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Vacher JP, Kok PJR, Rodrigues MT, Lima A, Hrbek T, Werneck FP, Manzi S, Thébaud C, Fouquet A. Diversification of the terrestrial frog genus Anomaloglossus (Anura, Aromobatidae) in the Guiana Shield proceeded from highlands to lowlands, with successive loss and reacquisition of endotrophy. Mol Phylogenet Evol 2024; 192:108008. [PMID: 38181828 DOI: 10.1016/j.ympev.2023.108008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 09/23/2023] [Accepted: 12/30/2023] [Indexed: 01/07/2024]
Abstract
Two main landscapes emerge from the Guiana Shield: the highlands to the west called the Pantepui region and the Amazonian lowlands to the east, both harbouring numerous endemic species. With 32 currently recognized species, the genus Anomaloglossus stands out among Neotropical frogs as one that diversified only within the Guiana Shield both in the highlands and the lowlands. We present a time-calibrated phylogeny obtained by using combined mitogenomic and nuclear DNA, which suggests that the genus originates from Pantepui where extant lineages started diversifying around 21 Ma, and subsequently (ca. 17 Ma) dispersed during the Miocene Climatic Optimum to the lowlands of the eastern Guiana Shield where the ability to produce endotrophic tadpoles evolved. Further diversification within the lowlands in the A. stepheni group notably led to an evolutionary reversal toward exotrophy in one species group during the late Miocene, followed by reacquisition of endotrophy during the Pleistocene. These successive shifts of reproductive mode seem to have accompanied climatic oscillations. Long dry periods might have triggered evolution of exotrophy, whereas wetter climates favoured endotrophic forms, enabling colonization of terrestrial habitats distant from water. Acquisition, loss, and reacquisition of endotrophy makes Anomaloglossus unique among frogs and may largely explain the current species diversity. The micro evolutionary processes involved in these rapid shifts of reproductive mode remain to be revealed.
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Affiliation(s)
- Jean-Pierre Vacher
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France.
| | - Philippe J R Kok
- Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, 12/16 Banacha Str, Łódź 90-237, Poland; Department of Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, United Kingdom
| | - Miguel Trefaut Rodrigues
- Universidade de São Paulo, Instituto de Biociências, Departamento de Zoologia, Caixa Postal 11.461, CEP 05508-090 São Paulo, Brazil
| | - Albertina Lima
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, 69080-971 Manaus, AM, Brazil
| | - Tomas Hrbek
- Departamento de Biologia, Instituto de Ciências Biológicas, Universidade Federal do Amazonas, 69080-900 Manaus, AM, Brazil
| | - Fernanda P Werneck
- Instituto Nacional de Pesquisas da Amazônia, Coordenação de Biodiversidade, Avenida André Araújo 2936, 69080-971 Manaus, AM, Brazil
| | - Sophie Manzi
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, France
| | - Antoine Fouquet
- Centre de Recherche sur la Biodiversité et l'Environnement (CRBE), UMR 5300 CNRS-IRD-TINP-UPS3, Université Paul Sabatier, Toulouse, 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Emerson BC, Borges PAV, Cardoso P, Convey P, deWaard JR, Economo EP, Gillespie RG, Kennedy S, Krehenwinkel H, Meier R, Roderick GK, Strasberg D, Thébaud C, Traveset A, Creedy TJ, Meramveliotakis E, Noguerales V, Overcast I, Morlon H, Papadopoulou A, Vogler AP, Arribas P, Andújar C. Collective and harmonized high throughput barcoding of insular arthropod biodiversity: Toward a Genomic Observatories Network for islands. Mol Ecol 2023; 32:6161-6176. [PMID: 36156326 DOI: 10.1111/mec.16683] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/11/2022] [Accepted: 08/19/2022] [Indexed: 12/01/2022]
Abstract
Current understanding of ecological and evolutionary processes underlying island biodiversity is heavily shaped by empirical data from plants and birds, although arthropods comprise the overwhelming majority of known animal species, and as such can provide key insights into processes governing biodiversity. Novel high throughput sequencing (HTS) approaches are now emerging as powerful tools to overcome limitations in the availability of arthropod biodiversity data, and hence provide insights into these processes. Here, we explored how these tools might be most effectively exploited for comprehensive and comparable inventory and monitoring of insular arthropod biodiversity. We first reviewed the strengths, limitations and potential synergies among existing approaches of high throughput barcode sequencing. We considered how this could be complemented with deep learning approaches applied to image analysis to study arthropod biodiversity. We then explored how these approaches could be implemented within the framework of an island Genomic Observatories Network (iGON) for the advancement of fundamental and applied understanding of island biodiversity. To this end, we identified seven island biology themes at the interface of ecology, evolution and conservation biology, within which collective and harmonized efforts in HTS arthropod inventory could yield significant advances in island biodiversity research.
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Affiliation(s)
- Brent C Emerson
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Paulo A V Borges
- Centre for Ecology, Evolution and Environmental Changes (cE3c)/Azorean Biodiversity Group, Faculty of Agricultural Sciences and Environment, CHANGE - Global Change and Sustainability Institute, University of the Azores, Angra do Heroísmo, Portugal
| | - Pedro Cardoso
- Centre for Ecology, Evolution and Environmental Changes (cE3c)/Azorean Biodiversity Group, Faculty of Agricultural Sciences and Environment, CHANGE - Global Change and Sustainability Institute, University of the Azores, Angra do Heroísmo, Portugal
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History Luomus, University of Helsinki, Helsinki, Finland
| | - Peter Convey
- British Antarctic Survey, NERC, Cambridge, UK
- Department of Zoology, University of Johannesburg, Auckland Park, South Africa
| | - Jeremy R deWaard
- Centre for Biodiversity Genomics, University of Guelph, Guelph, Canada
- School of Environmental Sciences, University of Guelph, Guelph, Canada
| | - Evan P Economo
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, Massachusetts, USA
| | - Rosemary G Gillespie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | - Susan Kennedy
- Biodiversity and Biocomplexity Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | | | - Rudolf Meier
- Center for Integrative Biodiversity Discovery, Leibniz Institute for Evolution and Biodiversity Science, Museum für Naturkunde, Berlin, Germany
- Department of Biological Sciences, National University of Singapore, Singapore City, Singapore
| | - George K Roderick
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, USA
| | | | - Christophe Thébaud
- UMR 5174 EDB Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier Toulouse III, CNRS, IRD, Toulouse, France
| | - Anna Traveset
- Global Change Research Group, Mediterranean Institut of Advanced Studies (CSIC-UIB), Mallorca, Spain
| | - Thomas J Creedy
- Department of Life Sciences, Natural History Museum, London, UK
| | | | - Víctor Noguerales
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Isaac Overcast
- Département de Biologie, École normale supérieure, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Université PSL, Paris, France
| | - Hélène Morlon
- Département de Biologie, École normale supérieure, Institut de Biologie de l'ENS (IBENS), CNRS, INSERM, Université PSL, Paris, France
| | - Anna Papadopoulou
- Department of Biological Sciences, University of Cyprus, Nicosia, Cyprus
| | - Alfried P Vogler
- Department of Life Sciences, Natural History Museum, London, UK
- Department of Life Sciences, Imperial College London, London, UK
| | - Paula Arribas
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
| | - Carmelo Andújar
- Island Ecology and Evolution Research Group, Institute of Natural Products and Agrobiology (IPNA-CSIC), San Cristóbal de la Laguna, Spain
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4
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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5
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Utami CY, Sholihah A, Condamine FL, Thébaud C, Hubert N. Cryptic diversity impacts model selection and macroevolutionary inferences in diversification analyses. Proc Biol Sci 2022; 289:20221335. [PMID: 36382998 PMCID: PMC9667750 DOI: 10.1098/rspb.2022.1335] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 10/26/2022] [Indexed: 12/02/2023] Open
Abstract
Species persist in landscapes through ecological dynamics but proliferate at wider spatial scales through evolutionary mechanisms. Disentangling the contribution of each dynamic is challenging, but the increasing use of dated molecular phylogenies opened new perspectives. First, the increasing use of DNA sequences in biodiversity inventory shed light on a substantial amount of cryptic diversity in species-rich ecosystems. Second, explicit diversification models accounting for various eco-evolutionary models are now available. Integrating both advances, we explored diversification trajectories among 10 lineages of freshwater fishes in Sundaland, for which time-calibrated and taxonomically rich phylogenies are available. By fitting diversification models to dated phylogenies and incorporating DNA-based species delimitation methods, the impact of cryptic diversity on diversification model selection and related inferences is explored. Eight clades display constant speciation rate model as the most likely if cryptic diversity is accounted, but nine display a signature of diversification slowdowns when cryptic diversity is ignored. Cryptic diversification occurs during the last 5 Myr for most groups, and palaeoecological models received little support. Most cryptic lineages display restricted range distribution, supporting geographical isolation across homogeneous landscapes as the main driver of diversification. These patterns question the persistence of cryptic diversity and its role during species proliferation.
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Affiliation(s)
- C. Y. Utami
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
- UMR 5174 EDB (CNRS, Université Paul Sabatier, IRD), 31062 Toulouse Cedex 9, France
| | - A. Sholihah
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
- School of Life Sciences and Technology, Institut Teknologi Bandung, Jalan Ganesha 10, Bandung 40132, Indonesia
| | - F. L. Condamine
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
| | - C. Thébaud
- UMR 5174 EDB (CNRS, Université Paul Sabatier, IRD), 31062 Toulouse Cedex 9, France
| | - N. Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France
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6
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Arida E, Ashari H, Dahruddin H, Fitriana YS, Hamidy A, Irham M, Kadarusman, Riyanto A, Wiantoro S, Zein MSA, Hadiaty RK, Apandi, Krey F, Kurnianingsih, Melmambessy EHP, Mulyadi, Ohee HL, Saidin, Salamuk A, Sauri S, Suparno, Supriatna N, Suruwaky AM, Laksono WT, Warikar EL, Wikanta H, Yohanita AM, Slembrouck J, Legendre M, Gaucher P, Cochet C, Delrieu-Trottin E, Thébaud C, Mila B, Fouquet A, Borisenko A, Steinke D, Hocdé R, Semiadi G, Pouyaud L, Hubert N. Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes. Mol Ecol Resour 2021; 21:2369-2387. [PMID: 33942522 DOI: 10.1111/1755-0998.13411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/06/2021] [Accepted: 04/13/2021] [Indexed: 11/27/2022]
Abstract
Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.
