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Horníková M, Lanier HC, Marková S, Escalante MA, Searle JB, Kotlík P. Genetic admixture drives climate adaptation in the bank vole. Commun Biol 2024; 7:863. [PMID: 39009753 PMCID: PMC11251159 DOI: 10.1038/s42003-024-06549-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 07/03/2024] [Indexed: 07/17/2024] Open
Abstract
Genetic admixture introduces new variants at relatively high frequencies, potentially aiding rapid responses to environmental changes. Here, we evaluate its role in adaptive variation related to climatic conditions in bank voles (Clethrionomys glareolus) in Britain, using whole-genome data. Our results reveal loci showing excess ancestry from one of the two postglacial colonist populations inconsistent with overall admixture patterns. Notably, loci associated with climate adaptation exhibit disproportionate amounts of excess ancestry, highlighting the impact of admixture between colonist populations on local adaptation. The results suggest strong and localized selection on climate-adaptive loci, as indicated by steep clines and/or shifted cline centres, during population replacement. A subset, including a haemoglobin gene, is associated with oxidative stress responses, underscoring a role of oxidative stress in local adaptation. Our study highlights the important contribution of admixture during secondary contact between populations from distinct climatic refugia enriching adaptive diversity. Understanding these dynamics is crucial for predicting future adaptive capacity to anthropogenic climate change.
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Affiliation(s)
- Michaela Horníková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Hayley C Lanier
- Department of Biology, Program in Ecology & Evolutionary Biology, University of Oklahoma, Norman, OK, USA
- Sam Noble Museum, University of Oklahoma, Norman, OK, USA
| | - Silvia Marková
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Marco A Escalante
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Petr Kotlík
- Laboratory of Molecular Ecology, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Liběchov, Czech Republic.
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As the Goose Flies: Migration Routes and Timing Influence Patterns of Genetic Diversity in a Circumpolar Migratory Herbivore. DIVERSITY 2022. [DOI: 10.3390/d14121067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
Migration schedules and the timing of other annual events (e.g., pair formation and molt) can affect the distribution of genetic diversity as much as where these events occur. The greater white-fronted goose (Anser albifrons) is a circumpolar goose species, exhibiting temporal and spatial variation of events among populations during the annual cycle. Previous range-wide genetic assessments of the nuclear genome based on eight microsatellite loci suggest a single, largely panmictic population despite up to five subspecies currently recognized based on phenotypic differences. We used double digest restriction-site associated DNA (ddRAD-seq) and mitochondrial DNA (mtDNA) sequence data to re-evaluate estimates of spatial genomic structure and to characterize how past and present processes have shaped the patterns of genetic diversity and connectivity across the Arctic and subarctic. We uncovered previously undetected inter-population differentiation with genetic clusters corresponding to sampling locales associated with current management groups. We further observed subtle genetic clustering within each management unit that can be at least partially explained by the timing and directionality of migration events along with other behaviors during the annual cycle. The Tule Goose (A. a. elgasi) and Greenland subspecies (A. a. flavirostris) showed the highest level of divergence among all sampling locales investigated. The recovery of previously undetected broad and fine-scale spatial structure suggests that the strong cultural transmission of migratory behavior restricts gene flow across portions of the species’ range. Our data further highlight the importance of re-evaluating previous assessments conducted based on a small number of highly variable genetic markers in phenotypically diverse species.
