551
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Percino-Daniel R, Recuero E, Vázquez-Domínguez E, Zamudio KR, Parra-Olea G. All grown-up and nowhere to go: paedomorphosis and local adaptation inAmbystomasalamanders in the Cuenca Oriental of Mexico. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12750] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Ruth Percino-Daniel
- Instituto de Biología; Universidad Nacional Autónoma de México; AP 70-153 Circuito Exterior Ciudad Universitaria México DF CP 04510 México
| | - Ernesto Recuero
- Departamento de Ecología de la Biodiversidad; Instituto de Ecología; Universidad Nacional Autónoma de México; Ap. Postal 70-275 Ciudad Universitaria México DF 04510 México
| | - Ella Vázquez-Domínguez
- Departamento de Ecología de la Biodiversidad; Instituto de Ecología; Universidad Nacional Autónoma de México; Ap. Postal 70-275 Ciudad Universitaria México DF 04510 México
| | - Kelly R. Zamudio
- Department of Ecology and Evolutionary Biology; Cornell University; Ithaca NY 14853 USA
| | - Gabriela Parra-Olea
- Instituto de Biología; Universidad Nacional Autónoma de México; AP 70-153 Circuito Exterior Ciudad Universitaria México DF CP 04510 México
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552
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Zinck JWR, Rajora OP. Post-glacial phylogeography and evolution of a wide-ranging highly-exploited keystone forest tree, eastern white pine (Pinus strobus) in North America: single refugium, multiple routes. BMC Evol Biol 2016; 16:56. [PMID: 26936598 PMCID: PMC4774161 DOI: 10.1186/s12862-016-0624-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/16/2016] [Indexed: 01/28/2023] Open
Abstract
Background Knowledge of the historical distribution and postglacial phylogeography and evolution of a species is important to better understand its current distribution and population structure and potential fate in the future, especially under climate change conditions, and conservation of its genetic resources. We have addressed this issue in a wide-ranging and heavily exploited keystone forest tree species of eastern North America, eastern white pine (Pinus strobus). We examined the range-wide population genetic structure, tested various hypothetical population history and evolutionary scenarios and inferred the location of glacial refugium and post-glacial recolonization routes. Our hypothesis was that eastern white pine survived in a single glacial refugium and expanded through multiple post-glacial recolonization routes. Results We studied the range-wide genetic diversity and population structure of 33 eastern white pine populations using 12 nuclear and 3 chloroplast microsatellite DNA markers. We used Approximate Bayesian Computation approach to test various evolutionary scenarios. We observed high levels of genetic diversity, and significant genetic differentiation (FST = 0.104) and population structure among eastern white pine populations across its range. A south to north trend of declining genetic diversity existed, consistent with repeated founder effects during post-glaciation migration northwards. We observed broad consensus from nuclear and chloroplast genetic markers supporting the presence of two main post-glacial recolonization routes that originated from a single southern refugium in the mid-Atlantic plain. One route gave rise to populations at the western margin of the species’ range in Minnesota and western Ontario. The second route gave rise to central-eastern populations, which branched into two subgroups: central and eastern. We observed minimal sharing of chloroplast haplotypes between recolonization routes but there was evidence of admixture between the western and west-central populations. Conclusions Our study reveals a single southern refugium, two recolonization routes and three genetically distinguishable lineages in eastern white pine that we suggest to be treated as separate Evolutionarily Significant Units. Like many wide-ranging North American species, eastern white pine retains the genetic signatures of post-glacial recolonization and evolution, and its contemporary population genetic structure reflects not just the modern distribution and effects of heavy exploitation but also routes northward from its glacial refugium. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0624-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John W R Zinck
- Faculty of Forestry and Environmental Management, University of New Brunswick, 28 Dineen Drive, Fredericton, NB, E3B 5A3, Canada. .,Present address: Athletigen Technologies Inc., 535 Legget Drive, Kanata, ON, K2K 3B8, Canada.
| | - Om P Rajora
- Faculty of Forestry and Environmental Management, University of New Brunswick, 28 Dineen Drive, Fredericton, NB, E3B 5A3, Canada.
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553
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Bai WN, Wang WT, Zhang DY. Phylogeographic breaks within Asian butternuts indicate the existence of a phytogeographic divide in East Asia. THE NEW PHYTOLOGIST 2016; 209:1757-72. [PMID: 26499508 DOI: 10.1111/nph.13711] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 09/15/2015] [Indexed: 05/16/2023]
Abstract
East Asia has been hypothesized to be subdivided into two distinct northern and southern areas, separated by a band of dry climate that was far more severe in the early Tertiary but still exists today. However, this biogeographic hypothesis has rarely been tested using a molecular phylogeographic approach. We genotyped 70 populations throughout the distributional range of Asian butternuts (Juglans section Cardiocaryon) using eight chloroplast DNA regions, one single-copy nuclear gene, and 17 nuclear microsatellite loci, supplemented with paleodistribution modeling of the major genetic clades. The genetic data consistently identified two clades, one northern, comprising Juglans mandshurica and Juglans ailantifolia, and one southern, comprising Juglans cathayensis. The two clades diverged through climate-induced vicariance of an ancestral northern range during the mid-Miocene and remained mostly separate thereafter, with geographical isolation of the Japanese Islands and refugial isolation or secondary contacts in the late Pleistocene producing further subdivision within the northern clade. But beyond all that, we also discovered a role of environmental adaptation in maintaining and/or reinforcing the north-south divergence. Asian butternuts offer a strong case for the existence of a biogeographic divide between the northern and southern parts of East Asia during the Neogene and into the Pleistocene.
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Affiliation(s)
- Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Wen-Ting Wang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
- School of Mathematics and Computer Science, Northwest University for Nationalities, Lanzhou, 730030, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
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554
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Taerum SJ, Konečný A, de Beer ZW, Cibrián-Tovar D, Wingfield MJ. Population genetics and symbiont assemblages support opposing invasion scenarios for the red turpentine beetle (Dendroctonus valens). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12781] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Stephen J. Taerum
- Department of Genetics; Forestry and Agricultural Biotechnology Institute (FABI); University of Pretoria; Pretoria 0002 South Africa
| | - Adam Konečný
- Department of Botany and Zoology; Faculty of Science; Masaryk University; Kotlářská 2 Brno 61137 Czech Republic
| | - Z. Wilhelm de Beer
- Department of Microbiology and Plant Pathology; Forestry and Agricultural Biotechnology Institute (FABI); University of Pretoria; Pretoria 0002 South Africa
| | - David Cibrián-Tovar
- División de Ciencias Forestales; Universidad Autónoma Chapingo; Km 38.5 Carretera México-Texcoco Chapingo Estado de México México
| | - Michael J. Wingfield
- Department of Genetics; Forestry and Agricultural Biotechnology Institute (FABI); University of Pretoria; Pretoria 0002 South Africa
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555
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Glotzbecker GJ, Alda F, Broughton RE, Neely DA, Mayden RL, Blum MJ. Geographic independence and phylogenetic diversity of red shiner introductions. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0822-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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556
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Attard CRM, Beheregaray LB, Jenner KCS, Gill PC, Jenner MNM, Morrice MG, Teske PR, Möller LM. Low genetic diversity in pygmy blue whales is due to climate-induced diversification rather than anthropogenic impacts. Biol Lett 2016; 11:20141037. [PMID: 25948571 DOI: 10.1098/rsbl.2014.1037] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Unusually low genetic diversity can be a warning of an urgent need to mitigate causative anthropogenic activities. However, current low levels of genetic diversity in a population could also be due to natural historical events, including recent evolutionary divergence, or long-term persistence at a small population size. Here, we determine whether the relatively low genetic diversity of pygmy blue whales (Balaenoptera musculus brevicauda) in Australia is due to natural causes or overexploitation. We apply recently developed analytical approaches in the largest genetic dataset ever compiled to study blue whales (297 samples collected after whaling and representing lineages from Australia, Antarctica and Chile). We find that low levels of genetic diversity in Australia are due to a natural founder event from Antarctic blue whales (Balaenoptera musculus intermedia) that occurred around the Last Glacial Maximum, followed by evolutionary divergence. Historical climate change has therefore driven the evolution of blue whales into genetically, phenotypically and behaviourally distinct lineages that will likely be influenced by future climate change.
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Affiliation(s)
- Catherine R M Attard
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Luciano B Beheregaray
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
| | - K Curt S Jenner
- Centre for Whale Research, PO Box 1622, Fremantle, Western Australia 6959, Australia
| | - Peter C Gill
- Blue Whale Study, C/- Post Office, Narrawong, Victoria 3285, Australia School of Life and Environmental Sciences, Deakin University, PO Box 423, Warrnambool, Victoria 3280, Australia
| | | | - Margaret G Morrice
- School of Life and Environmental Sciences, Deakin University, PO Box 423, Warrnambool, Victoria 3280, Australia
| | - Peter R Teske
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia Molecular Zoology Laboratory (Aquatic Division), Department of Zoology, University of Johannesburg, Auckland Park 2006, South Africa
| | - Luciana M Möller
- School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, South Australia 5001, Australia
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557
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Klütsch CFC, Manseau M, Trim V, Polfus J, Wilson PJ. The eastern migratory caribou: the role of genetic introgression in ecotype evolution. ROYAL SOCIETY OPEN SCIENCE 2016; 3:150469. [PMID: 26998320 PMCID: PMC4785971 DOI: 10.1098/rsos.150469] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 01/06/2016] [Indexed: 06/05/2023]
Abstract
Understanding the evolutionary history of contemporary animal groups is essential for conservation and management of endangered species like caribou (Rangifer tarandus). In central Canada, the ranges of two caribou subspecies (barren-ground/woodland caribou) and two woodland caribou ecotypes (boreal/eastern migratory) overlap. Our objectives were to reconstruct the evolutionary history of the eastern migratory ecotype and to assess the potential role of introgression in ecotype evolution. STRUCTURE analyses identified five higher order groups (i.e. three boreal caribou populations, eastern migratory ecotype and barren-ground). The evolutionary history of the eastern migratory ecotype was best explained by an early genetic introgression from barren-ground into a woodland caribou lineage during the Late Pleistocene and subsequent divergence of the eastern migratory ecotype during the Holocene. These results are consistent with the retreat of the Laurentide ice sheet and the colonization of the Hudson Bay coastal areas subsequent to the establishment of forest tundra vegetation approximately 7000 years ago. This historical reconstruction of the eastern migratory ecotype further supports its current classification as a conservation unit, specifically a Designatable Unit, under Canada's Species at Risk Act. These findings have implications for other sub-specific contact zones for caribou and other North American species in conservation unit delineation.
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Affiliation(s)
| | - Micheline Manseau
- Protected Areas Establishment and Conservation Directorate, Parks Canada, Gatineau, Quebec, Canada J8X 0B3
- Natural Resources Institute, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Vicki Trim
- Manitoba Conservation and Water Stewardship, PO Box 28, 59 Elizabeth Drive, Thompson, Manitoba, Canada R8N 1X4
| | - Jean Polfus
- Natural Resources Institute, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Paul J. Wilson
- Biology Department, Trent University, Peterborough, Ontario, Canada K9J 7B8
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558
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Wrange AL, Charrier G, Thonig A, Alm Rosenblad M, Blomberg A, Havenhand JN, Jonsson PR, André C. The Story of a Hitchhiker: Population Genetic Patterns in the Invasive Barnacle Balanus(Amphibalanus) improvisus Darwin 1854. PLoS One 2016; 11:e0147082. [PMID: 26821161 PMCID: PMC4731558 DOI: 10.1371/journal.pone.0147082] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 12/27/2015] [Indexed: 11/17/2022] Open
Abstract
Understanding the ecological and evolutionary forces that determine the genetic structure and spread of invasive species is a key component of invasion biology. The bay barnacle, Balanus improvisus (= Amphibalanus improvisus), is one of the most successful aquatic invaders worldwide, and is characterised by broad environmental tolerance. Although the species can spread through natural larval dispersal, human-mediated transport through (primarily) shipping has almost certainly contributed to the current global distribution of this species. Despite its worldwide distribution, little is known about the phylogeography of this species. Here, we characterize the population genetic structure and model dispersal dynamics of the barnacle B. improvisus, and describe how human-mediated spreading via shipping as well as natural larval dispersal may have contributed to observed genetic variation. We used both mitochondrial DNA (cytochrome c oxidase subunit I: COI) and nuclear microsatellites to characterize the genetic structure in 14 populations of B. improvisus on a global and regional scale (Baltic Sea). Genetic diversity was high in most populations, and many haplotypes were shared among populations on a global scale, indicating that long-distance dispersal (presumably through shipping and other anthropogenic activities) has played an important role in shaping the population genetic structure of this cosmopolitan species. We could not clearly confirm prior claims that B. improvisus originates from the western margins of the Atlantic coasts; although there were indications that Argentina could be part of a native region. In addition to dispersal via shipping, we show that natural larval dispersal may play an important role for further colonisation following initial introduction.
