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Fusco NA, Cosentino BJ, Gibbs JP, Allen ML, Blumenfeld AJ, Boettner GH, Carlen EJ, Collins M, Dennison C, DiGiacopo D, Drapeau Picard AP, Edmonson J, Fisher-Reid MC, Fyffe R, Gallo T, Grant A, Harbold W, Heard SB, Lafferty DJR, Lehtinen RM, Marino S, McDonald JE, Mortelliti A, Murray M, Newman A, Oswald KN, Ott-Conn C, Richardson JL, Rimbach R, Salaman P, Steele M, Stothart MR, Urban MC, Vandegrift K, Vanek JP, Vanderluit SN, Vezina L, Caccone A. Population genomic structure of a widespread, urban-dwelling mammal: The eastern grey squirrel (Sciurus carolinensis). Mol Ecol 2024; 33:e17230. [PMID: 38078558 DOI: 10.1111/mec.17230] [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: 01/24/2023] [Revised: 11/19/2023] [Accepted: 11/21/2023] [Indexed: 01/25/2024]
Abstract
Urbanization is a persistent and widespread driver of global environmental change, potentially shaping evolutionary processes due to genetic drift and reduced gene flow in cities induced by habitat fragmentation and small population sizes. We tested this prediction for the eastern grey squirrel (Sciurus carolinensis), a common and conspicuous forest-dwelling rodent, by obtaining 44K SNPs using reduced representation sequencing (ddRAD) for 403 individuals sampled across the species' native range in eastern North America. We observed moderate levels of genetic diversity, low levels of inbreeding, and only a modest signal of isolation-by-distance. Clustering and migration analyses show that estimated levels of migration and genetic connectivity were higher than expected across cities and forested areas, specifically within the eastern portion of the species' range dominated by urbanization, and genetic connectivity was less than expected within the western range where the landscape is fragmented by agriculture. Landscape genetic methods revealed greater gene flow among individual squirrels in forested regions, which likely provide abundant food and shelter for squirrels. Although gene flow appears to be higher in areas with more tree cover, only slight discontinuities in gene flow suggest eastern grey squirrels have maintained connected populations across urban areas in all but the most heavily fragmented agricultural landscapes. Our results suggest urbanization shapes biological evolution in wildlife species depending strongly on the composition and habitability of the landscape matrix surrounding urban areas.
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Affiliation(s)
- Nicole A Fusco
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - Bradley J Cosentino
- Department of Biology, Hobart and William Smith Colleges, Geneva, New York, USA
| | - James P Gibbs
- Department of Environmental Biology, State University of New York College of Environmental Science and Forestry, Syracuse, New York, USA
| | - Maximilian L Allen
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Alexander J Blumenfeld
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
| | - George H Boettner
- Department of Environmental Conservation, University of Massachusetts-Amherst, Amherst, Massachusetts, USA
| | - Elizabeth J Carlen
- Department of Biology, Washington University-St. Louis Campus, St. Louis, Missouri, USA
| | - Merri Collins
- Department of Environmental Science and Technology, University of Maryland, College Park, Maryland, USA
| | | | - Devin DiGiacopo
- Yreka Fish and Wildlife Office, U.S. Fish and Wildlife Service, Yreka, CA, USA
| | | | - Jonathan Edmonson
- Sonderegger Science Center, Edgewood College, Madison, Wisconsin, USA
| | - M Caitlin Fisher-Reid
- Department of Biological Sciences, Bridgewater State University, Bridgewater, Massachusetts, USA
| | - Rebecca Fyffe
- Landmark Pest Management, ABC Humane Wildlife Control & Prevention Inc., Arlington Heights, Illinois, USA
| | - Travis Gallo
- Department of Environmental Science and Technology, University of Maryland, College Park, Maryland, USA
| | - Alannah Grant
- Department of Integrative Biology, College of Biological Sciences, University of Guelph, Guelph, Ontario, Canada
| | - William Harbold
- Maryland Department of Natural Resources, Monitoring and Non-Tidal Assessment Division, Annapolis, Maryland, USA
| | - Stephen B Heard
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Diana J R Lafferty
- Department of Biology, Northern Michigan University, Marqeutte, Michigan, USA
| | | | - Shealyn Marino
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, USA
| | - John E McDonald
- Department of Environmental Science, Westfield State University, Westfield, Massachusetts, USA
| | | | - Maureen Murray
- Department of Conservation and Science, Lincoln Park Zoo, Chicago, Illinois, USA
| | - Amy Newman
- Maryland Department of Natural Resources, Monitoring and Non-Tidal Assessment Division, Annapolis, Maryland, USA
| | - Krista N Oswald
- Mitrani Department of Desert Ecology, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Caitlin Ott-Conn
- Michigan Department of Natural Resources, Wildlife Disease Laboratory - Wildlife Division, Naubinway, Michigan, USA
| | | | - Rebecca Rimbach
- Department of Behavioural Biology, University of Münster, Münster, Germany
| | - Paul Salaman
- Galapagos Conservancy, Washington, District of Columbia, USA
| | - Michael Steele
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, USA
| | - Mason R Stothart
- Department of Ecosystem and Public Health, University of Calgary, Calgary, Alberta, Canada
| | - Mark C Urban
- Department of Ecology and Evolutionary Biology and Center of Biological Risk, University of Connecticut, Storrs, Connecticut, USA
| | - Kurt Vandegrift
- Department of Biology, Center for Infectious Disease Dynamics, The Pennsylvania State University, State College, Pennsylvania, USA
| | - John P Vanek
- New York Natural Heritage Program, Albany, New York, USA
| | | | - Lucie Vezina
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
| | - Adalgisa Caccone
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
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Wishingrad V, Thomson RC. Biogeographic inferences across spatial and evolutionary scales. Mol Ecol 2023; 32:2055-2070. [PMID: 36695049 DOI: 10.1111/mec.16861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/05/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
The field of biogeography unites landscape genetics and phylogeography under a common conceptual framework. Landscape genetics traditionally focuses on recent-time, population-based, spatial genetics processes at small geographical scales, while phylogeography typically investigates deep past, lineage- and species-based processes at large geographical scales. Here, we evaluate the link between landscape genetics and phylogeographical methods using the western fence lizard (Sceloporus occidentalis) as a model species. First, we conducted replicated landscape genetics studies across several geographical scales to investigate how population genetics inferences change depending on the spatial extent of the study area. Then, we carried out a phylogeographical study of population structure at two evolutionary scales informed by inferences derived from landscape genetics results to identify concordance and conflict between these sets of methods. We found significant concordance in landscape genetics processes at all but the largest geographical scale. Phylogeographical results indicate major clades are restricted to distinct river drainages or distinct hydrological regions. At a more recent timescale, we find minor clades are restricted to single river canyons in the majority of cases, while the remainder of river canyons include samples from at most two clades. Overall, the broad-scale pattern implicating stream and river valleys as key features linking populations in the landscape genetics results, and high degree of clade specificity within major topographic subdivisions in the phylogeographical results, is consistent. As landscape genetics and phylogeography share many of the same objectives, synthesizing theory, models and methods between these fields will help bring about a better understanding of ecological and evolutionary processes structuring genetic variation across space and time.
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Affiliation(s)
- Van Wishingrad
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA.,Hawai'i, Institute of Marine Biology, Kāne'ohe, Hawai'i, USA
| | - Robert C Thomson
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
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