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Femerling G, van Oosterhout C, Feng S, Bristol RM, Zhang G, Groombridge J, P Gilbert MT, Morales HE. Genetic Load and Adaptive Potential of a Recovered Avian Species that Narrowly Avoided Extinction. Mol Biol Evol 2023; 40:msad256. [PMID: 37995319 DOI: 10.1093/molbev/msad256] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 10/26/2023] [Accepted: 11/16/2023] [Indexed: 11/25/2023] Open
Abstract
High genetic diversity is a good predictor of long-term population viability, yet some species persevere despite having low genetic diversity. Here we study the genomic erosion of the Seychelles paradise flycatcher (Terpsiphone corvina), a species that narrowly avoided extinction after having declined to 28 individuals in the 1960s. The species recovered unassisted to over 250 individuals in the 1990s and was downlisted from Critically Endangered to Vulnerable in the International Union for the Conservation of Nature Red List in 2020. By comparing historical, prebottleneck (130+ years old) and modern genomes, we uncovered a 10-fold loss of genetic diversity. Highly deleterious mutations were partly purged during the bottleneck, but mildly deleterious mutations accumulated. The genome shows signs of historical inbreeding during the bottleneck in the 1960s, but low levels of recent inbreeding after demographic recovery. Computer simulations suggest that the species long-term small Ne reduced the masked genetic load and made the species more resilient to inbreeding and extinction. However, the reduction in genetic diversity due to the chronically small Ne and the severe bottleneck is likely to have reduced the species adaptive potential to face environmental change, which together with a higher load, compromises its long-term population viability. Thus, small ancestral Ne offers short-term bottleneck resilience but hampers long-term adaptability to environmental shifts. In light of rapid global rates of population decline, our work shows that species can continue to suffer the effect of their decline even after recovery, highlighting the importance of considering genomic erosion and computer modeling in conservation assessments.
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Affiliation(s)
- Georgette Femerling
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | - Shaohong Feng
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Rachel M Bristol
- Mahe, Seychelles
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - Guojie Zhang
- Center for Evolutionary & Organismal Biology, Zhejiang University School of Medicine, Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
- Innovation Center of Yangtze River Delta, Zhejiang University, Jiashan, China
| | - Jim Groombridge
- Division of Human and Social Sciences, Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, Kent, CT2 7NR, UK
| | - M Thomas P Gilbert
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Hernán E Morales
- Section for Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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Deepak V, Maddock ST, Williams R, Nagy ZT, Conradie W, Rocha S, James Harris D, Perera A, Gvoždík V, Doherty-Bone TM, Kamei RG, Menegon M, Labisko J, Morel C, Cooper N, Day JJ, Gower DJ. Molecular phylogenetics of sub-Saharan African natricine snakes, and the biogeographic origins of the Seychelles endemic Lycognathophis seychellensis. Mol Phylogenet Evol 2021; 161:107152. [PMID: 33741534 DOI: 10.1016/j.ympev.2021.107152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 03/08/2021] [Accepted: 03/08/2021] [Indexed: 10/21/2022]
Abstract
Phylogenetic relationships of sub-Saharan African natricine snakes are understudied and poorly understood, which in turn has precluded analyses of the historical biogeography of the Seychelles endemic Lycognathophis seychellensis. We inferred the phylogenetic relationships of Seychelles and mainland sub-Saharan natricines by analysing a multilocus DNA sequence dataset for three mitochondrial (mt) and four nuclear (nu) genes. The mainland sub-Saharan natricines and L. seychellensis comprise a well-supported clade. Two maximally supported sets of relationships within this clade are (Limnophis,Natriciteres) and (Afronatrix,(Hydraethiops,Helophis)). The relationships of L. seychellensis with respect to these two lineages are not clearly resolved by analysing concatenated mt and nu data. Analysed separately, nu data best support a sister relationship of L. seychellensis with (Afronatrix,(Hydraethiops,Helophis)) and mt data best support a sister relationship with all mainland sub-Saharan natricines. Methods designed to cope with incomplete lineage sorting strongly favour the former hypothesis. Genetic variation among up to 33 L. seychellensis from five Seychelles islands is low. Fossil calibrated divergence time estimates support an overseas dispersal of the L. seychellensis lineage to the Seychelles from mainland Africa ca. 43-25 million years before present (Ma), rather than this taxon being a Gondwanan relic.