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Affiliation(s)
- Anna-Lisa Wrange
- University of Gothenburg, Department of Marine Sciences-Tjärnö, Sweden
| | - Gregory Charrier
- Institut Universitaire Européen de la Mer (IUEM), Technopôle Brest-Iroise, Plouzané, France
| | - Anne Thonig
- Roskilde University, Department of Environmental, Social and Spatial Change, Roskilde, Denmark
| | - Magnus Alm Rosenblad
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, Sweden
| | - Anders Blomberg
- University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, Sweden
| | | | - Per R Jonsson
- University of Gothenburg, Department of Marine Sciences-Tjärnö, Sweden
| | - Carl André
- University of Gothenburg, Department of Marine Sciences-Tjärnö, Sweden
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559
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Ornelas JF, González C, Hernández-Baños BE, García-Moreno J. Molecular and iridescent feather reflectance data reveal recent genetic diversification and phenotypic differentiation in a cloud forest hummingbird. Ecol Evol 2016; 6:1104-27. [PMID: 26811749 PMCID: PMC4722824 DOI: 10.1002/ece3.1950] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/14/2015] [Accepted: 12/15/2015] [Indexed: 01/31/2023] Open
Abstract
The present day distribution and spatial genetic diversity of Mesoamerican biota reflects a long history of responses to habitat change. The hummingbird Lampornis amethystinus is distributed in northern Mesoamerica, with geographically disjunct populations. Based on sampling across the species range using mitochondrial DNA (mtDNA) sequences and nuclear microsatellites jointly analysed with phenotypic and climatic data, we (1) test whether the fragmented distribution is correlated with main evolutionary lineages, (2) assess body size and plumage color differentiation of populations in geographic isolation, and (3) evaluate a set of divergence scenarios and demographic patterns of the hummingbird populations. Analysis of genetic variation revealed four main groups: blue‐throated populations (Sierra Madre del Sur); two groups of amethyst‐throated populations (Trans‐Mexican Volcanic Belt and Sierra Madre Oriental); and populations east of the Isthmus of Tehuantepec (IT) with males showing an amethyst throat. The most basal split is estimated to have originated in the Pleistocene, 2.39–0.57 million years ago (MYA), and corresponded to groups of populations separated by the IT. However, the estimated recent divergence time between blue‐ and amethyst‐throated populations does not correspond to the 2‐MY needed to be in isolation for substantial plumage divergence, likely because structurally iridescent colors are more malleable than others. Results of species distribution modeling and Approximate Bayesian Computation analysis fit a model of lineage divergence west of the Isthmus after the Last Glacial Maximum (LGM), and that the species’ suitable habitat was disjunct during past and current conditions. These results challenge the generality of the contraction/expansion glacial model to cloud forest‐interior species and urges management of cloud forest, a highly vulnerable ecosystem to climate change and currently facing destruction, to prevent further loss of genetic diversity or extinction.
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Affiliation(s)
- Juan Francisco Ornelas
- Departamento de Biología Evolutiva Instituto de Ecología AC (INECOL) Xalapa Veracruz 91070 Mexico
| | - Clementina González
- Departamento de Biología Evolutiva Instituto de Ecología AC (INECOL) Xalapa Veracruz 91070 Mexico; Instituto de Investigaciones sobre los Recursos Naturales Universidad Michoacana de San Nicolás de Hidalgo Morelia Michoacán Mexico
| | - Blanca E Hernández-Baños
- Museo de Zoología Departamento de Biología Evolutiva Facultad de Ciencias Universidad Nacional Autónoma de México México DF 04510 Mexico
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560
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Gargan LM, Cornette R, Yearsley JM, Montgomery WI, Paupério J, Alves PC, Butler F, Pascal M, Tresset A, Herrel A, Lusby J, Tosh DG, Searle JB, McDevitt AD. Molecular and morphological insights into the origin of the invasive greater white-toothed shrew (Crocidura russula) in Ireland. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1056-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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561
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Piertney SB, Black A, Watt L, Christie D, Poncet S, Collins MA. Resolving patterns of population genetic and phylogeographic structure to inform control and eradication initiatives for brown ratsRattus norvegicuson South Georgia. J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12589] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stuart B. Piertney
- Institute of Biological and Environmental Sciences; University of Aberdeen; Zoology Building, Tillydrone Avenue Aberdeen AB24 2TZ UK
| | - Andy Black
- Government of South Georgia & South Sandwich Islands; Government House Stanley Falkland Islands
| | - Laura Watt
- Institute of Biological and Environmental Sciences; University of Aberdeen; Zoology Building, Tillydrone Avenue Aberdeen AB24 2TZ UK
| | - Darren Christie
- Government of South Georgia & South Sandwich Islands; Government House Stanley Falkland Islands
| | - Sally Poncet
- Government of South Georgia & South Sandwich Islands; Government House Stanley Falkland Islands
| | - Martin A. Collins
- Government of South Georgia & South Sandwich Islands; Government House Stanley Falkland Islands
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562
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Feng L, Zheng QJ, Qian ZQ, Yang J, Zhang YP, Li ZH, Zhao GF. Genetic Structure and Evolutionary History of Three Alpine Sclerophyllous Oaks in East Himalaya-Hengduan Mountains and Adjacent Regions. FRONTIERS IN PLANT SCIENCE 2016. [PMID: 27891142 DOI: 10.3389/fgls.2016.01688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The East Himalaya-Hengduan Mountains (EH-HM) region has a high biodiversity and harbors numerous endemic alpine plants. This is probably the result of combined orographic and climate oscillations occurring since late Tertiary. Here, we determined the genetic structure and evolutionary history of alpine oak species (including Quercus spinosa, Quercus aquifolioides, and Quercus rehderiana) using both cytoplasmic-nuclear markers and ecological niche models (ENMs), and elucidated the impacts of climate oscillations and environmental heterogeneity on their population demography. Our results indicate there were mixed genetic structure and asymmetric contemporary gene flow within them. The ENMs revealed a similar demographic history for the three species expanded their ranges from the last interglacial (LIG) to the last glacial maximum (LGM), which was consistent with effective population sizes changes. Effects of genetic drift and fragmentation of habitats were responsible for the high differentiation and the lack of phylogeographic structure. Our results support that geological and climatic factors since Miocene triggered the differentiation, evolutionary origin and range shifts of the three oak species in the studied area and also emphasize that a multidisciplinary approach combining molecular markers, ENMs and population genetics can yield deep insights into diversification and evolutionary dynamics of species.
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Affiliation(s)
- Li Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University Xi'an, China
| | - Qi-Jian Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University Xi'an, China
| | - Zeng-Qiang Qian
- College of Life Sciences, Shaanxi Normal University Xi'an, China
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University Xi'an, China
| | - Yan-Ping Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University Xi'an, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University Xi'an, China
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University Xi'an, China
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563
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Castellanos-Morales G, Gámez N, Castillo-Gámez RA, Eguiarte LE. Peripatric speciation of an endemic species driven by Pleistocene climate change: The case of the Mexican prairie dog ( Cynomys mexicanus ). Mol Phylogenet Evol 2016; 94:171-81. [DOI: 10.1016/j.ympev.2015.08.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/26/2015] [Accepted: 08/31/2015] [Indexed: 02/02/2023]
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564
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Feng L, Zheng QJ, Qian ZQ, Yang J, Zhang YP, Li ZH, Zhao GF. Genetic Structure and Evolutionary History of Three Alpine Sclerophyllous Oaks in East Himalaya-Hengduan Mountains and Adjacent Regions. FRONTIERS IN PLANT SCIENCE 2016; 7:1688. [PMID: 27891142 PMCID: PMC5104984 DOI: 10.3389/fpls.2016.01688] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 10/26/2016] [Indexed: 05/20/2023]
Abstract
The East Himalaya-Hengduan Mountains (EH-HM) region has a high biodiversity and harbors numerous endemic alpine plants. This is probably the result of combined orographic and climate oscillations occurring since late Tertiary. Here, we determined the genetic structure and evolutionary history of alpine oak species (including Quercus spinosa, Quercus aquifolioides, and Quercus rehderiana) using both cytoplasmic-nuclear markers and ecological niche models (ENMs), and elucidated the impacts of climate oscillations and environmental heterogeneity on their population demography. Our results indicate there were mixed genetic structure and asymmetric contemporary gene flow within them. The ENMs revealed a similar demographic history for the three species expanded their ranges from the last interglacial (LIG) to the last glacial maximum (LGM), which was consistent with effective population sizes changes. Effects of genetic drift and fragmentation of habitats were responsible for the high differentiation and the lack of phylogeographic structure. Our results support that geological and climatic factors since Miocene triggered the differentiation, evolutionary origin and range shifts of the three oak species in the studied area and also emphasize that a multidisciplinary approach combining molecular markers, ENMs and population genetics can yield deep insights into diversification and evolutionary dynamics of species.
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Affiliation(s)
- Li Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
| | - Qi-Jian Zheng
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
| | - Zeng-Qiang Qian
- College of Life Sciences, Shaanxi Normal UniversityXi'an, China
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
| | - Yan-Ping Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest UniversityXi'an, China
- *Correspondence: Gui-Fang Zhao
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565
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Twomey E, Vestergaard JS, Venegas PJ, Summers K. Mimetic Divergence and the Speciation Continuum in the Mimic Poison Frog Ranitomeya imitator. Am Nat 2015; 187:205-24. [PMID: 26807748 DOI: 10.1086/684439] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
While divergent ecological adaptation can drive speciation, understanding the factors that facilitate or constrain this process remains a major goal in speciation research. Here, we study two mimetic transition zones in the poison frog Ranitomeya imitator, a species that has undergone a Müllerian mimetic radiation to establish four morphs in Peru. We find that mimetic morphs are strongly phenotypically differentiated, producing geographic clines with varying widths. However, distinct morphs show little neutral genetic divergence, and landscape genetic analyses implicate isolation by distance as the primary determinant of among-population genetic differentiation. Mate choice experiments suggest random mating at the transition zones, although certain allopatric populations show a preference for their own morph. We present evidence that this preference may be mediated by color pattern specifically. These results contrast with an earlier study of a third transition zone, in which a mimetic shift was associated with reproductive isolation. Overall, our results suggest that the three known mimetic transition zones in R. imitator reflect a speciation continuum, which we have characterized at the geographic, phenotypic, behavioral, and genetic levels. We discuss possible explanations for variable progress toward speciation, suggesting that multifarious selection on both mimetic color pattern and body size may be responsible for generating reproductive isolation.
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566
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Collins CJ, Chilvers BL, Taylor M, Robertson BC. Historical population size of the threatened New Zealand sea lion
Phocarctos hookeri. J Mammal 2015. [DOI: 10.1093/jmammal/gyv187] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Marine mammal species were exploited worldwide during periods of commercial sealing in the 18th and 19th centuries. For many of these species, an estimate of the pre-exploitation abundance of the species is lacking, as historical catch records are generally scarce and inaccurate. Genetic estimates of long-term effective population size provide a means to estimate the pre-exploitation abundance. Here, we apply genetic methods to estimate the long-term effective population size of the subantarctic lineage of the New Zealand sea lion (NZ sea lion), Phocarctos hookeri . This species is predominantly restricted to the subantarctic islands, south of mainland New Zealand, following commercial sealing in the 19th century. Today, the population consists of ~9,880 animals and population growth is slow. Auckland Island breeding colonies of NZ sea lion are currently impacted by commercial trawl fisheries via regular sea lion deaths as bycatch. In order to estimate sustainable levels of bycatch, an estimate of the population’s carrying capacity ( K ) is required. We apply the genetically estimated long-term effective population size of NZ sea lions as a proxy for the estimated historical carrying capacity of the subantarctic population. The historical abundance of subantarctic NZ sea lions was significantly higher than the target values of K employed by the contemporary management. The current management strategy may allow unsustainable bycatch levels, thereby limiting the recovery of the NZ sea lion population toward historical carrying capacity.
