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Boria RA, Blois JL. Phylogeography within the Peromyscus maniculatus species group: Understanding past distribution of genetic diversity and areas of refugia in western North America. Mol Phylogenet Evol 2023; 180:107701. [PMID: 36623612 DOI: 10.1016/j.ympev.2023.107701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 12/09/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
The effects of anthropogenic climate change on biodiversity have been recognized on every continent, ocean, and across different taxonomic groups. Here, we study the range dynamics and demography of a cosmopolitan species: the deer mouse, Peromyscus maniculatus. We generated a multilocus SNP dataset using the ddRADseq protocol for 218 individuals across the geographic range within three western North American lineages of this species group. We evaluated population structure using several methods and explored the correlation between geographic and genetic distances. We modeled the demographic history using a site frequency spectrum approach and used a machine learning algorithm to infer current and past (Last Glacial Maximum; LGM) environmental suitability. Lastly, we explored the origin of population expansion for the identified lineages. The genome-wide SNP dataset was able to identify-three regionally distinct groups- 1) P. m. gambelii (southern California); 2) P. keeni (Pacific Northwest); 3) P. m. sonoriensis (a broad population spanning the Pacific Northwest through central California and across the Rocky Mountains into the Great Plains). Demographic analysis indicated the splits between the three populations occurred within the last 500 thousand years, with one very recent (late Holocene) split. Ecological niche models for each of these lineages predicted suitable environment present throughout their known ranges for current conditions, and a severe reduction of northern habitat in the past. The deer mouse has responded to past climate changes by expanding its range during interglacial periods and contracting its range during glacial periods leading to strong population differentiation. But lower magnitude climate change or other processes within the Holocene interglacial period led to population differentiation as well, which is likely still ongoing today given the substantial anthropogenic climate change and other landscape transformations caused by humans during the Anthropocene. By understanding the historical processes that led to the contemporary geographic distribution of biodiversity, we can determine the relative importance of different factors that shape biodiversity, now and into the future.
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Affiliation(s)
- Robert A Boria
- School of Natural Sciences, University of California- Merced, Merced, CA 95343, USA; Present address: Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Jessica L Blois
- School of Natural Sciences, University of California- Merced, Merced, CA 95343, USA
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Lucid M, Cushman S, Robinson L, Kortello A, Hausleitner D, Mowat G, Ehlers S, Gillespie S, Svancara LK, Sullivan J, Rankin A, Paetkau D. Carnivore Contact: A Species Fracture Zone Delineated Amongst Genetically Structured North American Marten Populations ( Martes americana and Martes caurina). Front Genet 2020; 11:735. [PMID: 32754203 PMCID: PMC7370953 DOI: 10.3389/fgene.2020.00735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/17/2020] [Indexed: 11/13/2022] Open
Abstract
North American martens are forest dependent, influenced by human activity, and climate vulnerable. They have long been managed and harvested throughout their range as the American marten (Martes americana). Recent work has expanded evidence for the original description of two species in North America — M. americana and the Pacific Coast marten, M. caurina — but the geographic boundary between these groups has not been described in detail. From 2010 to 2016 we deployed 734 multi-taxa winter bait stations across a 53,474 km2 study area spanning seven mountain ranges within the anticipated contact zone along the border of Canada and the United States. We collected marten hair samples and developed genotypes for 15 polymorphic microsatellite loci for 235 individuals, and 493 base-pair sequences of the mtDNA gene COI for 175 of those individuals. Both nuclear and mitochondrial genetic structure identified a sharp break across the Clark Fork Valley, United States with M. americana and M. caurina occurring north and south of the break, respectively. We estimated global effective population size (Ne) for each mountain range, clinal genetic neighborhood sizes (NS), calculated observed (Ho) and expected (He) heterozygosity, fixation index (FST), and clinal measures of allelic richness (Ar), Ho, and inbreeding coefficient (FIS). Despite substantial genetic structure, we detected hybridization along the fracture zone with both contemporary (nuclear DNA) and historic (mtDNA) gene flow. Marten populations in our study area are highly structured and the break across the fracture zone being the largest documented in North America (FST range 0.21–0.34, mean = 0.27). With the exception of the Coeur d’Alene Mountains, marten were well distributed across higher elevation portions of our sampling area. Clinal NS values were variable suggesting substantial heterogeneity in marten density and movement. For both M. americana and M. caurina, elevationaly dependent gene flow and high genetic population structure suggest that connectivity corridors will be important to ensuring long-term population persistence. Our study is an example of how a combination of global and clinal molecular data analyses can provide important information for natural resource management.