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Affiliation(s)
- V Deepak
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK.
| | - Simon T Maddock
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK; School of Biology, Chemistry and Forensic Science, Wolverhampton University, WV1 1LY, UK; Island Biodiversity and Conservation Centre, University of Seychelles, Mahé, Seychelles
| | - Rhiannon Williams
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK; NRA Environmental Consultants, Cairns, Queensland 4870, Australia
| | | | - Werner Conradie
- Port Elizabeth Museum (Bayworld), Humewood, Port Elizabeth 6013, South Africa; Department of Nature Conservation Management, Natural Resource Science and Management Cluster, Faculty of Science, George Campus, Nelson Mandela University, George, South Africa
| | - Sara Rocha
- Biomedical Research Center (CINBIO), University of Vigo & Galicia Sur Health Institute, Vigo, Spain
| | - D James Harris
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, University of Porto, 4485-661 Vairão, Portugal
| | - Ana Perera
- CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, University of Porto, 4485-661 Vairão, Portugal
| | - Václav Gvoždík
- Institute of Vertebrate Biology of the Czech Academy of Sciences, Brno, Czech Republic; National Museum, Department of Zoology, Prague, Czech Republic
| | - Thomas M Doherty-Bone
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK; Conservation Programs, Royal Zoological Society of Scotland, Edinburgh EH12 6TL, UK
| | - Rachunliu G Kamei
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Michele Menegon
- Division of Biology & Conservation Ecology, Manchester Metropolitan University, UK; PAMS Foundation, P.O. Box 16556, Arusha, Tanzania
| | - Jim Labisko
- Island Biodiversity and Conservation Centre, University of Seychelles, Mahé, Seychelles; Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury CT2 7NR, UK; Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - Natalie Cooper
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK
| | - Julia J Day
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - David J Gower
- Department of Life Sciences, Natural History Museum, London SW7 5BD, UK; Island Biodiversity and Conservation Centre, University of Seychelles, Mahé, Seychelles
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The roles of vicariance and isolation by distance in shaping biotic diversification across an ancient archipelago: evidence from a Seychelles caecilian amphibian. BMC Evol Biol 2020; 20:110. [PMID: 32847507 PMCID: PMC7448330 DOI: 10.1186/s12862-020-01673-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 08/12/2020] [Indexed: 11/16/2022] Open
Abstract
Background Island systems offer excellent opportunities for studying the evolutionary histories of species by virtue of their restricted size and easily identifiable barriers to gene flow. However, most studies investigating evolutionary patterns and processes shaping biotic diversification have focused on more recent (emergent) rather than ancient oceanic archipelagos. Here, we focus on the granitic islands of the Seychelles, which are unusual among island systems because they have been isolated for a long time and are home to a monophyletic radiation of caecilian amphibians that has been separated from its extant sister lineage for ca. 65–62 Ma. We selected the most widespread Seychelles caecilian species, Hypogeophis rostratus, to investigate intraspecific morphological and genetic (mitochondrial and nuclear) variation across the archipelago (782 samples from nine islands) to identify patterns and test processes that shaped their evolutionary history within the Seychelles. Results Overall a signal of strong geographic structuring with distinct northern- and southern-island clusters were identified across all datasets. We suggest that these distinct groups have been isolated for ca. 1.26 Ma years without subsequent migration between them. Populations from the somewhat geographically isolated island of Frégate showed contrasting relationships to other islands based on genetic and morphological data, clustering alternatively with northern-island (genetic) and southern-island (morphological) populations. Conclusions Although variation in H. rostratus across the Seychelles is explained more by isolation-by-distance than by adaptation, the genetic-morphological incongruence for affinities of Frégate H. rostratus might be caused by local adaptation over-riding the signal from their vicariant history. Our findings highlight the need of integrative approaches to investigate fine-scale geographic structuring to uncover underlying diversity and to better understand evolutionary processes on ancient, continental islands.