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Affiliation(s)
- Evy Arida
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Hidayat Ashari
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Hadi Dahruddin
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Yuli Sulistya Fitriana
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Amir Hamidy
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Mohammad Irham
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Kadarusman
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Awal Riyanto
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Sigit Wiantoro
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Moch Syamsul Arifin Zein
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Renny K Hadiaty
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Apandi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Frengky Krey
- Jurusan Perikanan, Fakultas Perikanan dan Ilmu Kelautan, Universitas Papua, Jl. Gunung Salju Amban, Manokwari, Indonesia
| | - Kurnianingsih
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Edy H P Melmambessy
- Program Studi Manajemen Sumberdaya Perairan, Fakultas Pertanian, Universitas Musamus, Jl. Kamizaun Mopah Lama, Rimba Jaya, Merauke, Indonesia
| | - Mulyadi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Henderite L Ohee
- Jurusan Biologi, Fakultas MIPA, Universitas Cendrawasih, Jl. Kamp Wolker Waena Jayapura, Jayapura, Indonesia
| | - Saidin
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Ayub Salamuk
- Dinas Kelautan dan Perikanan Kabupaten Kaimana, Jl.Utarum Kampung Coa, Kaimana, Indonesia
| | - Sopian Sauri
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Suparno
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Nanang Supriatna
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Amir M Suruwaky
- Politeknik Kelautan dan Perikanan Sorong, Jl. Kapitan Pattimura, Suprau, Indonesia
| | - Wahyudi Tri Laksono
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Evie L Warikar
- Jurusan Biologi, Fakultas MIPA, Universitas Cendrawasih, Jl. Kamp Wolker Waena Jayapura, Jayapura, Indonesia
| | - Hadi Wikanta
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Aksamina M Yohanita
- Jurusan Biologi, Fakultas MIPA, Universitas Papua Jl. Gunung Salju - Amban, Manokwari, Indonesia
| | - Jacques Slembrouck
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Marc Legendre
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Philippe Gaucher
- USR LEEISA- Laboratoire Ecologie, Evolution, Interactions des Systèmes amazoniens, Centre de Recherche de Montabo, cayenne, French Guiana
| | - Christophe Cochet
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | | | | | - Borja Mila
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish National Research Council (CSIC), Madrid, Spain
| | - Antoine Fouquet
- UMR 5174 EDB CNRS, Université Paul Sabatier, IRD, Toulouse, France
| | - Alex Borisenko
- Department of Integrative Biology, Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Dirk Steinke
- Department of Integrative Biology, Centre for Biodiversity Genomics, University of Guelph, Guelph, ON, Canada
| | - Régis Hocdé
- UMR 9190 MARBEC (IRD, UM, CNRS, IFREMER), Université de Montpellier, Montpellier, France
| | - Gono Semiadi
- Division of Zoology, Research Center for Biology, Indonesian Institute of Sciences (LIPI), Cibinong, Indonesia
| | - Laurent Pouyaud
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
| | - Nicolas Hubert
- UMR 5554 ISEM (IRD, UM, CNRS, EPHE), Université de Montpellier, Montpellier, France
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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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Valente L, Phillimore AB, Melo M, Warren BH, Clegg SM, Havenstein K, Tiedemann R, Illera JC, Thébaud C, Aschenbach T, Etienne RS. A simple dynamic model explains the diversity of island birds worldwide. Nature 2020; 579:92-96. [PMID: 32076267 DOI: 10.1038/s41586-020-2022-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 01/22/2020] [Indexed: 12/17/2022]
Abstract
Colonization, speciation and extinction are dynamic processes that influence global patterns of species richness1-6. Island biogeography theory predicts that the contribution of these processes to the accumulation of species diversity depends on the area and isolation of the island7,8. Notably, there has been no robust global test of this prediction for islands where speciation cannot be ignored9, because neither the appropriate data nor the analytical tools have been available. Here we address both deficiencies to reveal, for island birds, the empirical shape of the general relationships that determine how colonization, extinction and speciation rates co-vary with the area and isolation of islands. We compiled a global molecular phylogenetic dataset of birds on islands, based on the terrestrial avifaunas of 41 oceanic archipelagos worldwide (including 596 avian taxa), and applied a new analysis method to estimate the sensitivity of island-specific rates of colonization, speciation and extinction to island features (area and isolation). Our model predicts-with high explanatory power-several global relationships. We found a decline in colonization with isolation, a decline in extinction with area and an increase in speciation with area and isolation. Combining the theoretical foundations of island biogeography7,8 with the temporal information contained in molecular phylogenies10 proves a powerful approach to reveal the fundamental relationships that govern variation in biodiversity across the planet.
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Affiliation(s)
- Luis Valente
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany. .,Naturalis Biodiversity Center, Leiden, The Netherlands. .,Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands. .,Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
| | | | - Martim Melo
- Museu de História Natural e da Ciência da Universidade do Porto, Porto, Portugal.,Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), InBio, Laboratório Associado, Universidade do Porto, Vairão, Portugal.,FitzPatrick Institute, DST-NRF Centre of Excellence, University of Cape Town, Cape Town, South Africa
| | - Ben H Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, UA, Paris, France
| | - Sonya M Clegg
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK.,Environmental Futures Research Institute, Griffith University, Brisbane, Queensland, Australia
| | - Katja Havenstein
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ralph Tiedemann
- Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Juan Carlos Illera
- Research Unit of Biodiversity (UO-CSIC-PA), Oviedo University, Mieres, Spain
| | - Christophe Thébaud
- Unité Mixte de Recherche 5174, CNRS-IRD-Paul Sabatier University, Toulouse, France
| | - Tina Aschenbach
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany
| | - Rampal S Etienne
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
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10
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Borges PA, Cardoso P, Fattorini S, Rigal F, Matthews TJ, Di Biase L, Amorim IR, Florencio M, Borda-de-Água L, Rego C, Pereira F, Nunes R, Carvalho R, Ferreira MT, López H, Pérez Delgado AJ, Otto R, Fernández Lugo S, De Nascimento L, Caujapé-Castells J, Casquet J, Danflous S, Fournel J, Sadeyen AM, Elias RB, Fernández-Palacios JM, Oromí P, Thébaud C, Strasberg D, Emerson BC. Community structure of woody plants on islands along a bioclimatic gradient. Frontiers of Biogeography 2018. [DOI: 10.21425/f5fbg40295] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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11
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Warren BH, Hagen O, Gerber F, Thébaud C, Paradis E, Conti E. Evaluating alternative explanations for an association of extinction risk and evolutionary uniqueness in multiple insular lineages. Evolution 2018; 72:2005-2024. [DOI: 10.1111/evo.13582] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/16/2018] [Accepted: 08/07/2018] [Indexed: 12/24/2022]
Affiliation(s)
- Ben H. Warren
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRSSorbonne Université EPHE, CP 51, 57 Rue Cuvier 75005 Paris France
- Department of Systematic and Evolutionary BotanyUniversity of Zurich Zollikerstrasse 107, 8008 Zurich Switzerland
| | - Oskar Hagen
- Swiss Federal Research Institute WSL 8903 Birmensdorf Switzerland
- Landscape EcologyInstitute of Terrestrial Ecosystems ETH Zurich 8092 Zurich Switzerland
| | - Florian Gerber
- Department of MathematicsUniversity of Zurich 8057 Zurich Switzerland
| | - Christophe Thébaud
- Laboratoire Evolution et Diversité BiologiqueUMR 5174 CNRS‐Université Paul Sabatier‐ENFA 31062 Toulouse Cedex 9 France
| | | | - Elena Conti
- Department of Systematic and Evolutionary BotanyUniversity of Zurich Zollikerstrasse 107, 8008 Zurich Switzerland
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12
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Bruxaux J, Gabrielli M, Ashari H, Prŷs-Jones R, Joseph L, Milá B, Besnard G, Thébaud C. Recovering the evolutionary history of crowned pigeons (Columbidae: Goura): Implications for the biogeography and conservation of New Guinean lowland birds. Mol Phylogenet Evol 2018; 120:248-258. [DOI: 10.1016/j.ympev.2017.11.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 11/27/2022]
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13
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Ducatez S, Giraudeau M, Thébaud C, Jacquin L. Colour polymorphism is associated with lower extinction risk in birds. Glob Chang Biol 2017; 23:3030-3039. [PMID: 28452164 DOI: 10.1111/gcb.13734] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 02/15/2017] [Accepted: 04/07/2017] [Indexed: 06/07/2023]
Abstract
Colour polymorphisms have played a major role in enhancing current understanding of how selection and demography can impact phenotypes. Because different morphs often display alternative strategies and exploit alternative ecological niches, colour polymorphism can be expected to promote adaptability to environmental changes. However, whether and how it could influence populations' and species' response to global changes remains debated. To address this question, we built an up-to-date and complete database on avian colour polymorphism based on the examination of available data from all 10,394 extant bird species. We distinguished between true polymorphism (where different genetically determined morphs co-occur in sympatry within the same population) and geographic variation (parapatric or allopatric colour variation), because these two patterns of variation are expected to have different consequences on populations' persistence. Using the IUCN red list, we then showed that polymorphic bird species are at lesser risk of extinction than nonpolymorphic ones, after controlling for a range of factors such as geographic range size, habitat breadth, life history, and phylogeny. This appears consistent with the idea that high genetic diversity and/or the existence of alternative strategies in polymorphic species promotes the ability to adaptively respond to changing environmental conditions. In contrast, polymorphic species were not less vulnerable than nonpolymorphic ones to specific drivers of extinction such as habitat alteration, direct exploitation, climate change, and invasive species. Thus, our results suggest that colour polymorphism acts as a buffer against environmental changes, although further studies are now needed to understand the underlying mechanisms. Developing accurate quantitative indices of sensitivity to specific threats is likely a key step towards a better understanding of species response to environmental changes.