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Affiliation(s)
- Michael Lucid
- Idaho Department of Fish and Game, Coeur d'Alene, ID, United States
| | - Sam Cushman
- US Forest Service, Rocky Mountain Research Station, Flagstaff, AZ, United States
| | - Lacy Robinson
- Idaho Department of Fish and Game, Coeur d'Alene, ID, United States.,Rainforest Ecological, Sandpoint, ID, United States
| | | | | | - Garth Mowat
- British Columbia Ministry of the Environment, Nelson, BC, Canada
| | - Shannon Ehlers
- Idaho Department of Fish and Game, Coeur d'Alene, ID, United States.,Kootenai Tribe of Idaho, Bonners Ferry, ID, United States
| | | | - Leona K Svancara
- Idaho Department of Fish and Game, Coeur d'Alene, ID, United States
| | - Jack Sullivan
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
| | - Andrew Rankin
- Department of Biological Sciences, University of Idaho, Moscow, ID, United States
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Sawyer YE, MacDonald SO, Lessa EP, Cook JA. Living on the edge: Exploring the role of coastal refugia in the Alexander Archipelago of Alaska. Ecol Evol 2019; 9:1777-1797. [PMID: 30847072 PMCID: PMC6392352 DOI: 10.1002/ece3.4861] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 11/27/2018] [Accepted: 12/04/2018] [Indexed: 12/14/2022] Open
Abstract
Although islands are of long-standing interest to biologists, only a handful of studies have investigated the role of climatic history in shaping evolutionary diversification in high-latitude archipelagos. In this study of the Alexander Archipelago (AA) of Southeast Alaska, we address the impact of glacial cycles on geographic genetic structure for three mammals co-distributed along the North Pacific Coast. We examined variation in mitochondrial and nuclear loci for long-tailed voles (Microtus longicaudus), northwestern deermice (Peromyscus keeni), and dusky shrews (Sorex monticola), and then tested hypotheses derived from Species Distribution Models, reconstructions of paleoshorelines, and island area and isolation. In all three species, we identified paleoendemic clades that likely originated in coastal refugia, a finding consistent with other paleoendemic lineages identified in the region such as ermine. Although there is spatial concordance at the regional level for endemism, finer scale spatial and temporal patterns are less clearly defined. Demographic expansion across the region for these distinctive clades is also evident and highlights the dynamic history of Late Quaternary contraction and expansion that characterizes high-latitude species.
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Affiliation(s)
- Yadéeh E. Sawyer
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew Mexico
| | - Stephen O. MacDonald
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew Mexico
| | - Enrique P. Lessa
- Departamento de Ecología y Evolución, Facultad de CienciasUniversidad de la RepúblicaMontevideoUruguay
| | - Joseph A. Cook
- Department of Biology and Museum of Southwestern BiologyUniversity of New MexicoAlbuquerqueNew Mexico
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Chavez AS, Maher SP, Arbogast BS, Kenagy GJ. DIVERSIFICATION AND GENE FLOW IN NASCENT LINEAGES OF ISLAND AND MAINLAND NORTH AMERICAN TREE SQUIRRELS (TAMIASCIURUS). Evolution 2014; 68:1094-109. [DOI: 10.1111/evo.12336] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 11/29/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Andreas S. Chavez
- Burke Museum and Department of Biology; University of Washington; Seattle Washington 98195
| | - Sean P. Maher
- Museum of Vertebrate Zoology; University of California; Berkeley California 94720
| | - Brian S. Arbogast
- Department of Biology and Marine Biology; University of North Carolina Wilmington; Wilmington North Carolina 28403
| | - G. J. Kenagy
- Burke Museum and Department of Biology; University of Washington; Seattle Washington 98195
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Ávila-Valle ZA, Castro-Campillo A, León-Paniagua L, Salgado-Ugalde IH, Navarro-Sigüenza AG, Hernández-Baños BE, Ramírez-Pulido J. Geographic variation and molecular evidence of the Blackish Deer Mouse complex (Peromyscus furvus, Rodentia: Muridae). Mamm Biol 2012. [DOI: 10.1016/j.mambio.2011.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Wilson AG, Arcese P, Chan YL, Patten MA. Micro-spatial genetic structure in song sparrows (Melospiza melodia). CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0134-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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SHAFER AARONBA, CULLINGHAM CATHERINEI, CÔTÉ STEEVED, COLTMAN DAVIDW. Of glaciers and refugia: a decade of study sheds new light on the phylogeography of northwestern North America. Mol Ecol 2010; 19:4589-621. [PMID: 20849561 DOI: 10.1111/j.1365-294x.2010.04828.x] [Citation(s) in RCA: 260] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- AARON B. A. SHAFER
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - CATHERINE I. CULLINGHAM
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - STEEVE D. CÔTÉ
- Département de Biologie and Centre for Northern Studies, Université Laval, Québec, Québec G1V 0A6, Canada
| | - DAVID W. COLTMAN
- Department of Biological Sciences, CW 405 Biological Sciences Building, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
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Weckworth BV, Talbot SL, Cook JA. Phylogeography of wolves (Canis lupus) in the Pacific Northwest. J Mammal 2010. [DOI: 10.1644/09-mamm-a-036.1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Latch EK, Amann RP, Jacobson JP, Rhodes OE. Competing hypotheses for the etiology of cryptorchidism in Sitka black-tailed deer: an evaluation of evolutionary alternatives. Anim Conserv 2008. [DOI: 10.1111/j.1469-1795.2008.00174.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Wilson A, Arcese P, Keller LF, Pruett CL, Winker K, Patten MA, Chan Y. The contribution of island populations to in situ genetic conservation. CONSERV GENET 2008. [DOI: 10.1007/s10592-008-9612-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Lucid M, Cook J. Cytochrome-b haplotypes suggest an undescribed Peromyscus species from the Yukon. CAN J ZOOL 2007. [DOI: 10.1139/z07-076] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Peromyscus maniculatus (Wagner, 1845) and Peromyscus keeni Merriam, 1897 are two species of deer mouse currently recognized in the Yukon. Phylogenetic analyses (Kimura two-parameter and maximum parsimony) of cytochrome-b sequences (560 base pairs) from deer mouse specimens (n = 4) collected near Haines Junction, Yukon, resulted in a monophyletic clade genetically distant from the two currently recognized species. We suggest that the Haines Junction specimens may represent a previously undescribed peromyscine species. Peromyscus arcticus is an available name.