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Mohan AV, Orozco-terWengel P, Shanker K, Vences M. The Andaman day gecko paradox: an ancient endemic without pronounced phylogeographic structure. Sci Rep 2020; 10:11745. [PMID: 32678130 PMCID: PMC7367275 DOI: 10.1038/s41598-020-68402-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 06/15/2020] [Indexed: 11/20/2022] Open
Abstract
The Andaman day gecko (Phelsuma andamanensis) is endemic to the Andaman Archipelago, located ~ 6000 km away from Madagascar where the genus Phelsuma likely evolved. We complemented existing phylogenetic data with additional markers to show that this species consistently branches off early in the evolution of the genus Phelsuma, and this early origin led us to hypothesize that island populations within the Andaman Archipelago could have further diversified. We sampled the Andaman day gecko from all major islands in the Andamans, developed new microsatellite markers and amplified mitochondrial markers to study population diversification. We detected high allelic diversity in microsatellites, but surprisingly poor geographical structuring. This study demonstrates that the Andaman day gecko has a panmictic population (K = 1), but with weak signals for two clusters that we name ‘North’ (North Andaman, Middle Andaman, Interview, Baratang, Neil, and Long Islands) and ‘South’ (Havelock, South Andaman, Little Andaman Islands). The mitochondrial COI gene uncovered wide haplotype sharing across islands with the presence of several private haplotypes (except for the Little Andaman Island, which only had an exclusive private haplotype) signalling ongoing admixture. This species differs from two other Andaman endemic geckos for which we provide comparative mitochondrial data, where haplotypes show a distinct phylogeographic structure. Testing population history scenarios for the Andaman day gecko using Approximate Bayesian Computation (ABC) supports two possible scenarios but fails to tease apart whether admixture or divergence produced the two weak clusters. Both scenarios agree that admixture and/or divergence prior to the onset of the last glacial maximum shaped the genetic diversity and structure detected in this study. ABC supports population expansion, possibly explained by anthropogenic food subsidies via plantations of cash crops, potentially coupled with human mediated dispersal resulting in the observed panmictic population. The Andaman day gecko may thus be a rare example of an island endemic reptile benefiting from habitat modification and increased movement in its native range.
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Affiliation(s)
- Ashwini V Mohan
- Department of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, 38106, Braunschweig, Germany. .,Centre for Ecological Sciences, Indian Institute of Science, Bangalore, 560012, India.
| | | | - Kartik Shanker
- Centre for Ecological Sciences, Indian Institute of Science, Bangalore, 560012, India
| | - Miguel Vences
- Department of Evolutionary Biology, Zoological Institute, Braunschweig University of Technology, 38106, Braunschweig, Germany
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Labisko J, Griffiths RA, Chong-Seng L, Bunbury N, Maddock ST, Bradfield KS, Taylor ML, Groombridge JJ. Endemic, endangered and evolutionarily significant: cryptic lineages in Seychelles’ frogs (Anura: Sooglossidae). Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/bly183] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jim Labisko
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
- Island Biodiversity and Conservation, Anse Royale, Mahé, Seychelles
| | - Richard A Griffiths
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | | | - Nancy Bunbury
- Seychelles Islands Foundation, Victoria, Mahé, Seychelles
- Centre for Ecology and Conservation, University of Exeter, UK
| | - Simon T Maddock
- Island Biodiversity and Conservation, Anse Royale, Mahé, Seychelles
- School of Biology, Chemistry and Forensic Science, Faculty of Science and Engineering, University of Wolverhampton, Wolverhampton, UK
- Department of Life Sciences, The Natural History Museum, London, UK
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | | | - Michelle L Taylor
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Jim J Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of Kent, Canterbury, UK
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Kurita T, Honda M, Toda M. Species delimitation and biogeography of the Ryukyu ground geckos, Goniurosaurus kuroiwaessp. (Squamata: Eublepharidae), by use of mitochondrial and nuclear DNA analyses. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Takaki Kurita
- Graduate School of Engineering and Science; University of the Ryukyus; Nishihara Okinawa Japan
| | - Masanao Honda
- Faculty of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki Japan
| | - Mamoru Toda
- Tropical Biosphere Research Center; University of the Ryukyus; Nishihara Okinawa Japan