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Affiliation(s)
- Simon Ducatez
- School of Biological Sciences, University of Sydney, Sydney, NSW, Australia
- Department of Biology, McGill University, Montréal, QC, Canada
- CREAF, Cerdanyola del Vallès, Spain
| | - Mathieu Giraudeau
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
- Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn, UK
| | - Christophe Thébaud
- CNRS, ENFA, UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
- CNRS, UMR 5174 EDB, Université Paul Sabatier, Toulouse, France
| | - Lisa Jacquin
- Department of Biology, McGill University, Montréal, QC, Canada
- CNRS, ENFA, UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), Université Toulouse 3 Paul Sabatier, Toulouse, France
- CNRS, UMR 5174 EDB, Université Paul Sabatier, Toulouse, France
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15
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Abbott RJ, Bretagnolle FC, Thébaud C. EVOLUTION OF A POLYMORPHISM FOR OUTCROSSING RATE IN SENECIO VULGARIS
: INFLUENCE OF GERMINATION BEHAVIOR. Evolution 2017; 52:1593-1601. [DOI: 10.1111/j.1558-5646.1998.tb02240.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/1997] [Accepted: 06/25/1998] [Indexed: 11/28/2022]
Affiliation(s)
- Richard J. Abbott
- School of Environmental and Evolutionary Biology; University of St. Andrews; St. Andrews Fife KY16 9TH United Kingdom
| | - Francois C. Bretagnolle
- School of Environmental and Evolutionary Biology; University of St. Andrews; St. Andrews Fife KY16 9TH United Kingdom
- Laboratoire de phanérogamie; Institut de botanique de l'Université; Chantemerle 18, CH-2007 Neuchâtel Switzerland
| | - Christophe Thébaud
- NERC Centre for Population Biology; Imperial College at Silwood Park; Ascot Berkshire SL5 7PY United Kingdom
- School of Biological Sciences; University of East Anglia; Norwich NR4 7TJ United Kingdom
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16
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Cicconardi F, Borges PAV, Strasberg D, Oromí P, López H, Pérez-Delgado AJ, Casquet J, Caujapé-Castells J, Fernández-Palacios JM, Thébaud C, Emerson BC. MtDNA metagenomics reveals large-scale invasion of belowground arthropod communities by introduced species. Mol Ecol 2017; 26:3104-3115. [PMID: 28139037 DOI: 10.1111/mec.14037] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/12/2016] [Accepted: 12/24/2016] [Indexed: 11/26/2022]
Abstract
Using a series of standardized sampling plots within forest ecosystems in remote oceanic islands, we reveal fundamental differences between the structuring of aboveground and belowground arthropod biodiversity that are likely due to large-scale species introductions by humans. Species of beetle and spider were sampled almost exclusively from single islands, while soil-dwelling Collembola exhibited more than tenfold higher species sharing among islands. Comparison of Collembola mitochondrial metagenomic data to a database of more than 80 000 Collembola barcode sequences revealed almost 30% of sampled island species are genetically identical, or near identical, to individuals sampled from often very distant geographic regions of the world. Patterns of mtDNA relatedness among Collembola implicate human-mediated species introductions, with minimum estimates for the proportion of introduced species on the sampled islands ranging from 45% to 88%. Our results call for more attention to soil mesofauna to understand the global extent and ecological consequences of species introductions.
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Affiliation(s)
- Francesco Cicconardi
- Institute of Ecology, University of Innsbruck, Technikerstrasse 25, a-6020, Innsbruck, Austria
| | - Paulo A V Borges
- CE3C - Centre for Ecology, Evolution and Environmental Changes/Azorean Biodiversity Group and Departamento de Ciências Agrárias e Ambiente, Universidade dos Açores, Rua Capitão João d'Ávila s/n, 9700-042, Angra do Heroísmo, Açores, Portugal
| | - Dominique Strasberg
- UMR PVBMT, Peuplements Végétaux et Bio-agresseurs en Milieu Tropical, Université de La Réunion, 15 avenue René Cassin, CS 93002, 97 744, Saint Denis Cedex 9, Reunion Island, France
| | - Pedro Oromí
- Departamento de Biología Animal y Edafología y Geología, Universidad de La Laguna, C/Astrofísico Francisco Sánchez, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Heriberto López
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Antonio J Pérez-Delgado
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Juliane Casquet
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
| | - Juli Caujapé-Castells
- Departamento de Biodiversidad Molecular y Banco de ADN, Jardín Botánico Canario 'Viera y Clavijo' - Unidad Asociada CSIC, Cabildo de Gran Canaria, Camino del Palmeral 15 de Tafira Alta, 35017, Las Palmas de Gran Canaria, Spain
| | - José María Fernández-Palacios
- Island Ecology and Biogeography Research Group, Instituto de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC), Universidad de La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Christophe Thébaud
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
| | - Brent C Emerson
- Island Ecology and Evolution Research Group, IPNA-CSIC, 38206, La Laguna, Tenerife, Canary Islands, Spain.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
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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. R Soc Open Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Emerson BC, Casquet J, López H, Cardoso P, Borges PAV, Mollaret N, Oromí P, Strasberg D, Thébaud C. A combined field survey and molecular identification protocol for comparing forest arthropod biodiversity across spatial scales. Mol Ecol Resour 2016; 17:694-707. [PMID: 27768248 DOI: 10.1111/1755-0998.12617] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 09/02/2016] [Accepted: 09/16/2016] [Indexed: 11/28/2022]
Abstract
Obtaining fundamental biodiversity metrics such as alpha, beta and gamma diversity for arthropods is often complicated by a lack of prior taxonomic information and/or taxonomic expertise, which can result in unreliable morphologically based estimates. We provide a set of standardized ecological and molecular sampling protocols that can be employed by researchers whose taxonomic skills may be limited, and where there may be a lack of robust a priori information regarding the regional pool of species. These protocols combine mass sampling of arthropods, classification of samples into parataxonomic units (PUs) and selective sampling of individuals for mtDNA sequencing to infer biological species. We sampled ten lowland rainforest plots located on the volcanic oceanic island of Réunion (Mascarene archipelago) for spiders, a group with limited taxonomic and distributional data for this region. We classified adults and juveniles into PUs and then demonstrated the reconciliation of these units with presumed biological species using mtDNA sequence data, ecological data and distributional data. Because our species assignment protocol is not reliant upon prior taxonomic information, or taxonomic expertise, it minimizes the problem of the Linnean shortfall to yield diversity estimates that can be directly compared across independent studies. Field sampling can be extended to other arthropod groups and habitats by adapting our field sampling protocol accordingly.
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Affiliation(s)
- Brent C Emerson
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología, C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, 38206, Spain.,School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Juliane Casquet
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
| | - Heriberto López
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología, C/Astrofísico Francisco Sánchez 3, La Laguna, Tenerife, Canary Islands, 38206, Spain
| | - Pedro Cardoso
- Finnish Museum of Natural History, University of Helsinki, P.O. Box 17, 00014, Helsinki, Finland.,Azorean Biodiversity Group, Departamento de Ciências e Engenharia do Ambiente, CE3C - Centre for Ecology, Evolution and Environmental Changes, Universidade dos Açores, Rua Capitão João d'Ávila s/n, 9700-042, Angra do Heroísmo, Açores, Portugal
| | - Paulo A V Borges
- Azorean Biodiversity Group, Departamento de Ciências e Engenharia do Ambiente, CE3C - Centre for Ecology, Evolution and Environmental Changes, Universidade dos Açores, Rua Capitão João d'Ávila s/n, 9700-042, Angra do Heroísmo, Açores, Portugal
| | - Noémy Mollaret
- Direction des collections, Invertébrés marins, Muséum National d'Histoire Naturelle, CP53, 61 rue Buffon, 75231, Paris Cedex 05, France
| | - Pedro Oromí
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, C/Astrofísico Francisco Sánchez, 38206, La Laguna, Tenerife, Canary Islands, Spain
| | - Dominique Strasberg
- UMR PVBMT, Peuplements Végétaux et Bio-agresseurs en Milieu Tropical, Université de La Réunion, 15 Avenue René Cassin, CS 93002, 97 744, Saint Denis, Cedex 9, Reunion Island, France
| | - Christophe Thébaud
- Laboratoire Evolution & Diversité Biologique, UMR 5174 CNRS-Université Paul Sabatier-ENFA, 31062, Toulouse Cedex 9, France
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19
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Mills JA, Teplitsky C, Arroyo B, Charmantier A, Becker PH, Birkhead TR, Bize P, Blumstein DT, Bonenfant C, Boutin S, Bushuev A, Cam E, Cockburn A, Côté SD, Coulson JC, Daunt F, Dingemanse NJ, Doligez B, Drummond H, Espie RHM, Festa-Bianchet M, Frentiu F, Fitzpatrick JW, Furness RW, Garant D, Gauthier G, Grant PR, Griesser M, Gustafsson L, Hansson B, Harris MP, Jiguet F, Kjellander P, Korpimäki E, Krebs CJ, Lens L, Linnell JDC, Low M, McAdam A, Margalida A, Merilä J, Møller AP, Nakagawa S, Nilsson JÅ, Nisbet ICT, van Noordwijk AJ, Oro D, Pärt T, Pelletier F, Potti J, Pujol B, Réale D, Rockwell RF, Ropert-Coudert Y, Roulin A, Sedinger JS, Swenson JE, Thébaud C, Visser ME, Wanless S, Westneat DF, Wilson AJ, Zedrosser A. Archiving Primary Data: Solutions for Long-Term Studies. Trends Ecol Evol 2016; 30:581-589. [PMID: 26411615 DOI: 10.1016/j.tree.2015.07.006] [Citation(s) in RCA: 83] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 07/14/2015] [Accepted: 07/15/2015] [Indexed: 11/25/2022]
Abstract
The recent trend for journals to require open access to primary data included in publications has been embraced by many biologists, but has caused apprehension amongst researchers engaged in long-term ecological and evolutionary studies. A worldwide survey of 73 principal investigators (Pls) with long-term studies revealed positive attitudes towards sharing data with the agreement or involvement of the PI, and 93% of PIs have historically shared data. Only 8% were in favor of uncontrolled, open access to primary data while 63% expressed serious concern. We present here their viewpoint on an issue that can have non-trivial scientific consequences. We discuss potential costs of public data archiving and provide possible solutions to meet the needs of journals and researchers.
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Affiliation(s)
| | - Céline Teplitsky
- Département Ecologie et Gestion de la Biodiversité, UMR 7204 CNRS/MNHN/UPMC, Muséum National d'Histoire Naturelle, Paris, France.