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Affiliation(s)
- Catherine J. Collins
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago , P.O. Box 56, Dunedin 9016 , New Zealand (CJC, MT, BCR)
- Department of Conservation, Marine Species and Threats , Wellington 6011 , New Zealand (BLC)
- Wildbase, IVABS, Massey University , Private Bag 11–222, Palmerston North 4442 , New Zealand (BLC)
| | - B. Louise Chilvers
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago , P.O. Box 56, Dunedin 9016 , New Zealand (CJC, MT, BCR)
- Department of Conservation, Marine Species and Threats , Wellington 6011 , New Zealand (BLC)
- Wildbase, IVABS, Massey University , Private Bag 11–222, Palmerston North 4442 , New Zealand (BLC)
| | - Matthew Taylor
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago , P.O. Box 56, Dunedin 9016 , New Zealand (CJC, MT, BCR)
- Department of Conservation, Marine Species and Threats , Wellington 6011 , New Zealand (BLC)
- Wildbase, IVABS, Massey University , Private Bag 11–222, Palmerston North 4442 , New Zealand (BLC)
| | - Bruce C. Robertson
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago , P.O. Box 56, Dunedin 9016 , New Zealand (CJC, MT, BCR)
- Department of Conservation, Marine Species and Threats , Wellington 6011 , New Zealand (BLC)
- Wildbase, IVABS, Massey University , Private Bag 11–222, Palmerston North 4442 , New Zealand (BLC)
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567
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Ortego J, Noguerales V, Gugger PF, Sork VL. Evolutionary and demographic history of the Californian scrub white oak species complex: an integrative approach. Mol Ecol 2015; 24:6188-208. [PMID: 26547661 DOI: 10.1111/mec.13457] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/30/2015] [Accepted: 11/03/2015] [Indexed: 01/17/2023]
Abstract
Understanding the factors promoting species formation is a major task in evolutionary research. Here, we employ an integrative approach to study the evolutionary history of the Californian scrub white oak species complex (genus Quercus). To infer the relative importance of geographical isolation and ecological divergence in driving the speciation process, we (i) analysed inter- and intraspecific patterns of genetic differentiation and employed an approximate Bayesian computation (ABC) framework to evaluate different plausible scenarios of species divergence. In a second step, we (ii) linked the inferred divergence pathways with current and past species distribution models (SDMs) and (iii) tested for niche differentiation and phylogenetic niche conservatism across taxa. ABC analyses showed that the most plausible scenario is the one considering the divergence of two main lineages followed by a more recent pulse of speciation. Genotypic data in conjunction with SDMs and niche differentiation analyses support that different factors (geography vs. environment) and modes of speciation (parapatry, allopatry and maybe sympatry) have played a role in the divergence process within this complex. We found no significant relationship between genetic differentiation and niche overlap, which probably reflects niche lability and/or that multiple factors, have contributed to speciation. Our study shows that different mechanisms can drive divergence even among closely related taxa representing early stages of species formation and exemplifies the importance of adopting integrative approaches to get a better understanding of the speciation process.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio s/n, E-41092, Seville, Spain
| | - Víctor Noguerales
- Department of Integrative Ecology, Estación Biológica de Doñana, EBD-CSIC, Avda. Américo Vespucio s/n, E-41092, Seville, Spain
| | - Paul F Gugger
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA
| | - Victoria L Sork
- Department of Ecology and Evolutionary Biology, University of California, Box 957239, Los Angeles, CA, 90095, USA.,Institute of the Environment and Sustainability, University of California, Box 951496, Los Angeles, CA, 90095-1496, USA
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568
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Chapuis MP, Plantamp C, Streiff R, Blondin L, Piou C. Microsatellite evolutionary rate and pattern in Schistocerca gregaria inferred from direct observation of germline mutations. Mol Ecol 2015; 24:6107-19. [PMID: 26562076 DOI: 10.1111/mec.13465] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 11/05/2015] [Accepted: 11/06/2015] [Indexed: 01/21/2023]
Abstract
Unravelling variation among taxonomic orders regarding the rate of evolution in microsatellites is crucial for evolutionary biology and population genetics research. The mean mutation rate of microsatellites tends to be lower in arthropods than in vertebrates, but data are scarce and mostly concern accumulation of mutations in model species. Based on parent-offspring segregations and a hierarchical Bayesian model, the mean rate of mutation in the orthopteran insect Schistocerca gregaria was estimated at 2.1e(-4) per generation per untranscribed dinucleotide locus. This is close to vertebrate estimates and one order of magnitude higher than estimates from species of other arthropod orders, such as Drosophila melanogaster and Daphnia pulex. We also found evidence of a directional bias towards expansions even for long alleles and exceptionally large ranges of allele sizes. Finally, at transcribed microsatellites, the mean rate of mutation was half the rate found at untranscribed loci and the mutational model deviated from that usually considered, with most mutations involving multistep changes that avoid disrupting the reading frame. Our direct estimates of mutation rate were discussed in the light of peculiar biological and genomic features of S. gregaria, including specificities in mismatch repair and the dependence of its activity to allele length. Shedding new light on the mutational dynamics of grasshopper microsatellites is of critical importance for a number of research fields. As an illustration, we showed how our findings improve microsatellite application in population genetics, by obtaining a more precise estimation of S. gregaria effective population size from a published data set based on the same microsatellites.
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Affiliation(s)
- M-P Chapuis
- CIRAD, UMR CBGP, Montpellier, F-34398, France
| | - C Plantamp
- Laboratoire de Biométrie et Biologie Evolutive, CNRS, UMR 5558, Université Lyon 1, Villeurbanne, 69622, France
| | - R Streiff
- INRA, UMR CBGP, Montpellier, F-34398, France.,INRA, UMR DGIMI, Montpellier, F-34000, France
| | - L Blondin
- CIRAD, UPR B-AMR, Montpellier, F-34398, France
| | - C Piou
- CIRAD, UMR CBGP, Montpellier, F-34398, France
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569
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Catarino D, Knutsen H, Veríssimo A, Olsen EM, Jorde PE, Menezes G, Sannæs H, Stanković D, Company JB, Neat F, Danovaro R, Dell'Anno A, Rochowski B, Stefanni S. The Pillars of Hercules as a bathymetric barrier to gene flow promoting isolation in a global deep-sea shark (Centroscymnus coelolepis). Mol Ecol 2015; 24:6061-79. [PMID: 26547144 DOI: 10.1111/mec.13453] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 10/29/2015] [Accepted: 11/02/2015] [Indexed: 11/26/2022]
Abstract
Knowledge of the mechanisms limiting connectivity and gene flow in deep-sea ecosystems is scarce, especially for deep-sea sharks. The Portuguese dogfish (Centroscymnus coelolepis) is a globally distributed and near threatened deep-sea shark. C. coelolepis population structure was studied using 11 nuclear microsatellite markers and a 497-bp fragment from the mtDNA control region. High levels of genetic homogeneity across the Atlantic (Φ(ST) = -0.0091, F(ST) = 0.0024, P > 0.05) were found suggesting one large population unit at this basin. The low levels of genetic divergence between Atlantic and Australia (Φ(ST) = 0.0744, P < 0.01; F(ST) = 0.0015, P > 0.05) further suggested that this species may be able to maintain some degree of genetic connectivity even across ocean basins. In contrast, sharks from the Mediterranean Sea exhibited marked genetic differentiation from all other localities studied (Φ(ST) = 0.3808, F(ST) = 0.1149, P < 0.001). This finding suggests that the shallow depth of the Strait of Gibraltar acts as a barrier to dispersal and that isolation and genetic drift may have had an important role shaping the Mediterranean shark population over time. Analyses of life history traits allowed the direct comparison among regions providing a complete characterization of this shark's populations. Sharks from the Mediterranean had markedly smaller adult body size and size at maturity compared to Atlantic and Pacific individuals. Together, these results suggest the existence of an isolated and unique population of C. coelolepis inhabiting the Mediterranean that most likely became separated from the Atlantic in the late Pleistocene.
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Affiliation(s)
- Diana Catarino
- MARE-Marine and Environmental Sciences Centre, Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, Horta, Azores, Portugal.,IMAR-Institute of Marine Research, Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, Horta, Azores, Portugal
| | - Halvor Knutsen
- Institute of Marine Research (IMR), Flødevigen, N-4817 His, Norway.,University of Agder, Kristiansand, N-4604, Norway.,Department of Biosciences, University of Oslo, Centre for Ecological and Evolutionary Synthesis (CEES), PO Box 1066 Blindern, Oslo, N-0316, Norway
| | - Ana Veríssimo
- CIBIO-U.P., Centro de Investigação em Biodiversidade e Recursos Genéticos, Campus Agrário de Vairão, Rua Padre Armando Quintas, Vairão, 4485-661, Portugal.,College of William and Mary, Virginia Institute of Marine Science, Route 1208, Greate Road, Gloucester Point, 23062, VA, USA
| | - Esben Moland Olsen
- Institute of Marine Research (IMR), Flødevigen, N-4817 His, Norway.,University of Agder, Kristiansand, N-4604, Norway.,Department of Biosciences, University of Oslo, Centre for Ecological and Evolutionary Synthesis (CEES), PO Box 1066 Blindern, Oslo, N-0316, Norway
| | - Per Erik Jorde
- Department of Biosciences, University of Oslo, Centre for Ecological and Evolutionary Synthesis (CEES), PO Box 1066 Blindern, Oslo, N-0316, Norway
| | - Gui Menezes
- MARE-Marine and Environmental Sciences Centre, Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, Horta, Azores, Portugal.,IMAR-Institute of Marine Research, Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, Horta, Azores, Portugal
| | - Hanne Sannæs
- Institute of Marine Research (IMR), Flødevigen, N-4817 His, Norway
| | - David Stanković
- Department of Life Sciences, University of Trieste, Via Licio Giorgieri 5, Trieste, 34127, Italy
| | - Joan Baptista Company
- Institut de Ciències del Mar, CSIC, Passeig Marítim de la Barceloneta 37-49, Barcelona, 08003, Spain
| | - Francis Neat
- Marine Laboratory, Marine Scotland-Science, PO Box 101, 375 Victoria Road, Aberdeen, AB11 9DB, UK
| | - Roberto Danovaro
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, 60131, Italy.,Stazione Zoologica Anton Dohrn, Villa Comunale, Naples, Italy
| | - Antonio Dell'Anno
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, Ancona, 60131, Italy
| | - Bastien Rochowski
- School of BioSciences, The University of Melbourne, Parkville, Vic., 3010, Australia
| | - Sergio Stefanni
- IMAR-Institute of Marine Research, Department of Oceanography and Fisheries, University of the Azores, Rua Prof. Dr. Frederico Machado, Horta, Azores, Portugal.,CNR-ISSIA, Via de Marini 6, Genova, 16149, Italy
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570
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Pudlo P, Marin JM, Estoup A, Cornuet JM, Gautier M, Robert CP. Reliable ABC model choice via random forests. ACTA ACUST UNITED AC 2015; 32:859-66. [PMID: 26589278 DOI: 10.1093/bioinformatics/btv684] [Citation(s) in RCA: 196] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 09/30/2015] [Indexed: 01/25/2023]
Abstract
MOTIVATION Approximate Bayesian computation (ABC) methods provide an elaborate approach to Bayesian inference on complex models, including model choice. Both theoretical arguments and simulation experiments indicate, however, that model posterior probabilities may be poorly evaluated by standard ABC techniques. RESULTS We propose a novel approach based on a machine learning tool named random forests (RF) to conduct selection among the highly complex models covered by ABC algorithms. We thus modify the way Bayesian model selection is both understood and operated, in that we rephrase the inferential goal as a classification problem, first predicting the model that best fits the data with RF and postponing the approximation of the posterior probability of the selected model for a second stage also relying on RF. Compared with earlier implementations of ABC model choice, the ABC RF approach offers several potential improvements: (i) it often has a larger discriminative power among the competing models, (ii) it is more robust against the number and choice of statistics summarizing the data, (iii) the computing effort is drastically reduced (with a gain in computation efficiency of at least 50) and (iv) it includes an approximation of the posterior probability of the selected model. The call to RF will undoubtedly extend the range of size of datasets and complexity of models that ABC can handle. We illustrate the power of this novel methodology by analyzing controlled experiments as well as genuine population genetics datasets. AVAILABILITY AND IMPLEMENTATION The proposed methodology is implemented in the R package abcrf available on the CRAN. CONTACT jean-michel.marin@umontpellier.fr SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pierre Pudlo
- Université de Montpellier, IMAG, Montpellier, Institut de Biologie Computationnelle (IBC), Montpellier
| | - Jean-Michel Marin
- Université de Montpellier, IMAG, Montpellier, Institut de Biologie Computationnelle (IBC), Montpellier