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Droghini A, Christie KS, Kelty RR, Schuette PA, Gotthardt T. Conservation status, threats, and information needs of small mammals in Alaska. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Amanda Droghini
- Alaska Center for Conservation Science University of Alaska Anchorage Anchorage Alaska USA
| | - Katherine S. Christie
- Threatened, Endangered, and Diversity Program Alaska Department of Fish and Game Anchorage Alaska USA
| | - Rachel R. Kelty
- Alaska Center for Conservation Science University of Alaska Anchorage Anchorage Alaska USA
| | - Paul A. Schuette
- Alaska Center for Conservation Science University of Alaska Anchorage Anchorage Alaska USA
- Marine Mammals Management US Fish and Wildlife Service Anchorage Alaska USA
| | - Tracey Gotthardt
- Threatened, Endangered, and Diversity Program Alaska Department of Fish and Game Anchorage Alaska USA
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Rankin AM, Schwartz RS, Floyd CH, Galbreath KE. Contrasting consequences of historical climate change for marmots at northern and temperate latitudes. J Mammal 2019. [DOI: 10.1093/jmammal/gyz025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Andrew M Rankin
- Department of Biological Sciences Program in Bioinformatics and Computational Biology, University of Idaho, Moscow, ID USA
| | - Rachel S Schwartz
- Department of Biological Sciences, University of Rhode Island, Kingston, RI, USA
| | - Chris H Floyd
- Department of Natural Resources Science, University of Rhode Island, Kingston, RI USA
| | - Kurt E Galbreath
- Department of Biology, Northern Michigan University, Marquette, MI USA (KEG)
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Ikeda H, Setoguchi H. Importance of Beringia for the divergence of two northern Pacific alpine plants, Phyllodoce aleutica and Phyllodoce glanduliflora (Ericaceae). Biol J Linn Soc Lond 2017. [DOI: 10.1093/biolinnean/blx071] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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An endemic rat species complex is evidence of moderate environmental changes in the terrestrial biodiversity centre of China through the late Quaternary. Sci Rep 2017; 7:46127. [PMID: 28393882 PMCID: PMC5385558 DOI: 10.1038/srep46127] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 03/13/2017] [Indexed: 11/08/2022] Open
Abstract
The underlying mechanisms that allow the Hengduan Mountains (HDM), the terrestrial biodiversity centre of China, to harbour high levels of species diversity remain poorly understood. Here, we sought to explore the biogeographic history of the endemic rat, Niviventer andersoni species complex (NASC), and to understand the long-term persistence of high species diversity in this region. In contrast to previous studies that have proposed regional refuges in eastern or southern of the HDM and emphasized the influence of climatic oscillations on local vertebrates, we found that HDM as a whole acted as refuge for the NASC and that the historical range shifts of NASC mainly occurred in the marginal regions. Demographic analyses revealed slight recent population decline in Yunnan and south-eastern Tibet, whereas of the populations in Sichuan and of the entire NASC were stable. This pattern differs greatly from classic paradigms of temperate or alpine and holarctic species. Interestingly, the mean elevation, area and climate of potential habitats of clade a (N. excelsior), an alpine inhabitant, showed larger variations than did those of clade b (N. andersoni), a middle-high altitude inhabitant. These species represent the evolutionary history of montane small mammals in regions that were less affected by the Quaternary climatic changes.
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Cook JA, McLean BS, Jackson DJ, Colella JP, Greiman SE, Tkach VV, Jung TS, Dunnum JL. First record of the Holarctic least shrew (Sorex minutissimus) and associated helminths from Canada: new light on northern Pleistocene refugia. CAN J ZOOL 2016. [DOI: 10.1139/cjz-2015-0212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We report the first Canadian record of the Holarctic least shrew (Sorex minutissimus Zimmermann, 1780) and associated helminth worms, collected along the Dempster Highway in central Yukon in 2014. We identify the specimen based on morphological characters, characterize the habitat, report other mammals and helminth species associated with this specimen, and use mitochondrial DNA sequences to place the specimen within a phylogenetic context and address Pleistocene refugial hypotheses. Although long considered an Eurasian endemic, the diminutive least shrew was first reported from Alaska in 1994. Our new record for Canada indicates that the species may occur at least as far east as the MacKenzie River and DNA variation suggests this species persisted only in the Beringian refugium in North America during the Last Glacial Maximum. The discovery of a new mammal and associated parasites for Canada points to the urgent need for more detailed information on high-latitude biotas in North America, data that are best obtained through museum-based field surveys, particularly for small, cryptic species.
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Affiliation(s)
- Joseph A. Cook
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Bryan S. McLean
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Donavan J. Jackson
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Jocelyn P. Colella
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Stephen E. Greiman
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Vasyl V. Tkach
- Department of Biology, University of North Dakota, Grand Forks, ND 58202, USA
| | - Thomas S. Jung
- Yukon Department of Environment, Whitehorse, YT Y1A 2C6, Canada
| | - Jonathan L. Dunnum
- Museum of Southwestern Biology and Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
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Lanier HC, Massatti R, He Q, Olson LE, Knowles LL. Colonization from divergent ancestors: glaciation signatures on contemporary patterns of genomic variation in Collared Pikas (Ochotona collaris). Mol Ecol 2015; 24:3688-705. [DOI: 10.1111/mec.13270] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 05/27/2015] [Accepted: 05/29/2015] [Indexed: 01/16/2023]
Affiliation(s)
- Hayley C. Lanier
- Department of Zoology and Physiology; University of Wyoming at Casper; Casper WY 82601 USA
| | - Rob Massatti
- Department of Ecology and Evolutionary Biology; The University of Michigan; Ann Arbor MI 41809-1079 USA
| | - Qixin He
- Department of Ecology and Evolutionary Biology; The University of Michigan; Ann Arbor MI 41809-1079 USA
| | - Link E. Olson
- University of Alaska Museum; University of Alaska Fairbanks; Fairbanks AK 99775 USA
| | - L. Lacey Knowles
- Department of Ecology and Evolutionary Biology; The University of Michigan; Ann Arbor MI 41809-1079 USA
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