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Colella JP, Frederick LM, Talbot SL, Cook JA. Extrinsically reinforced hybrid speciation within Holarctic ermine (
Mustela
spp.) produces an insular endemic. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Jocelyn P. Colella
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
- Biodiversity Institute University of Kansas Lawrence KS USA
| | - Lindsey M. Frederick
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
- New Mexico Museum of Natural History and Science Albuquerque NM USA
| | | | - Joseph A. Cook
- Department of Biology and Museum of Southwestern Biology University of New Mexico Albuquerque NM USA
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2
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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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3
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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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Weinell JL, Branch WR, Colston TJ, Jackman TR, Kuhn A, Conradie W, Bauer AM. A species-level phylogeny of Trachylepis (Scincidae: Mabuyinae) provides insight into their reproductive mode evolution. Mol Phylogenet Evol 2019; 136:183-195. [DOI: 10.1016/j.ympev.2019.04.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/24/2019] [Accepted: 04/01/2019] [Indexed: 10/27/2022]
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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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Mekonnen A, Rueness EK, Stenseth NC, Fashing PJ, Bekele A, Hernandez-Aguilar RA, Missbach R, Haus T, Zinner D, Roos C. Population genetic structure and evolutionary history of Bale monkeys (Chlorocebus djamdjamensis) in the southern Ethiopian Highlands. BMC Evol Biol 2018; 18:106. [PMID: 29986642 PMCID: PMC6038355 DOI: 10.1186/s12862-018-1217-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 06/13/2018] [Indexed: 12/31/2022] Open
Abstract
Background Species with a restricted geographic distribution, and highly specialized habitat and dietary requirements, are particularly vulnerable to extinction. The Bale monkey (Chlorocebus djamdjamensis) is a little-known arboreal, bamboo-specialist primate endemic to the southern Ethiopian Highlands. While most Bale monkeys inhabit montane forests dominated by bamboo, some occupy forest fragments where bamboo is much less abundant. We used mitochondrial DNA (mtDNA) sequences to analyse the genetic structure and evolutionary history of Bale monkeys covering the majority of their remaining distribution range. We analysed 119 faecal samples from their two main habitats, continuous forest (CF) and fragmented forests (FF), and sequenced 735 bp of the hypervariable region I (HVI) of the control region. We added 12 orthologous sequences from congeneric vervets (C. pygerythrus) and grivets (C. aethiops) as well as animals identified as hybrids, previously collected in southern Ethiopia. Results We found strong genetic differentiation (with no shared mtDNA haplotypes) between Bale monkey populations from CF and FF. Phylogenetic analyses revealed two distinct and highly diverged clades: a Bale monkey clade containing only Bale monkeys from CF and a green monkey clade where Bale monkeys from FF cluster with grivets and vervets. Analyses of demographic history revealed that Bale monkey populations (CF and FF) have had stable population sizes over an extended period, but have all recently experienced population declines. Conclusions The pronounced genetic structure and deep mtDNA divergence between Bale monkey populations inhabiting CF and FF are likely to be the results of hybridization and introgression of the FF population with parapatric Chlorocebus species, in contrast to the CF population, which was most likely not impacted by hybridization. Hybridization in the FF population was probably enhanced by an alteration of the bamboo forest habitat towards a more open woodland habitat, which enabled the parapatric Chlorocebus species to invade the Bale monkey's range and introgress the FF population. We therefore propose that the CF and FF Bale monkey populations should be managed as separate units when developing conservation strategies for this threatened species. Electronic supplementary material The online version of this article (10.1186/s12862-018-1217-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Addisu Mekonnen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway. .,Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia.
| | - Eli K Rueness
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - Nils Chr Stenseth
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway.,Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia
| | - Peter J Fashing
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway.,Department of Anthropology and Environmental Studies Program, California State University Fullerton, Fullerton, CA, 92834, USA
| | - Afework Bekele
- Department of Zoological Sciences, Addis Ababa University, P.O. Box: 1176, Addis Ababa, Ethiopia
| | - R Adriana Hernandez-Aguilar
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, N-0316, Oslo, Norway
| | - Rose Missbach
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Tanja Haus
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
| | - Christian Roos
- Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany.,Gene Bank of Primates, German Primate Center, Leibniz Institute for Primate Research, Göttingen, Germany
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Weigand H, Leese F. Detecting signatures of positive selection in non-model species using genomic data. Zool J Linn Soc 2018. [DOI: 10.1093/zoolinnean/zly007] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Hannah Weigand
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg-Essen, Universitätsstraße, Essen, Germany
- Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Universitätsstraße, Essen, Germany
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Mclean AJ, Joseph L, Toon A, Schmidt DJ, Drew A, Mason IJ, Hughes JM. Reassessment of a possible case of intraspecific gene flow across Australia’s Great Dividing Range in the variegated fairy wren, Malurus lamberti (Aves: Maluridae), and its systematic consequences. Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx054] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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