| | - Arnaud Estoup
- Institut de Biologie Computationnelle (IBC), Montpellier, CBGP, INRA, Montpellier
| | | | - Mathieu Gautier
- Institut de Biologie Computationnelle (IBC), Montpellier, CBGP, INRA, Montpellier
| | - Christian P Robert
- Université Paris Dauphine, CEREMADE, Paris, France and University of Warwick, Coventry, UK
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571
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Niedziałkowska M, Hundertmark KJ, Jędrzejewska B, Sidorovich VE, Zalewska H, Veeroja R, Solberg EJ, Laaksonen S, Sand H, Solovyev VA, Sagaydak A, Tiainen J, Juškaitis R, Done G, Borodulin VA, Tulandin EA, Niedziałkowski K. The contemporary genetic pattern of European moose is shaped by postglacial recolonization, bottlenecks, and the geographical barrier of the Baltic Sea. Biol J Linn Soc Lond 2015. [DOI: 10.1111/bij.12713] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Kris J. Hundertmark
- Mammal Research Institute; Polish Academy of Sciences; Białowieża 17-230 Poland
- Institute of Arctic Biology and Department of Biology and Wildlife; University of Alaska; Fairbanks P.O. Box 757000 AK 99775-7000 USA
| | | | - Vadim E. Sidorovich
- Institute of Zoology; Scientific and Practical Centre for Biological Resources; National Academy of Sciences of Belarus; Minsk BY-220072 Republic of Belarus
| | - Hanna Zalewska
- Mammal Research Institute; Polish Academy of Sciences; Białowieża 17-230 Poland
| | - Rauno Veeroja
- Department of Zoology; Institute of Ecology and Earth Science; University of Tartu; Tartu 51014 Estonia
| | - Erling J. Solberg
- Norwegian Institute for Nature Research; P.O. Box 5685 Sluppen Trondheim NO-7485 Norway
| | | | - Håkan Sand
- Grimsö Research Station; Swedish University of Agricultural Sciences; 73091 Riddarhyttan Sweden
| | - Vyacheslav A. Solovyev
- Department of Animal Ecology; B. M. Zhitkov Russian Research Institute of Game Management and Fur Farming; Kirov 610000 Russia
| | - Andrey Sagaydak
- Mizhrichynskyi Regional Landscape Park; Otrokhy; Kozelets Raion Chernihiv Oblast, Ukraine
| | - Juha Tiainen
- Natural Resources Institute Finland; Helsinki 00790 Finland
| | - Rimvydas Juškaitis
- Institute of Ecology; Nature Research Centre; Vilnius LT-08412 Lithuania
| | - Gundega Done
- Latvian State Forest Research Institute ‘Silava’; Salaspils 2169 Latvia
| | - Vadim A. Borodulin
- Inter-regional Non-governmental Organization ‘Leningrad Association of Hunters and Fishermen’; Sankt Petersburg 190121 Russia
| | - Evgenii A. Tulandin
- Non-commercial Partnership ‘Union of Gamekeepers of the Kostroma Region’; Kostroma Russia
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572
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Chau LM, Hanna C, Jenkins LT, Kutner RE, Burns EA, Kremen C, Goodisman MAD. Population genetic structure of the predatory, social wasp Vespula pensylvanica in its native and invasive range. Ecol Evol 2015; 5:5573-87. [PMID: 27069607 PMCID: PMC4813109 DOI: 10.1002/ece3.1757] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/27/2015] [Accepted: 08/28/2015] [Indexed: 01/09/2023] Open
Abstract
Invasive species cause extensive damage to their introduced ranges. Ocean archipelagos are particularly vulnerable to invasive taxa. In this study, we used polymorphic microsatellite markers to investigate the genetic structure of the social wasp Vespula pensylvanica in its native range of North America and its introduced range in the archipelago of Hawaii. Our goal was to gain a better understanding of the invasion dynamics of social species and the processes affecting biological invasions. We found that V. pensylvanica showed no significant genetic isolation by distance and little genetic structure over a span of 2000 km in its native range. This result suggests that V. pensylvanica can successfully disperse across large distances either through natural- or human-mediated mechanisms. In contrast to the genetic patterns observed in the native range, we found substantial genetic structure in the invasive V. pensylvanica range in Hawaii. The strong patterns of genetic differentiation within and between the Hawaiian Islands may reflect the effects of geographic barriers and invasion history on gene flow. We also found some evidence for gene flow between the different islands of Hawaii which was likely mediated through human activity. Overall, this study provides insight on how geographic barriers, invasion history, and human activity can shape population genetic structure of invasive species.
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Affiliation(s)
- Linh M Chau
- School of Biology Georgia Institute of Technology Atlanta Georgia 30332
| | - Cause Hanna
- Environmental Science and Resource Management California State University Camarillo California 93012
| | - Laurel T Jenkins
- School of Biology Georgia Institute of Technology Atlanta Georgia 30332
| | - Rachel E Kutner
- School of Biology Georgia Institute of Technology Atlanta Georgia 30332
| | - Elizabeth A Burns
- School of Biology Georgia Institute of Technology Atlanta Georgia 30332
| | - Claire Kremen
- Environmental Science, Policy and Management University of California Berkeley California 94720
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573
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Jacquet S, Garros C, Lombaert E, Walton C, Restrepo J, Allene X, Baldet T, Cetre-Sossah C, Chaskopoulou A, Delecolle JC, Desvars A, Djerbal M, Fall M, Gardes L, de Garine-Wichatitsky M, Goffredo M, Gottlieb Y, Gueye Fall A, Kasina M, Labuschagne K, Lhor Y, Lucientes J, Martin T, Mathieu B, Miranda M, Pages N, Pereira da Fonseca I, Ramilo DW, Segard A, Setier-Rio ML, Stachurski F, Tabbabi A, Talla Seck M, Venter G, Zimba M, Balenghien T, Guis H, Chevillon C, Bouyer J, Huber K. Colonization of the Mediterranean basin by the vector biting midge speciesCulicoides imicola: an old story. Mol Ecol 2015; 24:5707-25. [DOI: 10.1111/mec.13422] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 10/06/2015] [Accepted: 10/09/2015] [Indexed: 11/27/2022]
Affiliation(s)
- S. Jacquet
- CIRAD UMR15 CMAEE; 34398 Montpellier France
- INRA UMR1309 CMAEE; 34398 Montpellier France
- CNRS; UMR 5290 Maladies Infectieuses & Vecteurs-Ecologie, Génétique, Ecologie, Contrôle (MIVEGEC); Université de Montpellier; Montpellier France
- IRD; UR 224 MIVEGEC; BP 64501, Agropolis 34394 Montpellier Cedex 5 France
| | - C. Garros
- CIRAD UMR15 CMAEE; 34398 Montpellier France
- INRA UMR1309 CMAEE; 34398 Montpellier France
| | - E. Lombaert
- INRA; UMR1355; Institut Sophia Agrobiotech; 06903 Sophia Antipolis France
| | - C. Walton
- Computational and Evolutionary Biology; Faculty of Life Sciences; University of Manchester; Manchester UK
| | - J. Restrepo
- CIRAD UMR15 CMAEE; 34398 Montpellier France
- INRA UMR1309 CMAEE; 34398 Montpellier France
| | - X. Allene
- CIRAD UMR15 CMAEE; 34398 Montpellier France
- INRA UMR1309 CMAEE; 34398 Montpellier France
| | - T. Baldet
- CIRAD UMR15 CMAEE; 34398 Montpellier France
- INRA UMR1309 CMAEE; 34398 Montpellier France
| | - C. Cetre-Sossah
- CIRAD UMR15 CMAEE; 34398 Montpellier France
- INRA UMR1309 CMAEE; 34398 Montpellier France
- Plateforme de recherche CYROI; CRVOI; Sainte Clotilde La Réunion France
| | - A. Chaskopoulou
- USDA-ARS European Biological Control Laboratory; 54623 Thessaloniki Greece
| | - J.-C. Delecolle
- Medicine Faculty; Institute of Parasitology and Tropical Pathology (IPPTS); EA7292 67000 Strasbourg France
| | - A. Desvars
- Department of Clinical Microbiology; Umea University; Umea Sweden
| | - M. Djerbal
- Regional Veterinary Laboratory of Draa-Ben-Kheda; Tizi-Ouzou Algeria
| | - M. Fall
- ISRA-LNERV; BP 2057 Dakar Senegal
| | - L. Gardes
- CIRAD UMR15 CMAEE; 34398 Montpellier France
- INRA UMR1309 CMAEE; 34398 Montpellier France
| | - M. de Garine-Wichatitsky
- Cirad; UPR AGIRs, RP-PCP; Harare Zimbabwe
- Cirad; UPR AGIRs; Montpellier France
- Department of Biological Sciences, Entomology; University of Zimbabwe; PO Box MP 167 Mount Pleasant Harare Zimbabwe
| | - M. Goffredo
- Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise ‘G. Caporale’; 64100 Teramo Italy
| | - Y. Gottlieb
- Koret School of Veterinary Medicine; The Robert H. Smith Faculty of Agriculture, Food and Environment; The Hebrew University of Jerusalem; Rehovot Israel
| | | | - M. Kasina
- Kenya Agricultural and Livestock Research Organization Sericulture; PO Box 7816 Code 01000 Thika Kenya
| | - K. Labuschagne
- Agricultural Research Council-Onderstepoort Veterinary Institute, Parasites, Vectors and Vector-borne Diseases; Onderstepoort 0110 South Africa
| | - Y. Lhor
- Office National de Sécurité Sanitaire des produits Alimentaires (ONSSA); Rabat Morocco
| | - J. Lucientes
- Departamento de Patología Animal; Facultad de Veterinaria; Universidad de Zaragoza; Zaragoza Spain
| | - T. Martin
- UR Hortsys; Cirad; Montpellier France
- Plant Health Department; ICIPE; Nairobi Kenya
| | - B. Mathieu
- Medicine Faculty; Institute of Parasitology and Tropical Pathology (IPPTS); EA7292 67000 Strasbourg France
- EID Méditerranée; 34184 Montpellier France
| | - M. Miranda
- Laboratory of Zoology; University of Balearics (UIB); Palma de Mallorca Spain
| | - N. Pages
- INRA UMR1309 CMAEE; 34398 Montpellier France
- Centre de Recerca en Sanitat Animal (CReSA); UAB-IRTA; Campus de la Universitat Autònoma de Barcelona 08193 Bellaterra (Cerdanyola del Vallès) Spain
- CIRAD; UMR CMAEE; 97170 Petit Bourg Guadeloupe France
| | | | - D. W. Ramilo
- Faculdade de Medicina Veterinária; CIISA; ULisboa; 1300-477 Lisboa Portugal
| | - A. Segard
- CNRS; UMR 5175 CEFE; Université de Montpellier; Montpellier France
- EPHE Campus CNRS; 1919 route de Mende 34293 Montpellier Cedex 5 France
| | | | - F. Stachurski
- CIRAD UMR15 CMAEE; 34398 Montpellier France
- INRA UMR1309 CMAEE; 34398 Montpellier France
| | - A. Tabbabi
- Lab of Medical Parasitology, Biotechnologies & Biomolecules (LR 11 IPT 06); Pasteur Institute of Tunis; Tunis Tunisia
| | | | - G. Venter
- Agricultural Research Council-Onderstepoort Veterinary Institute, Parasites, Vectors and Vector-borne Diseases; Onderstepoort 0110 South Africa
| | - M. Zimba
- Department of Biological Sciences, Entomology; University of Zimbabwe; PO Box MP 167 Mount Pleasant Harare Zimbabwe
| | - T. Balenghien
- CIRAD UMR15 CMAEE; 34398 Montpellier France
- INRA UMR1309 CMAEE; 34398 Montpellier France
| | - H. Guis
- CIRAD UMR15 CMAEE; 34398 Montpellier France
- INRA UMR1309 CMAEE; 34398 Montpellier France
| | - C. Chevillon
- CNRS; UMR 5290 Maladies Infectieuses & Vecteurs-Ecologie, Génétique, Ecologie, Contrôle (MIVEGEC); Université de Montpellier; Montpellier France
- IRD; UR 224 MIVEGEC; BP 64501, Agropolis 34394 Montpellier Cedex 5 France
| | - J. Bouyer
- CIRAD UMR15 CMAEE; 34398 Montpellier France
- INRA UMR1309 CMAEE; 34398 Montpellier France
- ISRA-LNERV; BP 2057 Dakar Senegal
| | - K. Huber
- CIRAD UMR15 CMAEE; 34398 Montpellier France
- INRA UMR1309 CMAEE; 34398 Montpellier France
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574
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Vandergast AG, Wood DA, Thompson AR, Fisher M, Barrows CW, Grant TJ. Drifting to oblivion? Rapid genetic differentiation in an endangered lizard following habitat fragmentation and drought. DIVERS DISTRIB 2015. [DOI: 10.1111/ddi.12398] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Amy G. Vandergast
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station. 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
| | - Dustin A. Wood
- U.S. Geological Survey; Western Ecological Research Center; San Diego Field Station. 4165 Spruance Road, Suite 200 San Diego CA 92101 USA
| | - Andrew R. Thompson
- Fisheries Resources Division; Southwest Fisheries Science Center; National Marine Fisheries Service; National Oceanic and Atmospheric Administration; La Jolla CA 92037 USA
| | - Mark Fisher
- Natural Reserve System; P.L. Boyd Deep Canyon Desert Research Center; University of California; 54900 Desert Research Tr. Indian Wells CA 92210 USA
| | - Cameron W. Barrows
- Center for Conservation Biology; University of California Riverside; Riverside CA 92251 USA
| | - Tyler J. Grant
- Department of Natural Resource Ecology and Management; Iowa State University; 339 Science II Ames IA 50011 USA
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575
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The genomics of ecological vicariance in threespine stickleback fish. Nat Commun 2015; 6:8767. [PMID: 26556609 PMCID: PMC4659939 DOI: 10.1038/ncomms9767] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 09/29/2015] [Indexed: 12/19/2022] Open
Abstract
Populations occurring in similar habitats and displaying similar phenotypes are increasingly used to explore parallel evolution at the molecular level. This generally ignores the possibility that parallel evolution can be mimicked by the fragmentation of an ancestral population followed by genetic exchange with ecologically different populations. Here we demonstrate such an ecological vicariance scenario in multiple stream populations of threespine stickleback fish divergent from a single adjacent lake population. On the basis of demographic and population genomic analyses, we infer the initial spread of a stream-adapted ancestor followed by the emergence of a lake-adapted population, that selective sweeps have occurred mainly in the lake population, that adaptive lake–stream divergence is maintained in the face of gene flow from the lake into the streams, and that this divergence involves major inversion polymorphisms also important to marine-freshwater stickleback divergence. Overall, our study highlights the need for a robust understanding of the demographic and selective history in evolutionary investigations. Threespine stickleback fish are adapted to lake and stream habitats in Central Europe. Here, the authors show colonization of a lake basin by a stream-adapted ancestor, followed by the emergence of a lake-adapted population in the face of gene flow across lake–stream boundaries.