| | - Beatriz Arroyo
- Instituto de Investigacion en Recursos Cinegeticos (IREC) (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13005 Ciudad, Real, Spain
| | - Anne Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175, Campus CNRS, 1919 Route de Mende, 34293 Montpellier CEDEX 5, France
| | - Peter H Becker
- Institute of Avian Research, 'Vogelwarte Helgoland', An der Vogelwarte 21 D26386 Wilhelmshaven, Germany
| | - Tim R Birkhead
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK
| | - Pierre Bize
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
| | - Daniel T Blumstein
- Department of Ecology and Evolutionary Biology, University of California, 621 Young Drive South, Los Angeles, CA 90095-1606, USA
| | - Christophe Bonenfant
- CNRS,Université Lyon 1, Université de Lyon, UMR 5558, Laboratoire Biométrie et Biologie Évolutive, 43 boulevard du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France
| | - Stan Boutin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Andrey Bushuev
- Department of Vertebrate Zoology, Faculty of Biology, Lomonosov Moscow State University, Leninskie Gory 1/12, 119234 Moscow, Russia
| | - Emmanuelle Cam
- UMR 5174 EDB Laboratoire Évolution et Diversité Biologique, CNRS, ENFA, Université Toulouse 3 Paul Sabatier, 31062 Toulouse CEDEX 9, France
| | - Andrew Cockburn
- Department of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Steeve D Côté
- Département de Biologie and Centre d'Etudes Nordiques, Université Laval, 1045 avenue de la Médecine, Québec G1V 0A6, Canada
| | | | - Francis Daunt
- Centre for Ecology and Hydrology, Bush Estate, Penicuik, EH26 0QB UK
| | - Niels J Dingemanse
- Behavioural Ecology, Department of Biology, Ludwig-Maximilians University of Munich, Planegg-Martinsried, Germany; Evolutionary Ecology of Variation Research Group, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Blandine Doligez
- CNRS,Université Lyon 1, Université de Lyon, UMR 5558, Laboratoire Biométrie et Biologie Évolutive, 43 boulevard du 11 Novembre 1918, 69622 Villeurbanne CEDEX, France
| | - Hugh Drummond
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, AP 70-275, México DF 04510, México
| | - Richard H M Espie
- Technical Resource Branch, Saskatchewan Ministry of Environment, 3211 Albert Street, Regina, Saskatchewan, S4S 5W6, Canada
| | - Marco Festa-Bianchet
- Département de Biologie, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Francesca Frentiu
- School of Biomedical Sciences and Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD 4059 Australia
| | - John W Fitzpatrick
- Cornell Lab of Ornithology, 159 Sapsucker Woods Road, Ithaca, NY 14850, USA
| | - Robert W Furness
- Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, UK
| | - Dany Garant
- Département de Biologie, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Gilles Gauthier
- Département de Biologie and Centre d'Etudes Nordiques, Université Laval, 1045 avenue de la Médecine, Québec G1V 0A6, Canada
| | - Peter R Grant
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544-1003, USA
| | - Michael Griesser
- Anthropological Institute and Museum, University of Zürich, Zürich, Switzerland
| | - Lars Gustafsson
- Department of Animal Ecology, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
| | - Bengt Hansson
- Department of Biology, Lund University, Ecology Building, 223 62, Lund, Sweden
| | - Michael P Harris
- Centre for Ecology and Hydrology, Bush Estate, Penicuik, EH26 0QB UK
| | - Frédéric Jiguet
- CESCO, UMR7204 Sorbonne Universités-MNHN-CNRS-UPMC, CP51, 55 Rue Buffon, 75005 Paris, France
| | - Petter Kjellander
- Grimso Wildlife Research Station, Department of Ecology, Swedish University of Agricultural Sciences (SLU) 73091, Riddarhyttan, Sweden
| | - Erkki Korpimäki
- Section of Ecology, Department of Biology, University of Turku, 20014 Turku, Finland
| | - Charles J Krebs
- Department of Zoology, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Luc Lens
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ledeganckstraat 35, 9000 Gent, Belgium
| | - John D C Linnell
- Norwegian Institute for Nature Research, PO Box 5685 Sluppen, 7485 Trondheim, Norway
| | - Matthew Low
- Department of Ecology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Andrew McAdam
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Antoni Margalida
- Faculty of Life Sciences and Engineering, University of Lleida, 25198 Lleida, Spain
| | - Juha Merilä
- Ecological Genetics Research Unit, Department of Biosciences, PO Box 65 (Biocenter 3, Viikinkaari 1), University of Helsinki, 00014 Helskinki, Finland
| | - Anders P Møller
- Laboratoire Ecologie, Systématique et Evolution, Equipe Diversité, Ecologie et Evolution Microbiennes, Bâtiment 362, 91405 Orsay CEDEX, France
| | - Shinichi Nakagawa
- Evolution and Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Jan-Åke Nilsson
- Department of Animal Ecology, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
| | - Ian C T Nisbet
- I.C.T. Nisbet and Company, 150 Alder Lane, North Falmouth, MA 02556, USA
| | - Arie J van Noordwijk
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700 AB Wageningen, The Netherlands
| | - Daniel Oro
- Institut Mediterrani d'Estudis Avançats IMEDEA (CSIC-UIB), Miquel Marques 21, 07190 Esporles, Mallorca, Spain
| | - Tomas Pärt
- Department of Ecology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Fanie Pelletier
- Département de Biologie, Université de Sherbrooke, 2500 Boulevard de l'Université, Sherbrooke, Québec J1K 2R1, Canada
| | - Jaime Potti
- Departamento de Ecologia Evolutiva, Estación Biológica de Doñana-CSIC, Av. Américo Vespucio s/n, 41092 Seville, Spain
| | - Benoit Pujol
- Department of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Denis Réale
- Département des Sciences Biologiques, Université du Québec A Montréal, CP 8888 Cuccursale Centre Ville, Montréal, Québec H3C 3P8, Canada
| | - Robert F Rockwell
- Vertebrate Zoology, American Museum of Natural History, New York, NY 10024 USA
| | - Yan Ropert-Coudert
- Institut Pluridisciplinaire Hubert Curien, CNRS UMR7178, 23 rue Becquerel 67087 Strasbourg, France
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - James S Sedinger
- Department of Natural Resources and Environmental Science, University of Nevada Reno, Reno NV 89512, USA
| | - Jon E Swenson
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, PO Box 5003, 1432 Ås, and Norway and Norwegian Institute for Nature Research, PO Box 5685 Sluppen, 7485 Trondheim, Norway
| | - Christophe Thébaud
- UMR 5174 EDB Laboratoire Évolution et Diversité Biologique, CNRS, ENFA, Université Toulouse 3 Paul Sabatier, 31062 Toulouse CEDEX 9, France
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), PO Box 50, 6700 AB Wageningen, The Netherlands
| | - Sarah Wanless
- Centre for Ecology and Hydrology, Bush Estate, Penicuik, EH26 0QB UK
| | - David F Westneat
- Department of Biology, Center for Ecology, Evolution, and Behavior, University of Kentucky, Lexington, KY, USA
| | - Alastair J Wilson
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Penryn TR10 9EZ, UK
| | - Andreas Zedrosser
- Faculty of Arts and Sciences, Department of Environmental and Health Studies, Telemark University College, 3800 Bø i Telemark, Norway
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Vacher JP, Fouquet A, Holota H, Thébaud C. The complete mitochondrial genome of Anomaloglossus baeobatrachus (Amphibia: Anura: Aromobatidae). Mitochondrial DNA B Resour 2016; 1:338-340. [PMID: 33644376 PMCID: PMC7871838 DOI: 10.1080/23802359.2016.1172053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The complete mitogenome of the rocket frog Anomaloglossus baeobatrachus was sequenced using a shotgun approach on an Illumina HiSeq 2500 platform (Illumina Inc., San Diego, CA), providing the first mitogenome for this genus. The genome was 17,572 bp long and presents the typical organization found in other neobatrachian anurans. A phylogenetic analysis including A. baeobatrachus and all other available mitogenomes of Hyloidea provided relationships in accordance with previous phylogenetic studies.
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Affiliation(s)
| | - Antoine Fouquet
- Laboratoire Écologie, Évolution, Interactions Des Systèmes Amazoniens (LEEISA), Université De Guyane, CNRS Guyane, Cayenne, French Guiana
| | - Hélène Holota
- Laboratoire EDB, UMR5174, CNRS-UPS-ENFA, Toulouse, France
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21
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Bourgeois YXC, Bertrand JAM, Delahaie B, Cornuault J, Duval T, Milá B, Thébaud C. Candidate Gene Analysis Suggests Untapped Genetic Complexity in Melanin-Based Pigmentation in Birds. J Hered 2016; 107:327-35. [PMID: 26995742 DOI: 10.1093/jhered/esw017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 03/15/2016] [Indexed: 12/22/2022] Open
Abstract
Studies on melanin-based color variation in a context of natural selection have provided a wealth of information on the link between phenotypic and genetic variation. Here, we evaluated associations between melanic plumage patterns and genetic polymorphism in the Réunion grey white-eye (Zosterops borbonicus), a species in which mutations on MC1R do not seem to play any role in explaining melanic variation. This species exhibits 5 plumage color variants that can be grouped into 3 color forms which occupy discrete geographic regions in the lowlands of Réunion, and a fourth high-elevation form which comprises 2 color morphs (grey and brown) and represents a true color polymorphism. We conducted a comprehensive survey of sequence variation in 96 individuals at a series of 7 candidate genes other than MC1R that have been previously shown to influence melanin-based color patterns in vertebrates, including genes that have rarely been studied in a wild bird species before: POMC, Agouti, TYR, TYRP1, DCT, Corin, and SLC24A5 Of these 7 genes, 2 (Corin and TYRP1) displayed an interesting shift in allele frequencies between lowland and highland forms and a departure from mutation-drift equilibrium consistent with balancing selection in the polymorphic highland form only. Sequence variation at Agouti, a gene frequently involved in melanin-based pigmentation patterning, was not associated with color forms or morphs. Thus, we suggest that functionally important changes in loci other than those classically studied are involved in the color polymorphism exhibited by the Réunion grey white-eye and possibly many other nonmodel species.
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Affiliation(s)
- Yann X C Bourgeois
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá).
