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Zhao L, Zhang JX, Zhang YH. Genetic boundary and gene flow between 2 parapatric subspecies of brown rats. Curr Zool 2020; 66:677-688. [PMID: 33391367 PMCID: PMC7769575 DOI: 10.1093/cz/zoaa027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/30/2020] [Indexed: 12/30/2022] Open
Abstract
Two parapatric Rattus norvegicus subspecies, R. n. humiliatus (RNH) and R. n. caraco (RNC), are classified according to morphological divergence and are mainly distributed in North and Northeast China. Here, we aimed to explore the population genetic structure, genetic boundary, and gene flow in these rats using 16 microsatellite loci. Structure analysis and principal component analysis revealed 3 ancestral clusters. We found that the intermediate cluster exhibited higher genetic diversity and a lower inbreeding coefficient than the other 2 clusters. The genetic differentiation between the 3 clusters was significant but weak, with a higher FST value being observed between the clusters on both sides. The subspecies boundary inferred from microsatellite markers may indicate the existence of an admixture or hybridization area covering Liaoning, Inner Mongolia, and Jilin Provinces, rather than corresponding to the administrative provincial boundaries between Liaoning and Jilin. The RNH and RNC subspecies presented moderate gene exchange and an asymmetric bidirectional gene flow pattern, with higher gene flow from the RNH subspecies to the RNC subspecies, constraining speciation. Such genetic characteristics might be explained by biological processes such as dispersal ability, mate choice, and dynamic lineage boundaries.
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Affiliation(s)
- Lei Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Xu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yao-Hua Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
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Schield DR, Perry BW, Adams RH, Card DC, Jezkova T, Pasquesi GIM, Nikolakis ZL, Row K, Meik JM, Smith CF, Mackessy SP, Castoe TA. Allopatric divergence and secondary contact with gene flow: a recurring theme in rattlesnake speciation. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz077] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Abstract
The study of recently diverged lineages whose geographical ranges come into contact can provide insight into the early stages of speciation and the potential roles of reproductive isolation in generating and maintaining species. Such insight can also be important for understanding the strategies and challenges for delimiting species within recently diverged species complexes. Here, we use mitochondrial and nuclear genetic data to study population structure, gene flow and demographic history across a geographically widespread rattlesnake clade, the western rattlesnake species complex (Crotalus cerberus, Crotalus viridis, Crotalus oreganus and relatives), which contains multiple lineages with ranges that overlap geographically or contact one another. We find evidence that the evolutionary history of this group does not conform to a bifurcating tree model and that pervasive gene flow has broadly influenced patterns of present-day genetic diversity. Our results suggest that lineage diversity has been shaped largely by drift and divergent selection in isolation, followed by secondary contact, in which reproductive isolating mechanisms appear weak and insufficient to prevent introgression, even between anciently diverged lineages. The complexity of divergence and secondary contact with gene flow among lineages also provides new context for why delimiting species within this complex has been difficult and contentious historically.
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Affiliation(s)
- Drew R Schield
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Blair W Perry
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Richard H Adams
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Daren C Card
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Museum of Comparative Zoology, Harvard University, Cambridge, MA, USA
| | - Tereza Jezkova
- Department of Biology, Miami University of Ohio, Oxford, OH, USA
| | | | | | - Kristopher Row
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
| | - Jesse M Meik
- Department of Biological Sciences, Tarleton State University, Stephenville, TX, USA
| | - Cara F Smith
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Stephen P Mackessy
- School of Biological Sciences, University of Northern Colorado, Greeley, CO, USA
| | - Todd A Castoe
- Department of Biology, University of Texas at Arlington, Arlington, TX, USA
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Lemos-Espinal JA, Smith GR, Rorabaugh JC. A conservation checklist of the amphibians and reptiles of Sonora, Mexico, with updated species lists. Zookeys 2019; 829:131-160. [PMID: 30914839 PMCID: PMC6422993 DOI: 10.3897/zookeys.829.32146] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/28/2019] [Indexed: 11/12/2022] Open
Abstract
Sonora has a rich natural diversity, including reptiles and amphibians. Sonora's location on the United States-Mexico border creates some unique conservation challenges for its wildlife. We compiled a list of the amphibian and reptile species currently known for Sonora, summarized the conservation status of these species, and compared our list of species with known species lists for adjacent states. The herpetofauna of Sonora comprises 200 species of amphibians and reptiles (38 amphibians and 162 reptiles). Overall, Sonora shares the most species with Chihuahua, Sinaloa, and Arizona. Approximately 11% of the amphibian and reptile species are IUCN listed, but 35.5% are placed in a protected category by SEMARNAT, and 32.6% are categorized as high risk by the Environmental Vulnerability Score.