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576
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Rijal DP, Alm T, Jahodová Š, Stenøien HK, Alsos IG. Reconstructing the invasion history of Heracleum persicum (Apiaceae) into Europe. Mol Ecol 2015; 24:5522-43. [PMID: 26454010 DOI: 10.1111/mec.13411] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 01/15/2023]
Abstract
Sparse, incomplete and inappropriate historical records of invasive species often hamper invasive species management interventions. Population genetic analyses of invaders might provide a suitable context for the identification of their source populations and possible introduction routes. Here, we describe the population genetics of Heracleum persicum Desf. ex Fisch and trace its route of introduction into Europe. Microsatellite markers revealed a significantly higher genetic diversity of H. persicum in its native range, and the loss of diversity in the introduced range may be attributed to a recent genetic bottleneck. Bayesian cluster analysis on regional levels identified three and two genetic clusters in the native and the introduced ranges, respectively. A global structure analysis revealed two worldwide distinct genetic groups: one primarily in Iran and Denmark, the other primarily in Norway. There were also varying degrees of admixture in England, Sweden, Finland and Latvia. Approximate Bayesian computation indicated two independent introductions of H. persicum from Iran to Europe: the first one in Denmark and the second one in England. Finland was subsequently colonized by English populations. In contrast to the contemporary hypothesis of English origin of Norwegian populations, we found Finland to be a more likely source for Norwegian populations, a scenario supported by higher estimated historical migration from Finland to Norway. Genetic diversity per se is not a primary determinant of invasiveness in H. persicum. Our results indicate that, due to either pre-adaptations or rapid local adaptations, introduced populations may have acquired invasiveness after subsequent introductions, once a suitable environment was encountered.
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Affiliation(s)
- Dilli P Rijal
- Department of Natural Sciences, Tromsø Museum, University of Tromsø-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Torbjørn Alm
- Department of Natural Sciences, Tromsø Museum, University of Tromsø-The Arctic University of Norway, 9037, Tromsø, Norway
| | - Šárka Jahodová
- Institute of Botany, The Czech Academy of Sciences, CZ-252 43, Průhonice, Czech Republic.,Department of Ecology, Faculty of Science, Charles University in Prague, Viničná 7, Prague, CZ-128 44, Czech Republic
| | - Hans K Stenøien
- Department of Natural History, Centre for Biodiversity Dynamics, NTNU University Museum, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Inger G Alsos
- Department of Natural Sciences, Tromsø Museum, University of Tromsø-The Arctic University of Norway, 9037, Tromsø, Norway
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577
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Smyth JF, Patten MA, Pruett CL. The evolutionary ecology of a species ring: a test of alternative models. FOLIA ZOOLOGICA 2015. [DOI: 10.25225/fozo.v64.i3.a5.2015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Jason F. Smyth
- Florida Institute of Technology, Department of Biological Sciences, Melbourne, FL 32901, U.S.A.
| | - Michael A. Patten
- University of Oklahoma, Oklahoma Biological Survey and Department of Biology, Norman, OK 73019, U.S.A.
| | - Christin L. Pruett
- Florida Institute of Technology, Department of Biological Sciences, Melbourne, FL 32901, U.S.A.
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578
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Zeng YF, Wang WT, Liao WJ, Wang HF, Zhang DY. Multiple glacial refugia for cool-temperate deciduous trees in northern East Asia: the Mongolian oak as a case study. Mol Ecol 2015; 24:5676-91. [DOI: 10.1111/mec.13408] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Yan-Fei Zeng
- State Key Laboratory of Tree Genetics and Breeding; Chinese Academy of Forestry; Beijing 100091 China
- Key Laboratory of Silviculture of the State Forestry Administration; Research Institute of Forestry; Chinese Academy of Forestry; Beijing 100091 China
| | - Wen-Ting Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering; Beijing Normal University; Beijing 100875 China
- School of Mathematics and Computer Science; Northwest University for Nationalities; Lanzhou 730030 China
| | - Wan-Jin Liao
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering; Beijing Normal University; Beijing 100875 China
| | - Hong-Fang Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering; Beijing Normal University; Beijing 100875 China
| | - Da-Yong Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering; Beijing Normal University; Beijing 100875 China
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579
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Louis M, Fontaine MC, Spitz J, Schlund E, Dabin W, Deaville R, Caurant F, Cherel Y, Guinet C, Simon-Bouhet B. Ecological opportunities and specializations shaped genetic divergence in a highly mobile marine top predator. Proc Biol Sci 2015; 281:rspb.2014.1558. [PMID: 25297864 DOI: 10.1098/rspb.2014.1558] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Environmental conditions can shape genetic and morphological divergence. Release of new habitats during historical environmental changes was a major driver of evolutionary diversification. Here, forces shaping population structure and ecotype differentiation ('pelagic' and 'coastal') of bottlenose dolphins in the North-east Atlantic were investigated using complementary evolutionary and ecological approaches. Inference of population demographic history using approximate Bayesian computation indicated that coastal populations were likely founded by the Atlantic pelagic population after the Last Glacial Maxima probably as a result of newly available coastal ecological niches. Pelagic dolphins from the Atlantic and the Mediterranean Sea likely diverged during a period of high productivity in the Mediterranean Sea. Genetic differentiation between coastal and pelagic ecotypes may be maintained by niche specializations, as indicated by stable isotope and stomach content analyses, and social behaviour. The two ecotypes were only weakly morphologically segregated in contrast to other parts of the World Ocean. This may be linked to weak contrasts between coastal and pelagic habitats and/or a relatively recent divergence. We suggest that ecological opportunity to specialize is a major driver of genetic and morphological divergence. Combining genetic, ecological and morphological approaches is essential to understanding the population structure of mobile and cryptic species.
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Affiliation(s)
- Marie Louis
- Centre d'Etudes Biologiques de Chizé, UMR 7372 CNRS-Université de La Rochelle, La Rochelle, France Littoral Environnement et Sociétés, UMR 7266 CNRS-Université de La Rochelle, La Rochelle, France Groupe d'Etude des Cétacés du Cotentin, Cherbourg-Octeville, France
| | - Michael C Fontaine
- Marine Evolution and Conservation, Centre of Evolutionary and Ecological Studies, University of Groningen, Groningen, The Netherlands Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Jérôme Spitz
- Observatoire PELAGIS, UMS 3462 CNRS-Université La Rochelle, La Rochelle, France
| | - Erika Schlund
- Littoral Environnement et Sociétés, UMR 7266 CNRS-Université de La Rochelle, La Rochelle, France Observatoire PELAGIS, UMS 3462 CNRS-Université La Rochelle, La Rochelle, France
| | - Willy Dabin
- Observatoire PELAGIS, UMS 3462 CNRS-Université La Rochelle, La Rochelle, France
| | - Rob Deaville
- Institute of Zoology, Zoological Society of London, London, UK
| | - Florence Caurant
- Centre d'Etudes Biologiques de Chizé, UMR 7372 CNRS-Université de La Rochelle, La Rochelle, France
| | - Yves Cherel
- Centre d'Etudes Biologiques de Chizé, UMR 7372 CNRS-Université de La Rochelle, La Rochelle, France
| | - Christophe Guinet
- Centre d'Etudes Biologiques de Chizé, UMR 7372 CNRS-Université de La Rochelle, La Rochelle, France
| | - Benoit Simon-Bouhet
- Centre d'Etudes Biologiques de Chizé, UMR 7372 CNRS-Université de La Rochelle, La Rochelle, France
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580
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Marescaux J, von Oheimb KCM, Etoundi E, von Oheimb PV, Albrecht C, Wilke T, Van Doninck K. Unravelling the invasion pathways of the quagga mussel (Dreissena rostriformis) into Western Europe. Biol Invasions 2015. [DOI: 10.1007/s10530-015-1005-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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581
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Razgour O, Salicini I, Ibáñez C, Randi E, Juste J. Unravelling the evolutionary history and future prospects of endemic species restricted to former glacial refugia. Mol Ecol 2015; 24:5267-83. [PMID: 26346923 DOI: 10.1111/mec.13379] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 11/28/2022]
Abstract
The contemporary distribution and genetic composition of biodiversity bear a signature of species' evolutionary histories and the effects of past climatic oscillations. For many European species, the Mediterranean peninsulas of Iberia, Italy and the Balkans acted as glacial refugia and the source of range recolonization, and as a result, they contain disproportionately high levels of diversity. As these areas are particularly threatened by future climate change, it is important to understand how past climatic changes affected their biodiversity. We use an integrated approach, combining markers with different evolutionary rates and combining phylogenetic analysis with approximate Bayesian computation and species distribution modelling across temporal scales. We relate phylogeographic processes to patterns of genetic variation in Myotis escalerai, a bat species endemic to the Iberian Peninsula. We found a distinct population structure at the mitochondrial level with a strong geographic signature, indicating lineage divergence into separate glacial refugia within the Iberian refugium. However, microsatellite markers suggest higher levels of gene flow resulting in more limited structure at recent time frames. The evolutionary history of M. escalerai was shaped by the effects of climatic oscillations and changes in forest cover and composition, while its future is threatened by climatically induced range contractions and the role of ecological barriers due to competition interactions in restricting its distribution. This study warns that Mediterranean peninsulas, which provided refuge for European biodiversity during past glaciation events, may become a trap for limited dispersal and ecologically limited endemic species under future climate change, resulting in loss of entire lineages.