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Santamaria CA, Bluemel JK, Bunbury N, Curran M. Cryptic biodiversity and phylogeographic patterns of Seychellois Ligia isopods. PeerJ 2017; 5:e3894. [PMID: 29018626 PMCID: PMC5633021 DOI: 10.7717/peerj.3894] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 09/15/2017] [Indexed: 12/02/2022] Open
Abstract
Ligia isopods are conspicuous inhabitants of rocky intertidal habitats exhibiting several biological traits that severely limit their dispersal potential. Their presence in patchy habitats and low vagility may lead to long term isolation, allopatric isolation and possible cryptic speciation. Indeed, various species of Ligia have been suggested to represent instead cryptic species complexes. Past studies; however, have largely focused in Eastern Pacific and Atlantic species of Ligia, leaving in doubt whether cryptic diversity occurs in other highly biodiverse areas. The Seychelles consists of 115 islands of different ages and geological origins spread across the western Indian Ocean. They are well known for their rich biodiversity with recent reports of cryptic species in terrestrial Seychellois organisms. Despite these studies, it is unclear whether coastal invertebrates from the Seychelles harbor any cryptic diversity. In this study, we examined patterns of genetic diversity and isolation within Ligia isopods across the Seychelles archipelago by characterizing individuals from locations across both inner and outer islands of the Seychelles using mitochondrial and nuclear markers. We report the presence of highly divergent lineages of independent origin. At Aldabra Atoll, we uncovered a lineage closely related to the Ligia vitiensis cryptic species complex. Within the inner islands of Cousine, Silhouette, and Mahé we detected the presence of two moderately divergent and geographically disjunct lineages most closely related to Ligia dentipes. Our findings suggest that the Seychelles may harbor at least three novel species of Ligia in need of description and that these species may have originated independently.
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Affiliation(s)
- Carlos A. Santamaria
- Biology Faculty, College of Science and Mathematics, University of South Florida Sarasota-Manatee, Sarasota, FL, United States of America
- Department of Biological Sciences, Sam Houston State University, Huntsville, TX, United States of America
| | - Joanna K. Bluemel
- Marine Conservation Society Seychelles, Mahé, Seychelles
- Lowestoft Laboratory, Centre for Environment, Fisheries and Aquaculture Science (CEFAS), Lowestoft, Suffolk, United Kingdom
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Oliver PM, Travers SL, Richmond JQ, Pikacha P, Fisher RN. At the end of the line: independent overwater colonizations of the Solomon Islands by a hyperdiverse trans-Wallacean lizard lineage (Cyrtodactylus: Gekkota: Squamata). Zool J Linn Soc 2017. [DOI: 10.1093/zoolinnean/zlx047] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Paul M Oliver
- Division of Ecology and Evolution, and Centre for Biodiversity Analysis, Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - Scott L Travers
- Department of Ecology and Evolutionary Biology; Biodiversity Institute, University of Kansas, Lawrence, KS, USA
| | | | - Patrick Pikacha
- Aquatic Research Group, School of Civil Engineering, University of Queensland, Brisbane, QLD, Australia
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Rocha S, Perera A, Bunbury N, Kaiser-Bunbury CN, Harris DJ. Speciation history and species-delimitation within the Seychelles Bronze geckos,Ailuronyxspp.: molecular and morphological evidence. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Sara Rocha
- Department of Biochemistry, Genetics and Immunology; University of Vigo; Campus Lagoas-Marcosende; 36310 Vigo Spain
| | - Ana Perera
- CIBIO-InBIO; Research Center in Biodiversity and Genetic Resources; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
| | - Nancy Bunbury
- Seychelles Islands Foundation; La Ciotat Building; Mont Fleuri PO Box 853 Victoria, Mahé Seychelles
| | | | - David J. Harris
- CIBIO-InBIO; Research Center in Biodiversity and Genetic Resources; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
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Rocha S, Perera A, Silva A, Posada D, Harris DJ. Evolutionary history ofTrachylepisskinks in the Seychelles islands: introgressive hybridization, morphological evolution and geographic structure. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12803] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sara Rocha
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
- Departamento de Bioquímica; Genética e Inmunología; Facultad de Biología; Universidad de Vigo; Vigo 36310 Spain
| | - Anna Perera
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
| | - Andreia Silva
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Rua do Campo Alegre FC4; 4169-007 Porto Portugal
| | - David Posada
