we demonstrate that this melanin-based colour polymorphism is controlled by a single locus on chromosome 1 with two large-effect alleles, which was not previously described as affecting hair or feather colour. Differences between colour morphs appear to rely upon complex cis-regulatory variation that either prevents the synthesis of pheomelanin in grey feathers, or increases its production in brown ones. We used coalescent analyses to show that, from a 'brown' ancestral population, the dominant 'grey' allele spread quickly once it arose from a new mutation. Since colour morphs are always found in mixture, this implies that the selected allele does not go to fixation, but instead reaches an intermediate frequency, as would be expected under balancing selection.
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Affiliation(s)
- Yann X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Mathieu Gautier
- INRA, UMR 1062 CBGP (INRA, IRD, Cirad, Montpellier SupAgro), Campus de Baillarguet, 34988 Montferrier-sur-Lez, France
| | - Emeline Lhuillier
- INRA, GeT-PlaGe, Genotoul, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
- INRA, UAR1209, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
| | - Pierre-Jean G. Malé
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Joris A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Josselin Cornuault
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Kazumasa Wakamatsu
- Department of Chemistry, Fujita Health University, School of Health Sciences, Toyoake Aichi 470-1192, Japan
| | - Olivier Bouchez
- INRA, GeT-PlaGe, Genotoul, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
- GenPhySE, Université de Toulouse, INRA, INPT, INP-ENVT, 24 chemin de Borde Rouge, Auzeville, CS 52627, 31326 Castanet-Tolosan, France
| | - Claire Mould
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Jade Bruxaux
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Hélène Holota
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
| | - Borja Milá
- National Museum of Natural Sciences, Spanish National Research Council (CSIC), 28006 Madrid, Spain
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS, Université Paul Sabatier – ENFA, 31062 Toulouse Cedex 9, France
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18
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Noguerales V, García-Navas V, Cordero PJ, Ortego J. The role of environment and core-margin effects on range-wide phenotypic variation in a montane grasshopper. J Evol Biol 2016; 29:2129-2142. [DOI: 10.1111/jeb.12915] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/31/2022]
Affiliation(s)
- V. Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM); Ciudad Real Spain
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Sevilla Spain
| | - V. García-Navas
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Sevilla Spain
| | - P. J. Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM); Ciudad Real Spain
| | - J. Ortego
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Sevilla Spain
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