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Affiliation(s)
- Orly Razgour
- Division of Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Irene Salicini
- Estación Biológica de Doñana (CSIC), Avda Americo Vespucio s/n, 41092, Seville, Spain
| | - Carlos Ibáñez
- Estación Biológica de Doñana (CSIC), Avda Americo Vespucio s/n, 41092, Seville, Spain
| | - Ettore Randi
- Laboratorio di Genetica, Istituto Superiore per la Protezione e Ricerca Ambientale, Via Ca' Fornacetta 9, Ozzano dell' Emilia, Bologna, Italy.,Department 18/ Section of Environmental Engineering, Aalborg University, Sohngårdsholmsvej 57, 9000, Aalborg, Denmark
| | - Javier Juste
- Estación Biológica de Doñana (CSIC), Avda Americo Vespucio s/n, 41092, Seville, Spain
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582
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Lv FH, Peng WF, Yang J, Zhao YX, Li WR, Liu MJ, Ma YH, Zhao QJ, Yang GL, Wang F, Li JQ, Liu YG, Shen ZQ, Zhao SG, Hehua E, Gorkhali NA, Farhad Vahidi SM, Muladno M, Naqvi AN, Tabell J, Iso-Touru T, Bruford MW, Kantanen J, Han JL, Li MH. Mitogenomic Meta-Analysis Identifies Two Phases of Migration in the History of Eastern Eurasian Sheep. Mol Biol Evol 2015; 32:2515-33. [PMID: 26085518 PMCID: PMC4576706 DOI: 10.1093/molbev/msv139] [Citation(s) in RCA: 104] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Despite much attention, history of sheep (Ovis aries) evolution, including its dating, demographic trajectory and geographic spread, remains controversial. To address these questions, we generated 45 complete and 875 partial mitogenomic sequences, and performed a meta-analysis of these and published ovine mitochondrial DNA sequences (n = 3,229) across Eurasia. We inferred that O. orientalis and O. musimon share the most recent female ancestor with O. aries at approximately 0.790 Ma (95% CI: 0.637-0.934 Ma) during the Middle Pleistocene, substantially predating the domestication event (∼8-11 ka). By reconstructing historical variations in effective population size, we found evidence of a rapid population increase approximately 20-60 ka, immediately before the Last Glacial Maximum. Analyses of lineage expansions showed two sheep migratory waves at approximately 4.5-6.8 ka (lineages A and B: ∼6.4-6.8 ka; C: ∼4.5 ka) across eastern Eurasia, which could have been influenced by prehistoric West-East commercial trade and deliberate mating of domestic and wild sheep, respectively. A continent-scale examination of lineage diversity and approximate Bayesian computation analyses indicated that the Mongolian Plateau region was a secondary center of dispersal, acting as a "transportation hub" in eastern Eurasia: Sheep from the Middle Eastern domestication center were inferred to have migrated through the Caucasus and Central Asia, and arrived in North and Southwest China (lineages A, B, and C) and the Indian subcontinent (lineages B and C) through this region. Our results provide new insights into sheep domestication, particularly with respect to origins and migrations to and from eastern Eurasia.
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Affiliation(s)
- Feng-Hua Lv
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Wei-Feng Peng
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ji Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
| | - Yong-Xin Zhao
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Wen-Rong Li
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Ming-Jun Liu
- Animal Biotechnology Research Institute, Xinjiang Academy of Animal Science, Urumqi, China
| | - Yue-Hui Ma
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Qian-Jun Zhao
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Guang-Li Yang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China College of Life Sciences, Shangqiu Normal University, Shangqiu, China
| | - Feng Wang
- Institute of Sheep and Goat Science, Nanjing Agricultural University, Nanjing, China
| | - Jin-Quan Li
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yong-Gang Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Zhi-Qiang Shen
- Shandong Binzhou Academy of Animal Science and Veterinary Medicine, Binzhou, China
| | - Sheng-Guo Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Eer Hehua
- Grass-Feeding Livestock Engineering Technology Research Center, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Neena A Gorkhali
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China Animal Breeding Division, National Animal Science Institute, Nepal Agriculture Research Council, Kathmandu, Nepal
| | - S M Farhad Vahidi
- Agricultural Biotechnology Research Institute of Iran-North Branch (ABRII), Rasht, Iran
| | - Muhammad Muladno
- Department of Animal Technology and Production Science, Bogor Agricultural University, Darmaga Campus, Bogor, Indonesia
| | - Arifa N Naqvi
- Faculty of Life Sciences, Karakoram International University, Gilgit, Baltistan, Pakistan
| | - Jonna Tabell
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland
| | - Terhi Iso-Touru
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland
| | - Michael W Bruford
- School of Biosciences and Sustainable Places Research Institute, Cardiff University, Cardiff, United Kingdom
| | - Juha Kantanen
- Green Technology, Natural Resources Institute Finland (LUKE), Jokioinen, Finland Department of Biology, University of Eastern Finland, Kuopio, Finland
| | - Jian-Lin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China International Livestock Research Institute (ILRI), Nairobi, Kenya
| | - Meng-Hua Li
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
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583
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Ingram CM, Troendle NJ, Gill CA, Braude S, Honeycutt RL. Challenging the inbreeding hypothesis in a eusocial mammal: population genetics of the naked mole-rat, Heterocephalus glaber. Mol Ecol 2015; 24:4848-65. [PMID: 26407630 DOI: 10.1111/mec.13358] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Revised: 07/30/2015] [Accepted: 08/24/2015] [Indexed: 11/28/2022]
Abstract
The role of genetic relatedness in the evolution of eusociality has been the topic of much debate, especially when contrasting eusocial insects with vertebrates displaying reproductive altruism. The naked mole-rat, Heterocephalus glaber, was the first described eusocial mammal. Although this discovery was based on an ecological constraints model of eusocial evolution, early genetic studies reported high levels of relatedness in naked mole-rats, providing a compelling argument that low dispersal rates and consanguineous mating (inbreeding as a mating system) are the driving forces for the evolution of this eusocial species. One caveat to accepting this long-held view is that the original genetic studies were based on limited sampling from the species' geographic distribution. A growing body of evidence supports a contrary view, with the original samples not representative of the species-rather reflecting a single founder event, establishing a small population south of the Athi River. Our study is the first to address these competing hypotheses by examining patterns of molecular variation in colonies sampled from north and south of the Athi and Tana rivers, which based on our results, serve to isolate genetically distinct populations of naked mole-rats. Although colonies south of the Athi River share a single mtDNA haplotype and are fixed at most microsatellite loci, populations north of the Athi River are considerably more variable. Our findings support the position that the low variation observed in naked mole-rat populations south of the Athi River reflects a founder event, rather than a consequence of this species' unusual mating system.
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Affiliation(s)
- Colleen M Ingram
- Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA.,Department of Biology, University of Virginia, Charlottesville, VA, 22901, USA
| | | | - Clare A Gill
- Department of Animal Science, Texas A&M University, College Station, TX, 77843, USA
| | - Stanton Braude
- International Center for Tropical Ecology, University of Missouri, St. Louis, MO, 63130, USA.,Washington University in St. Louis, St. Louis, MO, 63130, USA
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584
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Wennerström L, Ryman N, Tison JL, Hasslow A, Dalén L, Laikre L. Genetic landscape with sharp discontinuities shaped by complex demographic history in moose (
Alces alces
). J Mammal 2015. [DOI: 10.1093/jmammal/gyv146] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
The moose ( Alces alces ) is the most intensely managed game species in Fennoscandia; approximately one-third of the population, ca. 160,000 animals, is harvested annually. Despite the species’ biological and socioeconomic importance, there are knowledge gaps with respect to its intraspecific diversity and genetic structure. Recent studies of moose in neighboring countries report 2 genetic groups in Finland, 3 in Norway with one of them suggested to be of ancient origin, and no indications of bottlenecks. To delineate the spatial genetic landscape of the Swedish moose, we used allozyme variability from over 20,000 georeferenced moose collected all over Sweden in combination with 12 microsatellites ( n > 1,200) and mitochondrial DNA (mtDNA) sequences ( n = 44). We combined individual-based and traditional statistical approaches with coalescence-based simulations. The results indicate a complex history with bottlenecks and recent expansions that is consistent with historical records. Swedish moose are separated into 2 major genetic groups, a northern and a southern one, where the southern group is further divided into 3 subgroups. The 2 main subpopulations are moderately differentiated ( FST = 0.1; RST = 0.07) and separated by sharp genetic discontinuities occurring over a relatively narrow transition zone in central Sweden that coincides with a similar, previously reported transition zone in Norway. This differentiation is not reflected in mtDNA variation, where no significant divergence was observed. Together with the FST and RST similarities, this suggests that the 2 major subpopulations in Sweden reflect divergence shaped after the postglacial recolonization of Scandinavia. Neighborhood size assessments indicate that gene flow is relatively restricted with an estimated average dispersal distance of 3.5–11.1 km, and spatial autocorrelograms suggest that genetic similarity decreases almost linearly over space resulting in continuous genetic clines within major subgroups. Management areas largely coincide with genetic clusters, simplifying the integration of genetic information into management.
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585
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Havrdová A, Douda J, Krak K, Vít P, Hadincová V, Zákravský P, Mandák B. Higher genetic diversity in recolonized areas than in refugia of Alnus glutinosa triggered by continent-wide lineage admixture. Mol Ecol 2015; 24:4759-77. [PMID: 26290117 DOI: 10.1111/mec.13348] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Revised: 08/03/2015] [Accepted: 08/16/2015] [Indexed: 02/05/2023]
Abstract
Genetic admixture is supposed to be an important trigger of species expansions because it can create the potential for selection of genotypes suitable for new climatic conditions. Up until now, however, no continent-wide population genetic study has performed a detailed reconstruction of admixture events during natural species expansions. To fill this gap, we analysed the postglacial history of Alnus glutinosa, a keystone species of European swamp habitats, across its entire distribution range using two molecular markers, cpDNA and nuclear microsatellites. CpDNA revealed multiple southern refugia located in the Iberian, Apennine, Balkan and Anatolian Peninsulas, Corsica and North Africa. Analysis of microsatellites variation revealed three main directions of postglacial expansion: (i) from the northern part of the Iberian Peninsula to Western and Central Europe and subsequently to the British Isles, (ii) from the Apennine Peninsula to the Alps and (iii) from the eastern part of the Balkan Peninsula to the Carpathians followed by expansion towards the Northern European plains. This challenges the classical paradigm that most European populations originated from refugial areas in the Carpathians. It has been shown that colonizing lineages have met several times and formed secondary contact zones with unexpectedly high population genetic diversity in Central Europe and Scandinavia. On the contrary, limited genetic admixture in southern refugial areas of A. glutinosa renders rear-edge populations in the Mediterranean region more vulnerable to extinction due to climate change.