| | - Joris A M Bertrand
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Boris Delahaie
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Josselin Cornuault
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Thomas Duval
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Borja Milá
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
| | - Christophe Thébaud
- From the Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174, Université Paul Sabatier, Toulouse 3-Centre National de la Recherche Scientifique (CNRS)-École Nationale de Formation Agronomique (ENFA), 118 route de Narbonne, F-31062 Toulouse, France (Bourgeois, Bertrand, Delahaie, Cornuault, and Thébaud); Hémisphères, BP 438, 98822 Poindimié, Nouvelle-Calédonie (Duval); and Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain (Milá)
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22
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Bertrand JAM, Delahaie B, Bourgeois YXC, Duval T, García-Jiménez R, Cornuault J, Pujol B, Thébaud C, Milá B. The role of selection and historical factors in driving population differentiation along an elevational gradient in an island bird. J Evol Biol 2016; 29:824-36. [DOI: 10.1111/jeb.12829] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Accepted: 01/10/2016] [Indexed: 01/31/2023]
Affiliation(s)
- J. A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique; UMR 5174; Université Paul Sabatier; Toulouse 3 - Centre National de la Recherche Scientifique (CNRS) - École Nationale de Formation Agronomique (ENFA); Toulouse Cedex 9 France
| | - B. Delahaie
- Laboratoire Évolution et Diversité Biologique; UMR 5174; Université Paul Sabatier; Toulouse 3 - Centre National de la Recherche Scientifique (CNRS) - École Nationale de Formation Agronomique (ENFA); Toulouse Cedex 9 France
| | - Y. X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique; UMR 5174; Université Paul Sabatier; Toulouse 3 - Centre National de la Recherche Scientifique (CNRS) - École Nationale de Formation Agronomique (ENFA); Toulouse Cedex 9 France
| | - T. Duval
- Hémisphères; Poindimié New Caledonia
| | - R. García-Jiménez
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
| | - J. Cornuault
- Laboratoire Évolution et Diversité Biologique; UMR 5174; Université Paul Sabatier; Toulouse 3 - Centre National de la Recherche Scientifique (CNRS) - École Nationale de Formation Agronomique (ENFA); Toulouse Cedex 9 France
| | - B. Pujol
- Laboratoire Évolution et Diversité Biologique; UMR 5174; Université Paul Sabatier; Toulouse 3 - Centre National de la Recherche Scientifique (CNRS) - École Nationale de Formation Agronomique (ENFA); Toulouse Cedex 9 France
| | - C. Thébaud
- Laboratoire Évolution et Diversité Biologique; UMR 5174; Université Paul Sabatier; Toulouse 3 - Centre National de la Recherche Scientifique (CNRS) - École Nationale de Formation Agronomique (ENFA); Toulouse Cedex 9 France
| | - B. Milá
- National Museum of Natural Sciences; Spanish National Research Council (CSIC); Madrid Spain
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23
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Besnard G, Bertrand JAM, Delahaie B, Bourgeois YXC, Lhuillier E, Thébaud C. Valuing museum specimens: high-throughput DNA sequencing on historical collections of New Guinea crowned pigeons (Goura). Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12494] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Joris A. M. Bertrand
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Institute of Oceanography; National Taiwan University; n°1, sec. 4, Roosevelt Road, Daan District Taipei 10617 Taiwan
| | - Boris Delahaie
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
| | - Yann X. C. Bourgeois
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
- Zoological Institute; Department of Evolutionary Biology; University of Basel; Vesalgasse 1 4051 Basel Switzerland
| | - Emeline Lhuillier
- INRA; GeT-PlaGe; UAR 1209 Département de Génétique Animale; INRA Auzeville; 31326 Castanet-Tolosan France
| | - Christophe Thébaud
- CNRS-UPS-ENFA; UMR5174 EDB (Laboratoire Évolution & Diversité Biologique); Université Paul Sabatier; 118 route de Narbonne 31062 Toulouse France
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24
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Courchamp F, Dunne JA, Le Maho Y, May RM, Thébaud C, Hochberg ME. Erratum: Fundamental ecology is fundamental. Trends Ecol Evol 2015. [DOI: 10.1016/j.tree.2015.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Warren BH, Simberloff D, Ricklefs RE, Aguilée R, Condamine FL, Gravel D, Morlon H, Mouquet N, Rosindell J, Casquet J, Conti E, Cornuault J, Fernández-Palacios JM, Hengl T, Norder SJ, Rijsdijk KF, Sanmartín I, Strasberg D, Triantis KA, Valente LM, Whittaker RJ, Gillespie RG, Emerson BC, Thébaud C. Islands as model systems in ecology and evolution: prospects fifty years after MacArthur-Wilson. Ecol Lett 2015; 18:200-17. [DOI: 10.1111/ele.12398] [Citation(s) in RCA: 279] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2014] [Revised: 07/01/2014] [Accepted: 11/10/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Ben H. Warren
- Institute of Systematic Botany; University of Zurich; Zollikerstrasse 107 8008 Zurich Switzerland
- Department of Ecology and Evolutionary Biology; University of Tennessee; Knoxville TN 37996 USA
- UMR PVBMT; Université de La Réunion-CIRAD; 7 chemin de l'IRAT Ligne Paradis 97410 Saint Pierre Réunion France
| | - Daniel Simberloff
- Department of Ecology and Evolutionary Biology; University of Tennessee; Knoxville TN 37996 USA
| | - Robert E. Ricklefs
- Department of Biology; University of Missouri at St. Louis; 8001 Natural Bridge Road St. Louis MO 63121 USA
| | - Robin Aguilée
- Laboratoire Evolution & Diversité Biologique; UMR 5174 CNRS-Université Paul Sabatier-ENFA; 31062 Toulouse Cedex 9 France
| | - Fabien L. Condamine
- CNRS; UMR 7641 Centre de Mathématiques Appliquées (Ecole Polytechnique); Route de Saclay 91128 Palaiseau France
| | - Dominique Gravel
- Département de Biologie; Université du Québec à Rimouski 300; Allée des Ursulines; Rimouski QC G5L 3A1 Canada
| | - Hélène Morlon
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS); UMR CNRS 8197; 46 rue d'Ulm 75005 Paris France
| | - Nicolas Mouquet
- Institut des Sciences de l'Evolution; UMR 5554; CNRS; Univ. Montpellier 2; CC 065 Place Eugène Bataillon 34095 Montpellier Cedex 05 France
| | - James Rosindell
- Department of Life Sciences; Imperial College London; Silwood Park Campus Ascot Berkshire SL5 7PY UK
| | - Juliane Casquet
- Laboratoire Evolution & Diversité Biologique; UMR 5174 CNRS-Université Paul Sabatier-ENFA; 31062 Toulouse Cedex 9 France
| | - Elena Conti
- Institute of Systematic Botany; University of Zurich; Zollikerstrasse 107 8008 Zurich Switzerland
| | - Josselin Cornuault
- Laboratoire Evolution & Diversité Biologique; UMR 5174 CNRS-Université Paul Sabatier-ENFA; 31062 Toulouse Cedex 9 France
| | - José María Fernández-Palacios
- Island Ecology and Biogeography Group; Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias (IUETSPC); Universidad de La Laguna; Tenerife Canary Islands Spain
| | - Tomislav Hengl
- ISRIC-World Soil Information; 6700 AJ Wageningen The Netherlands
| | - Sietze J. Norder
- Institute for Biodiversity and Ecosystem Dynamics; Institute for Interdisciplinary Studies; University of Amsterdam; Science Park 904 1098XH Amsterdam The Netherlands
| | - Kenneth F. Rijsdijk
- Institute for Biodiversity and Ecosystem Dynamics; Institute for Interdisciplinary Studies; University of Amsterdam; Science Park 904 1098XH Amsterdam The Netherlands
| | - Isabel Sanmartín
- Real Jardín Botánico; RJB-CSIC; Plaza de Murillo 2 28014 Madrid Spain
| | - Dominique Strasberg
- UMR PVBMT; Université de La Réunion-CIRAD; 7 chemin de l'IRAT Ligne Paradis 97410 Saint Pierre Réunion France
| | - Kostas A. Triantis
- Department of Ecology and Taxonomy; Faculty of Biology; National and Kapodistrian University; Athens 15784 Greece
- Oxford University Centre for the Environment; South Parks Road Oxford OX1 3QY UK
| | - Luis M. Valente
- Unit of Evolutionary Biology/Systematic Zoology; Institute of Biochemistry and Biology; University of Potsdam; Karl-Liebknecht-Strasse 24-25 14476 Potsdam Germany
| | - Robert J. Whittaker
- Oxford University Centre for the Environment; South Parks Road Oxford OX1 3QY UK
| | - Rosemary G. Gillespie
- Division of Organisms and Environment; University of California; Berkeley CA 94720 USA
| | - Brent C. Emerson
- Island Ecology and Evolution Research Group; Instituto de Productos Naturales y Agrobiología (IPNA-CSIC); C/Astrofísico Francisco Sánchez 3 La Laguna 38206 Tenerife Canary Islands Spain
| | - Christophe Thébaud
- Laboratoire Evolution & Diversité Biologique; UMR 5174 CNRS-Université Paul Sabatier-ENFA; 31062 Toulouse Cedex 9 France
- CESAB / FRB; Domaine du Petit Arbois; Av Louis Philibert Aix-en-Provence 13100 France
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Courchamp F, Dunne JA, Le Maho Y, May RM, Thébaud C, Hochberg ME. Fundamental ecology is fundamental. Trends Ecol Evol 2015; 30:9-16. [DOI: 10.1016/j.tree.2014.11.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/10/2014] [Accepted: 11/12/2014] [Indexed: 12/22/2022]
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Cornuault J, Delahaie B, Bertrand JAM, Bourgeois YXC, Milá B, Heeb P, Thébaud C. Morphological and plumage colour variation in the Réunion grey white-eye (Aves:Zosterops borbonicus): assessing the role of selection. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12428] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Josselin 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); 118 Route de Narbonne F-31062 Toulouse France
| | - Boris 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); 118 Route de Narbonne F-31062 Toulouse France
| | - Joris 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); 118 Route de Narbonne F-31062 Toulouse France
| | - Yann 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); 118 Route de Narbonne F-31062 Toulouse France
| | - Borja Milá
- National Museum of Natural Sciences; Spanish Research Council (CSIC); Madrid 28006 Spain
| | - Philipp Heeb
- Laboratoire Évolution et Diversité Biologique (EDB); UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier - Ecole Nationale de Formation Agronomique (ENFA); 118 Route de Narbonne F-31062 Toulouse France
| | - Christophe 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); 118 Route de Narbonne F-31062 Toulouse France
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Guidot A, Jiang W, Ferdy JB, Thébaud C, Barberis P, Gouzy J, Genin S. Multihost experimental evolution of the pathogen Ralstonia solanacearum unveils genes involved in adaptation to plants. Mol Biol Evol 2014; 31:2913-28. [PMID: 25086002 DOI: 10.1093/molbev/msu229] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Ralstonia solanacearum, the causal agent of a lethal bacterial wilt plant disease, infects an unusually wide range of hosts. These hosts can further be split into plants where R. solanacearum is known to cause disease (original hosts) and those where this bacterium can grow asymptomatically (distant hosts). Moreover, this pathogen is able to adapt to many plants as supported by field observations reporting emergence of strains with enlarged pathogenic properties. To investigate the genetic bases of host adaptation, we conducted evolution experiments by serial passages of a single clone of the pathogen on three original and two distant hosts over 300 bacterial generations and then analyzed the whole-genome of nine evolved clones. Phenotypic analysis of the evolved clones showed that the pathogen can increase its fitness on both original and distant hosts although the magnitude of fitness increase was greater on distant hosts. Only few genomic modifications were detected in evolved clones compared with the ancestor but parallel evolutionary changes in two genes were observed in independent evolved populations. Independent mutations in the regulatory gene efpR were selected for in three populations evolved on beans, a distant host. Reverse genetic approaches confirmed that these mutations were associated with fitness gain on bean plants. This work provides a first step toward understanding the within-host evolutionary dynamics of R. solanacearum during infection and identifying bacterial genes subjected to in planta selection. The discovery of EfpR as a determinant conditioning host adaptation of the pathogen illustrates how experimental evolution coupled with whole-genome sequencing is a potent tool to identify novel molecular players involved in central life-history traits.
