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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Mould MC, Huet M, Senegas L, Milá B, Thébaud C, Bourgeois Y, Chaine AS. Beyond morphs: Inter-individual colour variation despite strong genetic determinism of colour morphs in a wild bird. J Evol Biol 2023; 36:82-94. [PMID: 36484624 PMCID: PMC10107803 DOI: 10.1111/jeb.14124] [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: 11/18/2020] [Revised: 05/06/2022] [Accepted: 06/15/2022] [Indexed: 12/13/2022]
Abstract
Categorizing individuals into discrete forms in colour polymorphic species can overlook more subtle patterns in coloration that can be of functional significance. Thus, quantifying inter-individual variation in these species at both within- and between-morph levels is critical to understand the evolution of colour polymorphisms. Here we present analyses of inter-individual colour variation in the Reunion grey white-eye (Zosterops borbonicus), a colour polymorphic wild bird endemic to the island of Reunion in which all highland populations contain two sympatric colour morphs, with birds showing predominantly grey or brown plumage, respectively. We first quantified colour variation across multiple body areas by using a continuous plumage colour score to assess variation in brown-grey coloration as well as smaller scale variation in light patches. To examine the possible causes of among-individual variation, we tested if colour variation in plumage component elements could be explained by genotypes at two markers near a major-effect locus previously related to back coloration in this species, and by other factors such as age, sex and body condition. Overall, grey-brown coloration was largely determined by genetic factors and was best described by three distinct clusters that were associated to genotypic classes (homozygotes and heterozygote), with no effect of age or sex, whereas variation in smaller light patches was primarily related to age and sex. Our results highlight the importance of characterizing subtle plumage variation beyond morph categories that are readily observable since multiple patterns of colour variation may be driven by different mechanisms, have different functions and will likely respond in different ways to selection.
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Affiliation(s)
- Maya C Mould
- Station d'Ecologie Théorique et Expérimentale du CNRS and Université Paul Sabatier (Toulouse III), UPR 2001, Moulis, France
| | - Michèle Huet
- Station d'Ecologie Théorique et Expérimentale du CNRS and Université Paul Sabatier (Toulouse III), UPR 2001, Moulis, France
| | - Lou Senegas
- Station d'Ecologie Théorique et Expérimentale du CNRS and Université Paul Sabatier (Toulouse III), UPR 2001, Moulis, 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 Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD), Université Paul Sabatier (Toulouse III), Toulouse Cedex, France
| | - Yann Bourgeois
- School of Biological Sciences, University of Portsmouth, Portsmouth, UK
| | - Alexis S Chaine
- Station d'Ecologie Théorique et Expérimentale du CNRS and Université Paul Sabatier (Toulouse III), UPR 2001, Moulis, France.,Institute for Advanced Studies in Toulouse, Toulouse, France
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3
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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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4
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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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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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Thurman TJ, Szejner-Sigal A, McMillan WO. Movement of a Heliconius hybrid zone over 30 years: A Bayesian approach. J Evol Biol 2019; 32:974-983. [PMID: 31216075 DOI: 10.1111/jeb.13499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/29/2019] [Accepted: 06/10/2019] [Indexed: 11/27/2022]
Abstract
Hybrid zones have long been of interest to biologists as natural laboratories where we can gain insight into the processes of adaptation and speciation. Repeated sampling of individual hybrid zones has been particularly useful in elucidating the dynamic balance between selection and dispersal that maintains most hybrid zones. Here, we revisit a hybrid zone between Heliconius erato butterflies in Panamá for a third time over more than 30 years. We combine a novel Bayesian extension of stepped-cline hybrid zone models with environmental data to understand the genetic and environmental causes of cline dynamics in this species. The cline has continued to move west, likely due to dominance drive, but has slowed and broadened. Environmental analyses suggest that widespread deforestation in Panamá could be leading to decreased avian predation and relaxed selection, causing the observed changes in cline dynamics.
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Affiliation(s)
- Timothy J Thurman
- Smithsonian Tropical Research Institute, Panamá, República de Panamá.,Redpath Museum and Department of Biology, McGill University, Montréal, Québec, Canada
| | - Andre Szejner-Sigal
- Smithsonian Tropical Research Institute, Panamá, República de Panamá.,Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Panamá, República de Panamá
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