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Affiliation(s)
- Alena Havrdová
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43, Průhonice, Czech Republic.,Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 - Suchdol, CZ-165 21, Czech Republic
| | - Jan Douda
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43, Průhonice, Czech Republic.,Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 - Suchdol, CZ-165 21, Czech Republic
| | - Karol Krak
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43, Průhonice, Czech Republic.,Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 - Suchdol, CZ-165 21, Czech Republic
| | - Petr Vít
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43, Průhonice, Czech Republic.,Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 - Suchdol, CZ-165 21, Czech Republic
| | - Věroslava Hadincová
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Petr Zákravský
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43, Průhonice, Czech Republic
| | - Bohumil Mandák
- Institute of Botany, Academy of Sciences of the Czech Republic, Zámek 1, CZ-252 43, Průhonice, Czech Republic.,Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 - Suchdol, CZ-165 21, Czech Republic
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586
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Nunez JCB, Seale TP, Fraser MA, Burton TL, Fortson TN, Hoover D, Travis J, Oleksiak MF, Crawford DL. Population Genomics of the Euryhaline Teleost Poecilia latipinna. PLoS One 2015; 10:e0137077. [PMID: 26335684 PMCID: PMC4559437 DOI: 10.1371/journal.pone.0137077] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 08/11/2015] [Indexed: 01/09/2023] Open
Abstract
Global climate change and increases in sea levels will affect coastal marine communities. The conservation of these ecologically important areas will be a challenge because of their wide geographic distribution, ecological diversity and species richness. To address this problem, we need to better understand how the genetic variation of the species in these communities is distributed within local populations, among populations and between distant regions. In this study we apply genotyping by sequencing (GBS) and examine 955 SNPs to determine Sailfin molly (Poecilia latipinna) genetic diversity among three geographically close mangrove salt marsh flats in the Florida Keys compared to populations in southern and northern Florida. The questions we are asking are whether there is sufficient genetic variation among isolated estuarine fish within populations and whether there are significant divergences among populations. Additionally, we want to know if GBS approaches agree with previous studies using more traditional molecular approaches. We are able to identify large genetic diversity within each saltmarsh community (π ≈ 36%). Additionally, among the Florida Key populations and the mainland or between southern and northern Florida regions, there are significant differences in allele frequencies seen in population structure and evolutionary relationships among individuals. Surprisingly, even though the cumulative FST value using all 955 SNPs within the three Florida Key populations is small, there are 29 loci with significant FST values, and 11 of these were outliers suggestive of adaptive divergence. These data suggest that among the salt marsh flats surveyed here, there is significant genetic diversity within each population and small but significant differences among populations. Much of the genetic variation within and among populations found here with GBS is very similar to previous studies using allozymes and microsatellites. However, the meaningful difference between GBS and these previous measures of genetic diversity is the number of loci examined, which allows more precise delineations of population structure as well as facilitates identifying loci with excessive FST values that could indicate adaptive divergence.
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Affiliation(s)
- J. C. B. Nunez
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
| | - T. P. Seale
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
| | - M. A. Fraser
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
| | - T. L. Burton
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
| | - T. N. Fortson
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
| | - D. Hoover
- Department of Biology, Florida State University, Tallahassee, FL 32306, United States of America
| | - J. Travis
- Department of Biology, Florida State University, Tallahassee, FL 32306, United States of America
| | - M. F. Oleksiak
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
| | - D. L. Crawford
- University of Miami, Rosenstiel School of Marine and Atmospheric Science, 4600 Rickenbacker Causeway, Miami, FL 33149, United States of America
- * E-mail:
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587
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Hope AG, Waltari E, Malaney JL, Payer DC, Cook JA, Talbot SL. Arctic biodiversity: increasing richness accompanies shrinking refugia for a cold-associated tundra fauna. Ecosphere 2015. [DOI: 10.1890/es15-00104.1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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588
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Hagenblad J, Hülskötter J, Acharya KP, Brunet J, Chabrerie O, Cousins SAO, Dar PA, Diekmann M, De Frenne P, Hermy M, Jamoneau A, Kolb A, Lemke I, Plue J, Reshi ZA, Graae BJ. Low genetic diversity despite multiple introductions of the invasive plant species Impatiens glandulifera in Europe. BMC Genet 2015; 16:103. [PMID: 26289555 PMCID: PMC4546075 DOI: 10.1186/s12863-015-0242-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/29/2015] [Indexed: 11/12/2022] Open
Abstract
Background Invasive species can be a major threat to native biodiversity and the number of invasive plant species is increasing across the globe. Population genetic studies of invasive species can provide key insights into their invasion history and ensuing evolution, but also for their control. Here we genetically characterise populations of Impatiens glandulifera, an invasive plant in Europe that can have a major impact on native plant communities. We compared populations from the species’ native range in Kashmir, India, to those in its invaded range, along a latitudinal gradient in Europe. For comparison, the results from 39 other studies of genetic diversity in invasive species were collated. Results Our results suggest that I. glandulifera was established in the wild in Europe at least twice, from an area outside of our Kashmir study area. Our results further revealed that the genetic diversity in invasive populations of I. glandulifera is unusually low compared to native populations, in particular when compared to other invasive species. Genetic drift rather than mutation seems to have played a role in differentiating populations in Europe. We find evidence of limitations to local gene flow after introduction to Europe, but somewhat less restrictions in the native range. I. glandulifera populations with significant inbreeding were only found in the species’ native range and invasive species in general showed no increase in inbreeding upon leaving their native ranges. In Europe we detect cases of migration between distantly located populations. Human activities therefore seem to, at least partially, have facilitated not only introductions, but also further spread of I. glandulifera across Europe. Conclusions Although multiple introductions will facilitate the retention of genetic diversity in invasive ranges, widespread invasive species can remain genetically relatively invariant also after multiple introductions. Phenotypic plasticity may therefore be an important component of the successful spread of Impatiens glandulifera across Europe. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0242-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jenny Hagenblad
- Norwegian University of Science and Technology, Department of Biology, NO-7491, Trondheim, Norway. .,IFM - Biology, Linköping University, SE-581 83, Linköping, Sweden.
| | - Jennifer Hülskötter
- Norwegian University of Science and Technology, Department of Biology, NO-7491, Trondheim, Norway. .,University of Applied Sciences Bremen, DE-28199, Bremen, Germany.
| | - Kamal Prasad Acharya
- Norwegian University of Science and Technology, Department of Biology, NO-7491, Trondheim, Norway.
| | - Jörg Brunet
- Swedish University of Agricultural Sciences, Southern Swedish Forest Research Centre, SE-230 53, Alnarp, Sweden.
| | - Olivier Chabrerie
- Plant Biodiversity Lab, FRE 3498 CNRS, Université de Picardie Jules Verne, FR-80037, Amiens, Cedex, France.
| | - Sara A O Cousins
- Department of Physical Geography and Quaternary Geology, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Pervaiz A Dar
- Department of Botany, University of Kashmir, Srinagar - 190006, Jammu & Kashmir, India.
| | - Martin Diekmann
- Vegetation Ecology and Conservation Biology, Institute of Ecology, University of Bremen, DE-28359, Bremen, Germany.
| | - Pieter De Frenne
- Forest & Nature Lab, Ghent University, BE-9090, Melle Gontrode, Belgium.
| | - Martin Hermy
- Division Forest, Nature and Landscape, University of Leuven, BE-3001, Leuven, Belgium.
| | - Aurélien Jamoneau
- Plant Biodiversity Lab, FRE 3498 CNRS, Université de Picardie Jules Verne, FR-80037, Amiens, Cedex, France.
| | - Annette Kolb
- Vegetation Ecology and Conservation Biology, Institute of Ecology, University of Bremen, DE-28359, Bremen, Germany.
| | - Isgard Lemke
- Vegetation Ecology and Conservation Biology, Institute of Ecology, University of Bremen, DE-28359, Bremen, Germany.
| | - Jan Plue
- Department of Physical Geography and Quaternary Geology, Stockholm University, SE-106 91, Stockholm, Sweden.
| | - Zafar A Reshi
- Department of Botany, University of Kashmir, Srinagar - 190006, Jammu & Kashmir, India.
| | - Bente Jessen Graae
- Norwegian University of Science and Technology, Department of Biology, NO-7491, Trondheim, Norway.
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589
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Interglacial refugia preserved high genetic diversity of the Chinese mole shrew in the mountains of southwest China. Heredity (Edinb) 2015; 116:23-32. [PMID: 26286667 DOI: 10.1038/hdy.2015.62] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 04/30/2015] [Accepted: 06/04/2015] [Indexed: 11/08/2022] Open
Abstract
The mountains of southwest China (MSC) harbor extremely high species diversity; however, the mechanism behind this diversity is unknown. We investigated to what degree the topography and climate change shaped the genetic diversity and diversification in these mountains, and we also sought to identify the locations of microrefugia areas in these mountains. For these purposes, we sampled extensively to estimate the intraspecific phylogenetic pattern of the Chinese mole shrew (Anourosorex squamipes) in southwest China throughout its range of distribution. Two mitochondrial genes, namely, cytochrome b (CYT B) and NADH dehydrogenase subunit 2 (ND2), from 383 archived specimens from 43 localities were determined for phylogeographic and demographic analyses. We used the continuous-diffusion phylogeographic model, extensive Bayesian skyline plot species distribution modeling (SDM) and approximate Bayesian computation (ABC) to explore the changes in population size and distribution through time of the species. Two phylogenetic clades were identified, and significantly higher genetic diversity was preserved in the southern subregion of the mountains. The results of the SDM, continuous-diffusion phylogeographic model, extensive Bayesian skyline plot and ABC analyses were congruent and supported that the Last Interglacial Maximum (LIG) was an unfavorable period for the mole shrews because of a high degree of seasonality; A. squamipes survived in isolated interglacial refugia mainly located in the southern subregion during the LIG and rapidly expanded during the last glacial period. These results furnished the first evidence for major Pleistocene interglacial refugia and a latitudinal effect in southwest China, and the results shedding light on the higher level of species richness in the southern subregion.
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590
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Jackson H, Strubbe D, Tollington S, Prys-Jones R, Matthysen E, Groombridge JJ. Ancestral origins and invasion pathways in a globally invasive bird correlate with climate and influences from bird trade. Mol Ecol 2015; 24:4269-85. [PMID: 26172573 PMCID: PMC4657503 DOI: 10.1111/mec.13307] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 06/28/2015] [Accepted: 07/06/2015] [Indexed: 01/15/2023]
Abstract
Invasive species present a major threat to global biodiversity. Understanding genetic patterns and evolutionary processes that reinforce successful establishment is paramount for elucidating mechanisms underlying biological invasions. Among birds, the ring-necked parakeet (Psittacula krameri) is one of the most successful invasive species, established in over 35 countries. However, little is known about the evolutionary genetic origins of this species and what population genetic signatures tell us about patterns of invasion. We reveal the ancestral origins of populations across the invasive range and explore the potential influence of climate and propagule pressure from the pet trade on observed genetic patterns. Ring-necked parakeet samples representing the ancestral native range (n = 96) were collected from museum specimens, and modern samples from the invasive range (n = 855) were gathered from across Europe, Mauritius and Seychelles, and sequenced for two mitochondrial DNA markers comprising 868 bp of cytochrome b and control region, and genotyped at 10 microsatellite loci. Invasive populations comprise birds that originate predominantly from Pakistan and northern areas of India. Haplotypes associated with more northerly distribution limits in the ancestral native range were more prevalent in invasive populations in Europe, and the predominance of Asian haplotypes in Europe is consistent with the higher number of Asian birds transported by the pet trade outside the native range. Successful establishment of invasive species is likely to be underpinned by a combination of environmental and anthropogenic influences.
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Affiliation(s)
- Hazel Jackson
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of KentMarlowe Building, Canterbury, Kent, CT2 7NR, UK
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western BankSheffield, South Yorkshire, S10 2TN, UK
| | - Diederik Strubbe
- Evolutionary Ecology Group, Department of Biology, University of AntwerpGroenenborgerlaan 171, Antwerp, 2020, Belgium
| | - Simon Tollington
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of KentMarlowe Building, Canterbury, Kent, CT2 7NR, UK
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western BankSheffield, South Yorkshire, S10 2TN, UK
| | - Robert Prys-Jones
- Bird Group, Department of Life Sciences, Natural History MuseumAkeman Street, Tring, Herts, HP23 6AP, UK
| | - Erik Matthysen
- Evolutionary Ecology Group, Department of Biology, University of AntwerpGroenenborgerlaan 171, Antwerp, 2020, Belgium
| | - Jim J Groombridge
- Durrell Institute of Conservation and Ecology, School of Anthropology and Conservation, University of KentMarlowe Building, Canterbury, Kent, CT2 7NR, UK
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591
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Sun H, Yang Z, Lin K, Liu S, Huang K, Wang X, Chu J, Huang X. The Adaptive Change of HLA-DRB1 Allele Frequencies Caused by Natural Selection in a Mongolian Population That Migrated to the South of China. PLoS One 2015; 10:e0134334. [PMID: 26230582 PMCID: PMC4521750 DOI: 10.1371/journal.pone.0134334] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 07/08/2015] [Indexed: 01/18/2023] Open
Abstract
Pathogen-driven balancing selection determines the richness of human leukocyte antigen (HLA) alleles. Changes in the pathogen spectrum may cause corresponding changes in HLA loci. Approximately 700 years ago, a Mongolian population moved from the north of China to the Yunnan region in the south of China. The pathogen spectrum in the south of China differs from that in the north. In this study, changes in the HLA genes in the Yunnan Mongolian population, as well as the underlying mechanism, were investigated. A sequence-based typing method (SBT) was used to genotype HLA-DRB1 in 470 individuals from two Mongolian populations and another five ethnic groups. Meanwhile, 10 autosomal short tandem repeats (STRs) were genotyped to assess the influence of genetic background on HLA-DRB1 frequencies. The frequencies of certain alleles changed significantly in the Mongolian population that migrated to Yunnan. For example, DRB1*12:02:01 increased from 6.1% to 35.4%. STR analysis excluded the possibility of a recent bottleneck and indicated that 50% of the genetic consistency between northern and southern Mongolians; Tajima's D value for HLA-DRB1 exon2 and dN/dS analysis showed that the HLA-DRB1 genes in both Mongolian populations were under balancing selection. However, the sites under natural selection changed. We proposed that the dramatically change of HLA frequencies in southern Mongolian was caused by a combination of inter-population gene flow and natural selection. Certain diseases specific to the south of China, such as malaria, may be the driving force behind the enhanced DRB1*12:02:01 frequency.