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Affiliation(s)
- Alice Guidot
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Wei Jiang
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Jean-Baptiste Ferdy
- UPS-CNRS-ENFA, Laboratoire Évolution et Diversité Biologique (EDB), UMR5174, Université Paul Sabatier, Toulouse, France
| | - Christophe Thébaud
- UPS-CNRS-ENFA, Laboratoire Évolution et Diversité Biologique (EDB), UMR5174, Université Paul Sabatier, Toulouse, France
| | - Patrick Barberis
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Jérôme Gouzy
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
| | - Stéphane Genin
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France
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Liberal IM, Burrus M, Suchet C, Thébaud C, Vargas P. The evolutionary history of Antirrhinum in the Pyrenees inferred from phylogeographic analyses. BMC Evol Biol 2014; 14:146. [PMID: 24970688 PMCID: PMC4099501 DOI: 10.1186/1471-2148-14-146] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 06/17/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The origin and colonisation history after the Quaternary ice ages remain largely unresolved for many plant lineages, mainly owing to a lack of fine-scale studies. Here, we present a molecular phylogeny and a phylogeographic analysis of Antirrhinum, an important model system in plant biology, in the Pyrenees range. Our goal was to reconstruct the evolutionary and colonisation history of four taxa endemic to this region (A. majus subsp. majus, A. majus. subsp. striatum, A. molle, and A. sempervirens) by using a dense sampling strategy, with a total of 452 individuals from 99 populations whose collective distribution spans nearly the entirety of the Pyrenees and adjacent mountains. RESULTS Phylogenetic and phylogeographic analyses of the sequences of two plastid (trnS-trnG and trnK-matK) regions revealed the following: (i) historical relationship between the Pyrenees and Iberia (but not with the Alps); (ii) the long persistence of populations in the Pyrenees, at least since the Late Pleistocene; (iii) three different colonisation histories for populations from the Western, Central, and Eastern Pyrenees; (iv) the deep phylogeographic separation of the eastern and western populations; and (v) the colonisation of southern France from the Eastern Pyrenees. CONCLUSIONS The present study underlines the enormous influence of the glacial history of the mountain ranges on the current configuration of intra- and inter-specific genetic diversity in Antirrhinum, as well as the importance of periglacial areas for the survival of species during glacial periods of the Quaternary.
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Affiliation(s)
- Isabel M Liberal
- Real Jardín Botánico de Madrid (CSIC), Plaza de Murillo 2, Madrid E-28014, Spain
| | - Monique Burrus
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, CNRS - Université de Toulouse (UPS)- ENFA, 118 route de Narbonne, Toulouse, Cedex 9 31062, France
| | - Claire Suchet
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, CNRS - Université de Toulouse (UPS)- ENFA, 118 route de Narbonne, Toulouse, Cedex 9 31062, France
| | - Christophe Thébaud
- Laboratoire Evolution et Diversité Biologique (EDB), UMR5174, CNRS - Université de Toulouse (UPS)- ENFA, 118 route de Narbonne, Toulouse, Cedex 9 31062, France
| | - Pablo Vargas
- Real Jardín Botánico de Madrid (CSIC), Plaza de Murillo 2, Madrid E-28014, Spain
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Cornuault J, Warren BH, Bertrand JAM, Milá B, Thébaud C, Heeb P. Timing and Number of Colonizations but Not Diversification Rates Affect Diversity Patterns in Hemosporidian Lineages on a Remote Oceanic Archipelago. Am Nat 2013; 182:820-33. [DOI: 10.1086/673724] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Bertrand JAM, Bourgeois YXC, Delahaie B, Duval T, García-Jiménez R, Cornuault J, Heeb P, Milá B, Pujol B, Thébaud C. Extremely reduced dispersal and gene flow in an island bird. Heredity (Edinb) 2013; 112:190-6. [PMID: 24084644 DOI: 10.1038/hdy.2013.91] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Revised: 07/02/2013] [Accepted: 08/15/2013] [Indexed: 11/09/2022] Open
Abstract
The Réunion grey white-eye, Zosterops borbonicus, a passerine bird endemic to Réunion Island in the Mascarene archipelago, represents an extreme case of microgeographical plumage colour variation in birds, with four distinct colour forms occupying different parts of this small island (2512 km(2)). To understand whether such population differentiation may reflect low levels of dispersal and gene flow at a very small spatial scale, we examined population structure and gene flow by analysing variation at 11 microsatellite loci among four geographically close localities (<26 km apart) sampled within the distribution range of one of the colour forms, the brown-headed brown form. Our results revealed levels of genetic differentiation that are exceptionally high for birds at such a small spatial scale. This strong population structure appears to reflect low levels of historical and contemporary gene flow among populations, unless very close geographically (<10 km). Thus, we suggest that the Réunion grey white-eye shows an extremely reduced propensity to disperse, which is likely to be related to behavioural processes.
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Affiliation(s)
- J A M Bertrand
- Laboratoire Evolution et Diversité Biologique, UMR 5174 Centre National de la Recherche Scientifique (CNRS)-Université Paul Sabatier-Ecole Nationale de Formation Agronomique, Toulouse, France
| | - Y X C Bourgeois
- Laboratoire Evolution et Diversité Biologique, UMR 5174 Centre National de la Recherche Scientifique (CNRS)-Université Paul Sabatier-Ecole Nationale de Formation Agronomique, Toulouse, France
| | - B Delahaie
- Laboratoire Evolution et Diversité Biologique, UMR 5174 Centre National de la Recherche Scientifique (CNRS)-Université Paul Sabatier-Ecole Nationale de Formation Agronomique, Toulouse, France
| | - T Duval
- Société Calédonienne d'Ornithologie Nord, Nouvelle-Calédonie, France
| | - R García-Jiménez
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish Research Council (CSIC), Madrid, Spain
| | - J Cornuault
- Laboratoire Evolution et Diversité Biologique, UMR 5174 Centre National de la Recherche Scientifique (CNRS)-Université Paul Sabatier-Ecole Nationale de Formation Agronomique, Toulouse, France
| | - P Heeb
- Laboratoire Evolution et Diversité Biologique, UMR 5174 Centre National de la Recherche Scientifique (CNRS)-Université Paul Sabatier-Ecole Nationale de Formation Agronomique, Toulouse, France
| | - B Milá
- Department of Biodiversity and Evolutionary Biology, National Museum of Natural Sciences, Spanish Research Council (CSIC), Madrid, Spain
| | - B Pujol
- Laboratoire Evolution et Diversité Biologique, UMR 5174 Centre National de la Recherche Scientifique (CNRS)-Université Paul Sabatier-Ecole Nationale de Formation Agronomique, Toulouse, France
| | - C Thébaud
- Laboratoire Evolution et Diversité Biologique, UMR 5174 Centre National de la Recherche Scientifique (CNRS)-Université Paul Sabatier-Ecole Nationale de Formation Agronomique, Toulouse, France
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Bourgeois YXC, Lhuillier E, Cézard T, Bertrand JAM, Delahaie B, Cornuault J, Duval T, Bouchez O, Milá B, Thébaud C. Mass production of
SNP
markers in a nonmodel passerine bird through
RAD
sequencing and contig mapping to the zebra finch genome. Mol Ecol Resour 2013; 13:899-907. [DOI: 10.1111/1755-0998.12137] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 05/24/2013] [Accepted: 06/04/2013] [Indexed: 01/01/2023]
Affiliation(s)
- Yann X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Emeline Lhuillier
- INRA UAR 1209 Département de Génétique Animale INRA Auzeville F‐31326 Castanet‐Tolosan France
- GeT‐PlaGe Genotoul INRA Auzeville F‐31326 Castanet‐Tolosan France
| | - Timothée Cézard
- The GenePool Ashworth Laboratories The University of Edinburgh The King's Building Edinburgh EH9 3JT UK
| | - Joris A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Boris Delahaie
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Josselin Cornuault
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
| | - Thomas Duval
- Société Calédonienne d'Ornithologie Nord BP 236 F‐98822 Poindimié Nouvelle Calédonie France
| | - Olivier Bouchez
- GeT‐PlaGe Genotoul INRA Auzeville F‐31326 Castanet‐Tolosan France
- INRA UMR 444 Laboratoire de Génétique Cellulaire INRA Auzeville F‐31326 Castanet‐Tolosan France
| | - Borja Milá
- Museo Nacional de Ciencias Naturales CSIC José Gutiérrez Abascal 2 Madrid 28006 Spain
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique UMR 5174 CNRS ‐ Université Paul Sabatier – ENFA 118 route de Narbonne, Bâtiment 4R1 F‐31062 Toulouse Cedex 9 France
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Bourgeois YXC, Bertrand JAM, Thébaud C, Milá B. Investigating the role of the melanocortin-1 receptor gene in an extreme case of microgeographical variation in the pattern of melanin-based plumage pigmentation. PLoS One 2012; 7:e50906. [PMID: 23227219 PMCID: PMC3515493 DOI: 10.1371/journal.pone.0050906] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Accepted: 10/26/2012] [Indexed: 11/19/2022] Open
Abstract
UNLABELLED The Réunion grey white-eye (Zosterops borbonicus) is a single-island endemic passerine bird that exhibits striking geographically structured melanic polymorphism at a very small spatial scale. We investigated the genetic basis of this color polymorphism by testing whether the melanocortin-1 receptor (MC1R), a gene often involved in natural melanic polymorphism in birds, was associated with the observed plumage variation. Although we found three non-synonymous mutations, we detected no association between MC1R variants and color morphs, and the main amino-acid variant found in the Réunion grey white-eye was also present at high frequency in the Mauritius grey white-eye (Zosterops mauritianus), its sister species which shows no melanic polymorphism. In addition, neutrality tests and analysis of population structure did not reveal any obvious pattern of positive or balancing selection acting on MC1R. Altogether these results indicate that MC1R does not play a role in explaining the melanic variation observed in the Réunion grey white-eye. We propose that other genes such as POMC, Agouti or any other genes involved in pigment synthesis will need to be investigated in future studies if we are to understand how selection shapes complex patterns of melanin-based plumage pigmentation. TRIAL REGISTRATION All sequences submitted to Genbank. Accession number: JX914505 to JX914564.