- Departamento de Bioquímica; Genética e Inmunología; Facultad de Biología; Universidad de Vigo; Vigo 36310 Spain
| | - D. James Harris
- CIBIO; Centro de Investigação em Biodiversidade e Recursos Genéticos; Campus Agrário de Vairão; Rua Padre Armando Quintas; 4485-661 Vairão Portugal
- Departamento de Biologia; Faculdade de Ciências; Rua do Campo Alegre FC4; 4169-007 Porto Portugal
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Spurgin LG, Wright DJ, van der Velde M, Collar NJ, Komdeur J, Burke T, Richardson DS. Museum DNA reveals the demographic history of the endangered Seychelles warbler. Evol Appl 2014; 7:1134-43. [PMID: 25553073 PMCID: PMC4231601 DOI: 10.1111/eva.12191] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/30/2014] [Indexed: 01/10/2023] Open
Abstract
The importance of evolutionary conservation – how understanding evolutionary forces can help guide conservation decisions – is widely recognized. However, the historical demography of many endangered species is unknown, despite the fact that this can have important implications for contemporary ecological processes and for extinction risk. Here, we reconstruct the population history of the Seychelles warbler (Acrocephalus sechellensis) – an ecological model species. By the 1960s, this species was on the brink of extinction, but its previous history is unknown. We used DNA samples from contemporary and museum specimens spanning 140 years to reconstruct bottleneck history. We found a 25% reduction in genetic diversity between museum and contemporary populations, and strong genetic structure. Simulations indicate that the Seychelles warbler was bottlenecked from a large population, with an ancestral Ne of several thousands falling to <50 within the last century. Such a rapid decline, due to anthropogenic factors, has important implications for extinction risk in the Seychelles warbler, and our results will inform conservation practices. Reconstructing the population history of this species also allows us to better understand patterns of genetic diversity, inbreeding and promiscuity in the contemporary populations. Our approaches can be applied across species to test ecological hypotheses and inform conservation.
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Affiliation(s)
- Lewis G Spurgin
- School of Biological Sciences, University of East Anglia Norwich, Norfolk, UK ; Behavioural Ecology and Self-organization Group, Centre for Ecological and Evolutionary Studies, University of Groningen Groningen, The Netherlands
| | - David J Wright
- School of Biological Sciences, University of East Anglia Norwich, Norfolk, UK ; Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield Sheffield, UK
| | - Marco van der Velde
- Behavioural Ecology and Self-organization Group, Centre for Ecological and Evolutionary Studies, University of Groningen Groningen, The Netherlands
| | - Nigel J Collar
- School of Biological Sciences, University of East Anglia Norwich, Norfolk, UK ; BirdLife International Cambridge, UK
| | - Jan Komdeur
- Behavioural Ecology and Self-organization Group, Centre for Ecological and Evolutionary Studies, University of Groningen Groningen, The Netherlands
| | - Terry Burke
- Department of Animal and Plant Sciences, NERC Biomolecular Analysis Facility, University of Sheffield Sheffield, UK
| | - David S Richardson
- School of Biological Sciences, University of East Anglia Norwich, Norfolk, UK ; Nature Seychelles Roche Caiman, Mahé, Republic of Seychelles
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Abstract
This article reviews the various models that have been used to describe the relationships between gene trees and species trees. Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are tightly linked, they are seldom identical, because genes duplicate, are lost or horizontally transferred, and because alleles can coexist in populations for periods that may span several speciation events. Building models describing the relationship between gene and species trees can thus improve the reconstruction of gene trees when a species tree is known, and vice versa. Several approaches have been proposed to solve the problem in one direction or the other, but in general neither gene trees nor species trees are known. Only a few studies have attempted to jointly infer gene trees and species trees. These models account for gene duplication and loss, transfer or incomplete lineage sorting. Some of them consider several types of events together, but none exists currently that considers the full repertoire of processes that generate gene trees along the species tree. Simulations as well as empirical studies on genomic data show that combining gene tree-species tree models with models of sequence evolution improves gene tree reconstruction. In turn, these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences. We predict that gene tree-species tree methods that can deal with genomic data sets will be instrumental to advancing our understanding of genomic evolution.