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Affiliation(s)
- Hao Sun
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Zhaoqing Yang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Keqin Lin
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Shuyuan Liu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Kai Huang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Xiuyun Wang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Jiayou Chu
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
| | - Xiaoqin Huang
- Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Kunming 650118, China
- * E-mail:
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592
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Wei S, Cao L, Gong Y, Shi B, Wang S, Zhang F, Guo X, Wang Y, Chen X. Population genetic structure and approximate
B
ayesian computation analyses reveal the southern origin and northward dispersal of the oriental fruit moth
G
rapholita molesta
(
L
epidoptera:
T
ortricidae) in its native range. Mol Ecol 2015; 24:4094-111. [DOI: 10.1111/mec.13300] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 06/22/2015] [Accepted: 06/29/2015] [Indexed: 11/30/2022]
Affiliation(s)
- Shu‐Jun Wei
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Li‐Jun Cao
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Ya‐Jun Gong
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Bao‐Cai Shi
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Su Wang
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Fan Zhang
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Xiao‐Jun Guo
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Yuan‐Min Wang
- Institute of Plant and Environmental Protection Beijing Academy of Agriculture and Forestry Sciences 9 Shuguanghuayuan Middle Road, Haidian District Beijing 100097 China
| | - Xue‐Xin Chen
- Institute of Insect Sciences Zhejiang University 866 Yuhangtang Road Hangzhou 310058 China
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593
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Vera-Escalona I, Habit E, Ruzzante DE. Echoes of a distant time: effects of historical processes on contemporary genetic patterns in Galaxias platei in Patagonia. Mol Ecol 2015; 24:4112-28. [PMID: 26147523 DOI: 10.1111/mec.13303] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Revised: 06/21/2015] [Accepted: 06/24/2015] [Indexed: 12/11/2022]
Abstract
Interpreting the genetic structure of a metapopulation as the outcome of gene flow over a variety of timescales is essential for the proper understanding of how changes in landscape affect biological connectivity. Here we contrast historical and contemporary connectivity in two metapopulations of the freshwater fish Galaxias platei in northern and southernmost Patagonia where paleolakes existed during the Holocene and Pleistocene, respectively. Contemporary gene flow was mostly high and asymmetrical in the northern system while extremely reduced in the southernmost system. Historical migration patterns were high and symmetric in the northern system and high and largely asymmetric in the southern system. Both systems showed a moderate structure with a clear pattern of isolation by distance (IBD). Effective population sizes were smaller in populations with low contemporary gene flow. An approximate Bayesian computation (ABC) approach suggests a late Holocene colonization of the lakes in the northern system and recent divergence of the populations from refugial populations from east and west of the Andes. For the southern system, the ABC approach reveals that some of the extant G. platei populations most likely derive from an ancestral population inhabiting a large Pleistocene paleolake while the rest derive from a higher-altitude lake. Our results suggest that neither historical nor contemporary processes individually fully explain the observed structure and geneflow patterns and both are necessary for a proper understanding of the factors that affect diversity and its distribution. Our study highlights the importance of a temporal perspective on connectivity to analyse the diversity of spatially complex metapopulations.
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Affiliation(s)
- Iván Vera-Escalona
- Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS, Canada
| | - Evelyn Habit
- Departamento de Sistemas Acuáticos, Facultad de Ciencias Ambientales y Centro EULA-Chile, Universidad de Concepción, Barrio Universitario s/n, Concepción, Chile
| | - Daniel E Ruzzante
- Department of Biology, Dalhousie University, 1355 Oxford St., Halifax, NS, Canada
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594
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Kvist L, Aminian L, Rouger R, Kreivi M, Laurila M, Hyvärinen M, Aspi J, Markkola A. A climatic relict or a long distance disperser: conservation genetics of an Arctic disjunct polyploid plant. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0756-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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595
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Brüniche-Olsen A, Jones ME, Austin JJ, Burridge CP, Holland BR. Extensive population decline in the Tasmanian devil predates European settlement and devil facial tumour disease. Biol Lett 2015; 10:20140619. [PMID: 25376800 DOI: 10.1098/rsbl.2014.0619] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Tasmanian devil (Sarcophilus harrisii) was widespread in Australia during the Late Pleistocene but is now endemic to the island of Tasmania. Low genetic diversity combined with the spread of devil facial tumour disease have raised concerns for the species' long-term survival. Here, we investigate the origin of low genetic diversity by inferring the species' demographic history using temporal sampling with summary statistics, full-likelihood and approximate Bayesian computation methods. Our results show extensive population declines across Tasmania correlating with environmental changes around the last glacial maximum and following unstable climate related to increased 'El Niño-Southern Oscillation' activity.
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Affiliation(s)
- Anna Brüniche-Olsen
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart 7001,Tasmania, Australia
| | - Menna E Jones
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart 7001,Tasmania, Australia
| | - Jeremy J Austin
- School of Earth and Environmental Sciences, University of Adelaide, North Terrace, South Australia 5005, Australia
| | - Christopher P Burridge
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart 7001,Tasmania, Australia
| | - Barbara R Holland
- School of Mathematics and Physics, University of Tasmania, Private Bag 37, Hobart 7001, Tasmania, Australia
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596
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597
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Population genetics of the speckled peacock bass (Cichla temensis), South America’s most important inland sport fishery. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0744-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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598
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Reed JM, Stockwell CA. Evaluating an icon of population persistence: the Devil's Hole pupfish. Proc Biol Sci 2015; 281:20141648. [PMID: 25232135 DOI: 10.1098/rspb.2014.1648] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The Devil's Hole pupfish Cyprinodon diabolis has iconic status among conservation biologists because it is one of the World's most vulnerable species. Furthermore, C. diabolis is the most widely cited example of a persistent, small, isolated vertebrate population; a chronic exception to the rule that small populations do not persist long in isolation. It is widely asserted that this species has persisted in small numbers (less than 400 adults) for 10 000-20 000 years, but this assertion has never been evaluated. Here, we analyse the time series of count data for this species, and we estimate time to coalescence from microsatellite data to evaluate this hypothesis. We conclude that mean time to extinction is approximately 360-2900 years (median 410-1800), with less than a 2.1% probability of persisting 10 000 years. Median times to coalescence varied from 217 to 2530 years, but all five approximations had wide credible intervals. Our analyses suggest that Devil's Hole pupfish colonized this pool well after the Pleistocene Lakes receded, probably within the last few hundred to few thousand years; this could have occurred through human intervention.
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Affiliation(s)
- J Michael Reed
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Craig A Stockwell
- Department of Biological Sciences, North Dakota State University, Fargo, ND 58108, USA
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599
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Shum P, Pampoulie C, Kristinsson K, Mariani S. Three-dimensional post-glacial expansion and diversification of an exploited oceanic fish. Mol Ecol 2015; 24:3652-67. [PMID: 26073046 PMCID: PMC4744735 DOI: 10.1111/mec.13262] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/22/2015] [Accepted: 05/29/2015] [Indexed: 01/27/2023]
Abstract
Vertical divergence in marine organisms is being increasingly documented, yet much remains to be carried out to understand the role of depth in the context of phylogeographic reconstruction and the identification of management units. An ideal study system to address this issue is the beaked redfish, Sebastes mentella – one of four species of ‘redfish’ occurring in the North Atlantic – which is known for a widely distributed ‘shallow‐pelagic’ oceanic type inhabiting waters between 250 and 550 m, and a more localized ‘deep‐pelagic’ population dwelling between 550 and 800 m, in the oceanic habitat of the Irminger Sea. Here, we investigate the extent of population structure in relation to both depth and geographic spread of oceanic beaked redfish throughout most of its distribution range. By sequencing the mitochondrial control region of 261 redfish collected over a decadal interval, and combining 160 rhodopsin coding nuclear sequences and previously genotyped microsatellite data, we map the existence of two strongly divergent evolutionary lineages with significantly different distribution patterns and historical demography, and whose genetic variance is mostly explained by depth. Combined genetic data, analysed via independent approaches, are consistent with a Late Pleistocene lineage split, where segregation by depth probably resulted from the interplay of climatic and oceanographic processes with life history and behavioural traits. The ongoing process of diversification in North Atlantic S. mentella may serve as an ‘hourglass’ to understand speciation and adaptive radiation in Sebastes and in other marine taxa distributed across a depth gradient.
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Affiliation(s)
- Peter Shum
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, UK
| | | | | | - Stefano Mariani
- Ecosystems and Environment Research Centre, School of Environment and Life Sciences, University of Salford, Salford, M5 4WT, UK
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600
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Xenikoudakis G, Ersmark E, Tison JL, Waits L, Kindberg J, Swenson JE, Dalén L. Consequences of a demographic bottleneck on genetic structure and variation in the Scandinavian brown bear. Mol Ecol 2015; 24:3441-54. [PMID: 26042479 DOI: 10.1111/mec.13239] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Revised: 05/07/2015] [Accepted: 05/08/2015] [Indexed: 11/30/2022]
Abstract
The Scandinavian brown bear went through a major decline in population size approximately 100 years ago, due to intense hunting. After being protected, the population subsequently recovered and today numbers in the thousands. The genetic diversity in the contemporary population has been investigated in considerable detail, and it has been shown that the population consists of several subpopulations that display relatively high levels of genetic variation. However, previous studies have been unable to resolve the degree to which the demographic bottleneck impacted the contemporary genetic structure and diversity. In this study, we used mitochondrial and microsatellite DNA markers from pre- and postbottleneck Scandinavian brown bear samples to investigate the effect of the bottleneck. Simulation and multivariate analysis suggested the same genetic structure for the historical and modern samples, which are clustered into three subpopulations in southern, central and northern Scandinavia. However, the southern subpopulation appears to have gone through a marked change in allele frequencies. When comparing the mitochondrial DNA diversity in the whole population, we found a major decline in haplotype numbers across the bottleneck. However, the loss of autosomal genetic diversity was less pronounced, although a significant decline in allelic richness was observed in the southern subpopulation. Approximate Bayesian computations provided clear support for a decline in effective population size during the bottleneck, in both the southern and northern subpopulations. These results have implications for the future management of the Scandinavian brown bear because they indicate a recent loss in genetic diversity and also that the current genetic structure may have been caused by historical ecological processes rather than recent anthropogenic persecution.
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Affiliation(s)
- G Xenikoudakis
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden.,Department of Zoology, Stockholm University, SE-106 91, Stockholm, Sweden
| | - E Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden.,Department of Zoology, Stockholm University, SE-106 91, Stockholm, Sweden
| | - J-L Tison
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - L Waits
- Department of Fish and Wildlife Sciences, University of Idaho, 875 Perimeter Drive MS 1136, Moscow, ID, 83844, USA
| | - J Kindberg
- Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, SE-90183, Umeå, Sweden
| | - J E Swenson
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, NO-1432, Ås, Norway.,Norwegian Institute for Nature Research, PO Box 5685 Sluppen, NO-7485, Trondheim, Norway
| | - L Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
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