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Affiliation(s)
- Julio A Lemos-Espinal
- Laboratorio de Ecología-UBIPRO, FES Iztacala UNAM, Avenida los Barrios 1, Los Reyes Iztacala, Tlalnepantla, edo. de Mexico, 54090, Mexico Universidad Nacional Autónoma de México Tlalnepantla Mexico
| | - Geoffrey R Smith
- Department of Biology, Denison University, Granville, Ohio 43023, USA Denison University Granville United States of America
| | - James C Rorabaugh
- P.O. Box 31, Saint David, Arizona 85630, USA Unaffilaited Phoenix United States of America
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Cox CL, Davis Rabosky AR, Holmes IA, Reyes-Velasco J, Roelke CE, Smith EN, Flores-Villela O, McGuire JA, Campbell JA. Synopsis and taxonomic revision of three genera in the snake tribe Sonorini. J NAT HIST 2018. [DOI: 10.1080/00222933.2018.1449912] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Christian L. Cox
- Department of Biology, Georgia Southern University, Statesboro, Georgia, USA
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
| | - Alison R. Davis Rabosky
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Iris A. Holmes
- Department of Ecology and Evolutionary Biology and Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | - Jacobo Reyes-Velasco
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
- Evolutionary Genomics Laboratory, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Corey E. Roelke
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
| | - Eric N. Smith
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
| | | | - Jimmy A. McGuire
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Jonathan A. Campbell
- Amphibian and Reptile Diversity Research Center, Department of Biology, University of Texas-Arlington, Arlington, TX, USA
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5
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Book Reviews. COPEIA 2017. [DOI: 10.1643/ot-17-687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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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: 2.3] [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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Yannic G, St-Laurent MH, Ortego J, Taillon J, Beauchemin A, Bernatchez L, Dussault C, Côté SD. Integrating ecological and genetic structure to define management units for caribou in Eastern Canada. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0795-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Edwards T, Berry KH, Inman RD, Esque TC, Nussear KE, Jones CA, Culver M. Testing Taxon Tenacity of Tortoises: evidence for a geographical selection gradient at a secondary contact zone. Ecol Evol 2015; 5:2095-114. [PMID: 26045959 PMCID: PMC4449762 DOI: 10.1002/ece3.1500] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/10/2015] [Accepted: 03/11/2015] [Indexed: 11/30/2022] Open
Abstract
We examined a secondary contact zone between two species of desert tortoise, Gopherus agassizii and G. morafkai. The taxa were isolated from a common ancestor during the formation of the Colorado River (4–8 mya) and are a classic example of allopatric speciation. However, an anomalous population of G. agassizii comes into secondary contact with G. morafkai east of the Colorado River in the Black Mountains of Arizona and provides an opportunity to examine reinforcement of species' boundaries under natural conditions. We sampled 234 tortoises representing G. agassizii in California (n - 103), G. morafkai in Arizona (n - 78), and 53 individuals of undetermined assignment in the contact zone including and surrounding the Black Mountains. We genotyped individuals for 25 STR loci and determined maternal lineage using mtDNA sequence data. We performed multilocus genetic clustering analyses and used multiple statistical methods to detect levels of hybridization. We tested hypotheses about habitat use between G. agassizii and G. morafkai in the region where they co-occur using habitat suitability models. Gopherus agassizii and G. morafkai maintain independent taxonomic identities likely due to ecological niche partitioning, and the maintenance of the hybrid zone is best described by a geographical selection gradient model.
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Affiliation(s)
- Taylor Edwards
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; University of Arizona Genetics Core, University of Arizona 1657 E. Helen Street, Tucson, Arizona, 85721
| | - Kristin H Berry
- Western Ecological Research Center, U.S. Geological Survey Falcon Business Park, 21803 Cactus Avenue, Suite F, Riverside, California, 92518
| | - Richard D Inman
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Todd C Esque
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Kenneth E Nussear
- Western Ecological Research Center, U.S. Geological Survey 160 North Stephanie St., Henderson, Nevada, 89074
| | - Cristina A Jones
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; Arizona Game and Fish Department, Nongame Wildlife Branch Phoenix, Arizona, 85086
| | - Melanie Culver
- School of Natural Resources and the Environment, The University of Arizona Tucson, Arizona, 85721 ; Arizona Cooperative Fish and Wildlife Research Unit, U.S. Geological Survey, University of Arizona Tucson, Arizona, 85721
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