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Affiliation(s)
- Gergely J Szöllősi
- ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France
| | - Eric Tannier
- ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France; ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France; ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France
| | - Vincent Daubin
- ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France; ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France
| | - Bastien Boussau
- ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France; ELTE-MTA "Lendület" Biophysics Research Group, Pázmány P. stny. 1A., 1117 Budapest, Hungary; Laboratoire de Biométrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5558, Université Lyon 1, F-69622 Villeurbanne, France; Université de Lyon, F-69000 Lyon, France; and Institut National de Recherche en Informatique et en Automatique Rhône-Alpes, F-38334 Montbonnot, France;
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13
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High risks of losing genetic diversity in an endemic Mauritian gecko: implications for conservation. PLoS One 2014; 9:e93387. [PMID: 24963708 PMCID: PMC4070904 DOI: 10.1371/journal.pone.0093387] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 03/05/2014] [Indexed: 02/01/2023] Open
Abstract
Genetic structure can be a consequence of recent population fragmentation and isolation, or a remnant of historical localised adaptation. This poses a challenge for conservationists since misinterpreting patterns of genetic structure may lead to inappropriate management. Of 17 species of reptile originally found in Mauritius, only five survive on the main island. One of these, Phelsuma guimbeaui (lowland forest day gecko), is now restricted to 30 small isolated subpopulations following severe forest fragmentation and isolation due to human colonisation. We used 20 microsatellites in ten subpopulations and two mitochondrial DNA (mtDNA) markers in 13 subpopulations to: (i) assess genetic diversity, population structure and genetic differentiation of subpopulations; (ii) estimate effective population sizes and migration rates of subpopulations; and (iii) examine the phylogenetic relationships of haplotypes found in different subpopulations. Microsatellite data revealed significant population structure with high levels of genetic diversity and isolation by distance, substantial genetic differentiation and no migration between most subpopulations. MtDNA, however, showed no evidence of population structure, indicating that there was once a genetically panmictic population. Effective population sizes of ten subpopulations, based on microsatellite markers, were small, ranging from 44 to 167. Simulations suggested that the chance of survival and allelic diversity of some subpopulations will decrease dramatically over the next 50 years if no migration occurs. Our DNA-based evidence reveals an urgent need for a management plan for the conservation of P. guimbeaui. We identified 18 threatened and 12 viable subpopulations and discuss a range of management options that include translocation of threatened subpopulations to retain maximum allelic diversity, and habitat restoration and assisted migration to decrease genetic erosion and inbreeding for the viable subpopulations.