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Affiliation(s)
- M.K. Lucid
- Idaho State University, Department of Biological Sciences, Pocatello, ID 83209, USA
| | - J.A. Cook
- Idaho State University, Department of Biological Sciences, Pocatello, ID 83209, USA
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Dragoo JW, Lackey JA, Moore KE, Lessa EP, Cook JA, Yates TL. Phylogeography of the deer mouse (Peromyscus maniculatus) provides a predictive framework for research on hantaviruses. J Gen Virol 2006; 87:1997-2003. [PMID: 16760402 DOI: 10.1099/vir.0.81576-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Phylogeographical partitioning of Sin Nombre and Monongahela viruses (hantaviruses) may reflect that of their primary rodent host, the deer mouse (Peromyscus maniculatus). Lack of a comprehensive assessment of phylogeographical variation of the host has precluded the possibility of predicting spatial limits of existing strains of these viruses or geographical regions where novel viral strains might emerge. The complete cytochrome b gene was sequenced for 206 deer mice collected from sites throughout North America to provide a foundation for future studies of spatial structure and evolution of this ubiquitous host. Bayesian analyses of these sequences partitioned deer mice into six largely allopatric lineages, some of which may represent unrecognized species. The geographical distributions of these lineages were probably shaped by Quaternary climatic events. Populations of mice were apparently restricted to refugia during glacial advances, where they experienced genetic divergence. Expansion of these populations, following climatic amelioration, brought genetically distinctive forms into contact. Occurrence of parallel changes in virus strains can now be explored in appropriate regions. In New Mexico, for example, near the location where Sin Nombre virus was first discovered, there are three genetically distinctive lineages of deer mice whose geographical ranges need to be delineated precisely. The phylogeography of P. maniculatus provides a framework for interpreting geographical variability, not only in hosts, but also in associated viral variants and disease transmission, and an opportunity to predict the potential geographical distribution of newly emerging viral strains.
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Affiliation(s)
- Jerry W Dragoo
- Department of Biology, Museum of Southwestern Biology (MSB), The University of New Mexico, Albuquerque, NM 87131, USA
| | - J Alden Lackey
- Department of Biological Sciences, Oswego State University, Oswego, NY 13126, USA
| | - Kathryn E Moore
- School of Medicine, The University of New Mexico, Albuquerque, NM 87131, USA
| | - Enrique P Lessa
- Laboratorio de Evolución, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Joseph A Cook
- Department of Biology, Museum of Southwestern Biology (MSB), The University of New Mexico, Albuquerque, NM 87131, USA
| | - Terry L Yates
- Department of Biology, Museum of Southwestern Biology (MSB), The University of New Mexico, Albuquerque, NM 87131, USA
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Weckworth BV, Talbot S, Sage GK, Person DK, Cook J. A signal for independent coastal and continental histories among North American wolves. Mol Ecol 2006; 14:917-31. [PMID: 15773925 DOI: 10.1111/j.1365-294x.2005.02461.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Relatively little genetic variation has been uncovered in surveys across North American wolf populations. Pacific Northwest coastal wolves, in particular, have never been analysed. With an emphasis on coastal Alaska wolf populations, variation at 11 microsatellite loci was assessed. Coastal wolf populations were distinctive from continental wolves and high levels of diversity were found within this isolated and relatively small geographical region. Significant genetic structure within southeast Alaska relative to other populations in the Pacific Northwest, and lack of significant correlation between genetic and geographical distances suggest that differentiation of southeast Alaska wolves may be caused by barriers to gene flow, rather than isolation by distance. Morphological research also suggests that coastal wolves differ from continental populations. A series of studies of other mammals in the region also has uncovered distinctive evolutionary histories and high levels of endemism along the Pacific coast. Divergence of these coastal wolves is consistent with the unique phylogeographical history of the biota of this region and re-emphasizes the need for continued exploration of this biota to lay a framework for thoughtful management of southeast Alaska.
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Affiliation(s)
- Byron V Weckworth
- Division of Biological Sciences, Idaho State University, Pocatello, ID 83209-8007, USA.
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