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Affiliation(s)
- Yann X. C. Bourgeois
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS - Université Paul Sabatier – ENFA, Toulouse, France
- * E-mail:
| | - Joris A. M. Bertrand
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS - Université Paul Sabatier – ENFA, Toulouse, France
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique, UMR5174 CNRS - Université Paul Sabatier – ENFA, Toulouse, France
| | - Borja Milá
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
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Strijk JS, Noyes RD, Strasberg D, Cruaud C, Gavory F, Chase MW, Abbott RJ, Thébaud C. In and out of Madagascar: dispersal to peripheral islands, insular speciation and diversification of Indian Ocean daisy trees (Psiadia, Asteraceae). PLoS One 2012; 7:e42932. [PMID: 22900068 PMCID: PMC3416790 DOI: 10.1371/journal.pone.0042932] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Accepted: 07/16/2012] [Indexed: 11/20/2022] Open
Abstract
Madagascar is surrounded by archipelagos varying widely in origin, age and structure. Although small and geologically young, these archipelagos have accumulated disproportionate numbers of unique lineages in comparison to Madagascar, highlighting the role of waif-dispersal and rapid in situ diversification processes in generating endemic biodiversity. We reconstruct the evolutionary and biogeographical history of the genus Psiadia (Asteraceae), a plant genus with near equal numbers of species in Madagascar and surrounding islands. Analyzing patterns and processes of diversification, we explain species accumulation on peripheral islands and aim to offer new insights on the origin and potential causes for diversification in the Madagascar and Indian Ocean Islands biodiversity hotspot. Our results provide support for an African origin of the group, with strong support for non-monophyly. Colonization of the Mascarenes took place by two evolutionary distinct lineages from Madagascar, via two independent dispersal events, each unique for their spatial and temporal properties. Significant shifts in diversification rate followed regional expansion, resulting in co-occurring and phenotypically convergent species on high-elevation volcanic slopes. Like other endemic island lineages, Psiadia have been highly successful in dispersing to and radiating on isolated oceanic islands, typified by high habitat diversity and dynamic ecosystems fuelled by continued geological activity. Results stress the important biogeographical role for Rodrigues in serving as an outlying stepping stone from which regional colonization took place. We discuss how isolated volcanic islands contribute to regional diversity by generating substantial numbers of endemic species on short temporal scales. Factors pertaining to the mode and tempo of archipelago formation and its geographical isolation strongly govern evolutionary pathways available for species diversification, and the potential for successful diversification of dispersed lineages, therefore, appears highly dependent on the timing of arrival, as habitat and resource properties change dramatically over the course of oceanic island evolution.
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Affiliation(s)
- Joeri S Strijk
- Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Mengla, Yunnan, People's Republic of China.
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Warren BH, Bermingham E, Bourgeois Y, Estep LK, Prys-Jones RP, Strasberg D, Thébaud C. HYBRIDIZATION AND BARRIERS TO GENE FLOW IN AN ISLAND BIRD RADIATION. Evolution 2012; 66:1490-505. [DOI: 10.1111/j.1558-5646.2011.01550.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Tastard E, Ferdy JB, Burrus M, Thébaud C, Andalo C. Patterns of floral colour neighbourhood and their effects on female reproductive success in an Antirrhinum hybrid zone. J Evol Biol 2011; 25:388-99. [PMID: 22188332 DOI: 10.1111/j.1420-9101.2011.02433.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The maintenance of genetic integrity of parental populations is often explained by selection against hybrids. However, the selection agents are usually unknown. The role of environmental biotic interactions is often suspected but has rarely been demonstrated. In plants for instance, mutualism with pollinators may be involved. After verification that pollen deposition is a limiting factor for fruit set, we used an individual-based study and a representation of pollinator colour perception to test the effects of local plant density and floral colour neighbourhood on female reproductive success in an Antirrhinum hybrid zone. In addition to flower colour and density effects, the composition of the floral neighbourhood was found to influence fruit set, suggesting that most plants were usually better fertilized when similar to their neighbours. However, the plants of one particular type were sometimes favoured when very different from their neighbours. The implications for hybrid zone dynamics are discussed.
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Affiliation(s)
- E Tastard
- Université de Toulouse, ENFA, UMR 5174 EDB (Laboratoire Évolution & Diversité Biologique), 118 route de Narbonne, Toulouse Cedex 9, France
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Khimoun A, Burrus M, Andalo C, Liu ZL, Vicédo-Cazettes C, Thébaud C, Pujol B. Locally asymmetric introgressions between subspecies suggest circular range expansion at the Antirrhinum majus global scale. J Evol Biol 2011; 24:1433-41. [PMID: 21545420 DOI: 10.1111/j.1420-9101.2011.02276.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Assessing processes of geographic expansion in contact zones is a crucial step towards an accurate prediction of the evolution of species genetic diversity. The geographic distribution of cytonuclear discordance often reflects genetic introgression patterns across a species geographic range. Antirrhinum majus pseudomajus and A. m. striatum are two interfertile subspecies that occupy nonoverlapping areas but enter in contact in many locations at the margin of their geographic distribution. We found that genetic introgression between both subspecies was asymmetric at the local scale and geographically oriented in opposite directions at both ends of their contact zone perimeter in the Pyrenees. Our results suggest that the geographic expansion of A. majus subspecies was circular around the perimeter of their contact zone and pinpoint the need to integrate different spatial scales to unravel complex patterns of species geographic expansion.
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Affiliation(s)
- A Khimoun
- Université de Toulouse; UPS; EDB (Laboratoire Évolution et Diversité Biologique); UMR5174; Toulouse Cedex 9, France.
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Warren BH, Strasberg D, Bruggemann JH, Prys-Jones RP, Thébaud C. Why does the biota of the Madagascar region have such a strong Asiatic flavour? Cladistics 2010; 26:526-538. [DOI: 10.1111/j.1096-0031.2009.00300.x] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Milá B, Warren BH, Heeb P, Thébaud C. The geographic scale of diversification on islands: genetic and morphological divergence at a very small spatial scale in the Mascarene grey white-eye (Aves: Zosterops borbonicus). BMC Evol Biol 2010; 10:158. [PMID: 20504327 PMCID: PMC2894829 DOI: 10.1186/1471-2148-10-158] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Accepted: 05/26/2010] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Oceanic islands provide unique scenarios for studying the roles of geography and ecology in driving population divergence and speciation. Assessing the relative importance of selective and neutral factors in driving population divergence is central to understanding how such divergence may lead to speciation in small oceanic islands, where opportunities for gene flow and population mixing are potentially high. Here we report a case of genetic and morphological structure in the Mascarene grey white-eye (Zosterops borbonicus) a species that shows a striking, geographically structured plumage polymorphism on the topographically and ecologically complex island of Réunion, yet is monotypic on the relatively uniform neighbouring island of Mauritius. RESULTS Analysis of 276 AFLP loci in 197 individuals revealed prolonged independent evolution of Réunion and Mauritius populations, which is congruent with previous mtDNA assessments. Furthermore, populations on Réunion showed significant differentiation into three main genetic groups separating lowland from highland areas despite the small geographic distances involved. Genetic differentiation along the altitudinal gradient is consistent with morphometric analysis of fitness-related traits. Birds in the highlands were larger, yet had relatively smaller beaks than in the lowlands, suggesting the role of selection in shaping morphology and restricting gene flow along the gradient. No genetic differentiation between plumage morphs was detected in neutral markers, suggesting that plumage differences are of recent origin. CONCLUSIONS Our results suggest a dual role of vicariance and natural selection in differentiating populations of a passerine bird in an oceanic island at very small spatial scales. We propose a combination of past microallopatry driven by volcanic activity and selection-constrained dispersal along steep ecological gradients to explain the striking levels of population structure found within the island, although the possibility that genetic differences evolved in situ along the gradient cannot be ruled out at present. The lack of congruence between genetic groups and plumage morphs suggests that the latter are of recent origin and likely due to social or sexual selection acting on few loci. The presence of sharp and stable contact zones between plumage morphs suggests that they could be on independent evolutionary trajectories, yet whether or not they represent incipient species will require further research to directly assess the degree of reproductive isolation among them.
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Affiliation(s)
- Borja Milá
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas (CSIC), José Gutiérrez Abascal 2, Madrid E-28006, Spain
| | - Ben H Warren
- UMR PVBMT, Université de La Réunion, 7 chemin de l'IRAT, F-97410 Saint Pierre, Réunion, France
| | - Philipp Heeb
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Christophe Thébaud
- Laboratoire Évolution et Diversité Biologique (EDB), UMR 5174 Centre National de la Recherche Scientifique (CNRS) - Université Paul Sabatier, 118 Route de Narbonne, F-31062 Toulouse, France
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Gonzalez MA, Baraloto C, Engel J, Mori SA, Pétronelli P, Riéra B, Roger A, Thébaud C, Chave J. Identification of Amazonian trees with DNA barcodes. PLoS One 2009. [PMID: 19834612 DOI: 10.137/journal.pone.0007483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
BACKGROUND Large-scale plant diversity inventories are critical to develop informed conservation strategies. However, the workload required for classic taxonomic surveys remains high and is particularly problematic for megadiverse tropical forests. METHODOLOGY/PRINCIPAL FINDINGS Based on a comprehensive census of all trees in two hectares of a tropical forest in French Guiana, we examined whether plant DNA barcoding could contribute to increasing the quality and the pace of tropical plant biodiversity surveys. Of the eight plant DNA markers we tested (rbcLa, rpoC1, rpoB, matK, ycf5, trnL, psbA-trnH, ITS), matK and ITS had a low rate of sequencing success. More critically, none of the plastid markers achieved a rate of correct plant identification greater than 70%, either alone or combined. The performance of all barcoding markers was noticeably low in few species-rich clades, such as the Laureae, and the Sapotaceae. A field test of the approach enabled us to detect 130 molecular operational taxonomic units in a sample of 252 juvenile trees. Including molecular markers increased the identification rate of juveniles from 72% (morphology alone) to 96% (morphology and molecular) of the individuals assigned to a known tree taxon. CONCLUSION/SIGNIFICANCE We conclude that while DNA barcoding is an invaluable tool for detecting errors in identifications and for identifying plants at juvenile stages, its limited ability to identify collections will constrain the practical implementation of DNA-based tropical plant biodiversity programs.
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Affiliation(s)
- Mailyn Adriana Gonzalez
- Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier and CNRS, UMR 5174, Toulouse, France
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Gonzalez MA, Baraloto C, Engel J, Mori SA, Pétronelli P, Riéra B, Roger A, Thébaud C, Chave J. Identification of Amazonian trees with DNA barcodes. PLoS One 2009; 4:e7483. [PMID: 19834612 PMCID: PMC2759516 DOI: 10.1371/journal.pone.0007483] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Accepted: 09/28/2009] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Large-scale plant diversity inventories are critical to develop informed conservation strategies. However, the workload required for classic taxonomic surveys remains high and is particularly problematic for megadiverse tropical forests. METHODOLOGY/PRINCIPAL FINDINGS Based on a comprehensive census of all trees in two hectares of a tropical forest in French Guiana, we examined whether plant DNA barcoding could contribute to increasing the quality and the pace of tropical plant biodiversity surveys. Of the eight plant DNA markers we tested (rbcLa, rpoC1, rpoB, matK, ycf5, trnL, psbA-trnH, ITS), matK and ITS had a low rate of sequencing success. More critically, none of the plastid markers achieved a rate of correct plant identification greater than 70%, either alone or combined. The performance of all barcoding markers was noticeably low in few species-rich clades, such as the Laureae, and the Sapotaceae. A field test of the approach enabled us to detect 130 molecular operational taxonomic units in a sample of 252 juvenile trees. Including molecular markers increased the identification rate of juveniles from 72% (morphology alone) to 96% (morphology and molecular) of the individuals assigned to a known tree taxon. CONCLUSION/SIGNIFICANCE We conclude that while DNA barcoding is an invaluable tool for detecting errors in identifications and for identifying plants at juvenile stages, its limited ability to identify collections will constrain the practical implementation of DNA-based tropical plant biodiversity programs.