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Maddock ST, Day JJ, Nussbaum RA, Wilkinson M, Gower DJ. Evolutionary origins and genetic variation of the Seychelles treefrog, Tachycnemis seychellensis (Duméril and Bibron, 1841) (Amphibia: Anura: Hyperoliidae). Mol Phylogenet Evol 2014; 75:194-201. [PMID: 24555995 PMCID: PMC4101239 DOI: 10.1016/j.ympev.2014.02.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 02/06/2014] [Accepted: 02/08/2014] [Indexed: 11/30/2022]
Abstract
The hyperoliid frog Tachycnemis seychellensis, the only species of its genus, is endemic to the four largest granitic islands of the Seychelles archipelago and is reliant on freshwater bodies for reproduction. Its presence in the Seychelles is thought to be the product of a transoceanic dispersal, diverging from the genus Heterixalus, its closest living relative (currently endemic to Madagascar), between approximately 10-35Ma. A previous study documented substantial intraspecific morphological variation among island populations and also among populations within the largest island (Mahé). To assess intraspecific genetic variation and to infer the closest living relative(s) of T. seychellensis, DNA sequence data were generated for three mitochondrial and four nuclear markers. These data support a sister-group relationship between T. seychellensis and Heterixalus, with the divergence between the two occurring between approximately 11-19Ma based on cytb p-distances. Low levels of genetic variation were found among major mitochondrial haplotype clades of T. seychellensis (maximum 0.7% p-distance concatenated mtDNA), and samples from each of the islands (except La Digue) comprised multiple mitochondrial haplotype clades. Two nuclear genes (rag1 and tyr) showed no variation, and the other two (rho and pomc) lacked any notable geographic structuring, counter to patterns observed within presumably more vagile Seychelles taxa such as lizards. The low levels of genetic variation and phylogeographic structure support an interpretation that there is a single but morphologically highly variable species of Seychelles treefrog. The contrasting genetic and morphological intraspecific variation may be attributable to relatively recent admixture during low sea-level stands, ecophenotypic plasticity, local adaptation to different environmental conditions, and/or current and previously small population sizes. Low genetic phylogeographic structure but substantial morphological variation is unusual within anurans.
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Affiliation(s)
- Simon T Maddock
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK.
| | - Julia J Day
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Ronald A Nussbaum
- Museum of Zoology and Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109-1079, USA
| | - Mark Wilkinson
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK; Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
| | - David J Gower
- Department of Life Sciences, The Natural History Museum, London SW7 5BD, UK
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15
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Engelhardt KAM, Ritchie ME, Powell JA. Body size mediated coexistence in swans. ScientificWorldJournal 2014; 2014:643694. [PMID: 24672347 PMCID: PMC3932214 DOI: 10.1155/2014/643694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 10/24/2013] [Indexed: 11/22/2022] Open
Abstract
Differences in body sizes may create a trade-off between foraging efficiency (foraging gains/costs) and access to resources. Such a trade-off provides a potential mechanism for ecologically similar species to coexist on one resource. We explored this hypothesis for tundra (Cygnus columbianus) and trumpeter swans (Cygnus buccinator), a federally protected species, feeding solely on sago pondweed (Stuckenia pectinata) tubers during fall staging and wintering in northern Utah. Foraging efficiency was higher for tundra swans because this species experienced lower foraging and metabolic costs relative to foraging gains; however, trumpeter swans (a) had longer necks and therefore had access to exclusive resources buried deep in wetland sediments and (b) were more aggressive and could therefore displace tundra swans from lucrative foraging locations. We conclude that body size differentiation is an important feature of coexistence among ecologically similar species feeding on one resource. In situations where resources are limiting and competition for resources is strong, conservation managers will need to consider the trade-off between foraging efficiency and access to resources to ensure ecologically similar species can coexist on a shared resource.
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Affiliation(s)
- Katharina A. M. Engelhardt
- Appalachian Laboratory, University of Maryland Center for Environmental Science, Frostburg, MD 21532-2307, USA
| | - Mark E. Ritchie
- Department of Biology, Syracuse University, Syracuse, NY 13244-1270, USA
| | - James A. Powell
- Department of Mathematics and Statistics, Utah State University, Logan, UT 84322-3900, USA
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Valente J, Rocha S, Harris DJ. Differentiation within the endemic burrowing skink Pamelaescincus gardineri, across the Seychelles islands, assessed by mitochondrial and nuclear markers. AFR J HERPETOL 2013. [DOI: 10.1080/21564574.2013.856354] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Joana Valente
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Universidade do Porto, Porto, Portugal
| | - Sara Rocha
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Universidade do Porto, Vairão, Portugal
- Departamento de Bioquímica, Genética e Inmunología, Universidad de Vigo, Vigo, Spain
| | - D. James Harris
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO), Universidade do Porto, Vairão, Portugal
- Departamento de Biologia, Universidade do Porto, Porto, Portugal
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