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Affiliation(s)
- Mailyn Adriana Gonzalez
- Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier and CNRS, UMR 5174, Toulouse, France
| | | | - Julien Engel
- Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier and CNRS, UMR 5174, Toulouse, France
| | - Scott A. Mori
- Institute of Systematic Botany, New York Botanical Garden, Bronx, New York, United States of America
| | - Pascal Pétronelli
- CIRAD, UMR Ecologie des Forêts de Guyane, Kourou, French Guiana, France
| | - Bernard Riéra
- Laboratoire Fonctionnement, Evolution et Mécanismes Régulateurs des Ecosystèmes Forestiers, CNRS, UMR 5176, Brunoy, France
| | - Aurélien Roger
- Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier and CNRS, UMR 5174, Toulouse, France
| | - Christophe Thébaud
- Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier and CNRS, UMR 5174, Toulouse, France
| | - Jérôme Chave
- Laboratoire Evolution et Diversité Biologique, Université Paul Sabatier and CNRS, UMR 5174, Toulouse, France
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Norden N, Chave J, Belbenoit P, Caubère A, Châtelet P, Forget PM, Thébaud C. Mast fruiting is a frequent strategy in woody species of eastern South America. PLoS One 2007; 2:e1079. [PMID: 17957261 PMCID: PMC2031917 DOI: 10.1371/journal.pone.0001079] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2007] [Accepted: 09/28/2007] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND It is thought that mast seeding is a rare reproductive strategy in the tropics, since tropical climates are less variable, and fruit consumers tend to be more generalist in these regions. However, previous tests of this hypothesis were based on only few tropical datasets, and none from tropical South America. Moreover, reproductive strategies have been quantified based on the coefficient of variation of interannual seed production, an index that potentially confounds masting and high interannual variability in seed production. METHODOLOGY/PRINCIPAL FINDINGS We developed a new approach to model the monthly variability in seed production for 28 tree species, and 20 liana species monitored during 5 years in a tropical forest of Central French Guiana. We found that 23% of the species showed a masting pattern, 54% an annual fruiting pattern, and 23% an irregular fruiting pattern. The majority of masting species were trees (8 out of 11), most of them animal-dispersed. The classification into reproductive strategies based on the coefficient of variation was inconsistent with our results in nearly half of the cases. CONCLUSIONS/SIGNIFICANCE Our study is the first to clearly evidence the frequency of the masting strategy in a tropical forest community of Eastern South America. The commonness of the masting strategy in tropical plants may promote species coexistence through storage dynamics.
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Affiliation(s)
- Natalia Norden
- Laboratoire Evolution et Diversité Biologique, UMR 5174 Université Paul Sabatier/CNRS, Toulouse, France
| | - Jérôme Chave
- Laboratoire Evolution et Diversité Biologique, UMR 5174 Université Paul Sabatier/CNRS, Toulouse, France
- * To whom correspondence should be addressed. E-mail:
| | - Pierre Belbenoit
- Département Ecologie et Gestion de la Biodiversité, UMR 5176 CNRS-MNHN, Brunoy, France
| | - Adeline Caubère
- Département Ecologie et Gestion de la Biodiversité, UMR 5176 CNRS-MNHN, Brunoy, France
| | - Patrick Châtelet
- Station d'Etudes des Nouragues, CNRS Guyane UPS 2561, French Guiana, France
| | - Pierre-Michel Forget
- Département Ecologie et Gestion de la Biodiversité, UMR 5176 CNRS-MNHN, Brunoy, France
| | - Christophe Thébaud
- Laboratoire Evolution et Diversité Biologique, UMR 5174 Université Paul Sabatier/CNRS, Toulouse, France
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Ukizintambara T, White L, Abernethy K, Thébaud C. Gallery forests versus bosquets: conservation of natural fragments at Lopé National Park in central Gabon. Afr J Ecol 2007. [DOI: 10.1111/j.1365-2028.2007.00757.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Lee White
- Wildlife Conservation Society, B.P. 7847 Libreville, Gabon
| | - Kate Abernethy
- Wildlife Conservation Society, B.P. 7847 Libreville, Gabon
| | - Christophe Thébaud
- Applied Ecology and Conservation Programme, School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK
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Warren BH, Bermingham E, Prys-Jones RP, Thébaud C. Immigration, species radiation and extinction in a highly diverse songbird lineage: white-eyes on Indian Ocean islands. Mol Ecol 2006; 15:3769-86. [PMID: 17032273 DOI: 10.1111/j.1365-294x.2006.03058.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Molecular phylogenetic hypotheses of species-rich lineages in regions where geological history can be reliably inferred may provide insights into the scale of processes driving diversification. Here we sample all extant or recently extinct white-eye (Zosterops) taxa of the southwest Indian Ocean, combined with samples from all principal continental lineages. Results support a high dispersal capability, with at least two independent continental sources for white-eyes of the region. An early (within 1.8 million years ago) expansion into the Indian Ocean may have originated either from Asia or Africa; the three resulting lineages show a disparate distribution consistent with considerable extinction following their arrival. Africa is supported as the origin of a later expansion into the region (within 1.2 million years ago). On two islands, a pair of Zosterops species derived from independent immigrations into the Indian Ocean co-occur or may have formerly co-occurred, providing strong support for their origin by double-island colonization rather than within-island (sympatric or microallopatric) speciation. On Mauritius and La Réunion, phylogenetic placement of sympatric white-eyes allow us to rule out a scenario in which independent within-island speciation occurred on both islands; one of the species pairs must have arisen by double colonization, while the other pair is likely to have arisen by the same mechanism. Long-distance immigration therefore appears to be responsible for much of the region's white-eye diversity. Independent immigrations into the region have resulted in lineages with mutually exclusive distributions and it seems likely that competition with congeneric species, rather than arrival frequency, may limit present-day diversity.
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Affiliation(s)
- Ben H Warren
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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Abstract
To understand evolutionary paths connecting diverse biological forms, we defined a three-dimensional genotypic space separating two flower color morphs of Antirrhinum. A hybrid zone between morphs showed a steep cline specifically at genes controlling flower color differences, indicating that these loci are under selection. Antirrhinum species with diverse floral phenotypes formed a U-shaped cloud within the genotypic space. We propose that this cloud defines an evolutionary path that allows flower color to evolve while circumventing less-adaptive regions. Hybridization between morphs located in different arms of the U-shaped path yields low-fitness genotypes, accounting for the observed steep clines at hybrid zones.
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Affiliation(s)
- Annabel C Whibley
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK
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Langlade NB, Feng X, Dransfield T, Copsey L, Hanna AI, Thébaud C, Bangham A, Hudson A, Coen E. Evolution through genetically controlled allometry space. Proc Natl Acad Sci U S A 2005; 102:10221-6. [PMID: 16009935 PMCID: PMC1177394 DOI: 10.1073/pnas.0504210102] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Understanding evolutionary change requires phenotypic differences between organisms to be placed in a genetic context. However, there are few cases where it has been possible to define an appropriate genotypic space for a range of species. Here we address this problem by defining a genetically controlled space that captures variation in shape and size between closely related species of Antirrhinum. The axes of the space are based on an allometric model of leaves from an F2 of an interspecific cross between Antirrhinum majus and Antirrhinum charidemi. Three principal components were found to capture most of the genetic variation in shape and size, allowing a three-dimensional allometric space to be defined. The contribution of individual genetic loci was determined from QTL analysis, allowing each locus to be represented as a vector in the allometric space. Leaf shapes and sizes of 18 different Antirrhinum taxa, encompassing a broad range of leaf morphologies, could be accurately represented as clouds within the space. Most taxa overlapped with, or were near to, at least one other species in the space, so that together they defined a largely interconnected domain of viable forms. It is likely that the pattern of evolution within this domain reflects a combination of directional selection and evolutionary tradeoffs within a high dimensional space.
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Affiliation(s)
- Nicolas B Langlade
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, United Kingdom
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Warren BH, Bermingham E, Bowie RCK, Prys-Jones RP, Thébaud C. Molecular phylogeography reveals island colonization history and diversification of western Indian Ocean sunbirds (Nectarinia: Nectariniidae). Mol Phylogenet Evol 2003; 29:67-85. [PMID: 12967608 DOI: 10.1016/s1055-7903(03)00063-0] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We constructed a phylogenetic hypothesis for western Indian Ocean sunbirds (Nectarinia) and used this to investigate the geographic pattern of their diversification among the islands of the Indian Ocean. A total of 1309 bp of mitochondrial sequence data was collected from the island sunbird taxa of the western Indian Ocean region, combined with sequence data from a selection of continental (African and Asian) sunbirds. Topological and branch length information combined with estimated divergence times are used to present hypotheses for the direction and sequence of colonization events in relation to the geological history of the Indian Ocean region. Indian Ocean sunbirds fall into two well-supported clades, consistent with two independent colonizations from Africa within the last 3.9 million years. The first clade contains island populations representing the species Nectarinia notata, while the second includes Nectarinia souimanga, Nectarinia humbloti, Nectarinia dussumieri, and Nectarinia coquereli. With respect to the latter clade, application of Bremer's [Syst. Biol. 41 (1992) 436] ancestral areas method permits us to posit the Comoros archipelago as the point of initial colonization in the Indian Ocean. The subsequent expansion of the souimanga clade across its Indian Ocean range occurred rapidly, with descendants of this early expansion remaining on the Comoros and granitic Seychelles. The data suggest that a more recent expansion from Anjouan in the Comoros group led to the colonization of Madagascar by sunbirds representing the souimanga clade. In concordance with the very young geological age of the Aldabra group, the sunbirds of this archipelago have diverged little from the Madagascar population; this is attributed to colonization of the Aldabra archipelago in recent times, in one or possibly two or more waves originating from Madagascar. The overall pattern of sunbird radiation across Indian Ocean islands indicates that these birds disperse across ocean barriers with relative ease, but that their subsequent evolutionary success probably depends on a variety of factors including prior island occupation by competing species.
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Affiliation(s)
- Ben H Warren
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK.
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Blondel J, Perret P, Anstett MC, Thébaud C. Evolution of sexual size dimorphism in birds: test of hypotheses using blue tits in contrasted Mediterranean habitats. J Evol Biol 2002. [DOI: 10.1046/j.1420-9101.2002.00397.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Thébaud C, Johnston A. Plant responces to global changes in Co2: unfinished business? Trends Ecol Evol 1997; 12:425-6. [DOI: 10.1016/s0169-5347(97)01203-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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