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Barbosa S, Andrews KR, Goldberg AR, Gour DS, Hohenlohe PA, Conway CJ, Waits LP. The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern. Mol Ecol 2021; 30:4673-4694. [PMID: 34324748 DOI: 10.1111/mec.16096] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 07/10/2021] [Accepted: 07/19/2021] [Indexed: 11/29/2022]
Abstract
Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus - NIDGS, and U. endemicus - SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both theinter- and intraspecific level, and identified putatively adaptive SNPs using population structure outlier detection and genotype-environment association (GEA) analyses. At the interspecific level, we detected a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation putatively linked to torpor patterns. At the intraspecific level, we found evidence of both neutral and adaptive differentiation. For NIDGS, elevation appears to be the main driver of adaptive differentiation, while neutral variation patterns match and expand information on the low connectivity between some populations identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected natural geographic barriers, while adaptive variation reflected differences in land cover and temperature, as well as elevation. These results clearly highlight the roles of neutral and adaptive processes for understanding the complexity of the processes leading to species and population differentiation, which can have important conservation implications in susceptible and threatened species.
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Affiliation(s)
- Soraia Barbosa
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
| | - Kimberly R Andrews
- University of Idaho, Institute for Bioinformatics and Evolutionary Studies (IBEST), Moscow, ID, 83844-1136, USA
| | - Amanda R Goldberg
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
| | - Digpal S Gour
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
| | - Paul A Hohenlohe
- University of Idaho, Institute for Bioinformatics and Evolutionary Studies (IBEST), Moscow, ID, 83844-1136, USA.,Department of Biological Sciences, College of Science, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-3051, USA
| | - Courtney J Conway
- U.S. Geological Survey, Idaho Cooperative Fish & Wildlife Research Unit, Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, Moscow, ID, 83844-1141, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, College of Natural Resources, University of Idaho, 875 Perimeter Drive, Moscow, ID, 83844-1136, USA
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Yensen E, Dyni EJ. Why is the Northern Idaho Ground Squirrel Rare? NORTHWEST SCIENCE 2020. [DOI: 10.3955/046.094.0101] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Eric Yensen
- Museum of Natural History, The College of Idaho, Caldwell, Idaho 83605 and Wildlife Toxicology Laboratory, Michigan State University, East Lansing, Michigan 48824
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Kelt DA, Heske EJ, Lambin X, Oli MK, Orrock JL, Ozgul A, Pauli JN, Prugh LR, Sollmann R, Sommer S. Advances in population ecology and species interactions in mammals. J Mammal 2019. [DOI: 10.1093/jmammal/gyz017] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
AbstractThe study of mammals has promoted the development and testing of many ideas in contemporary ecology. Here we address recent developments in foraging and habitat selection, source–sink dynamics, competition (both within and between species), population cycles, predation (including apparent competition), mutualism, and biological invasions. Because mammals are appealing to the public, ecological insight gleaned from the study of mammals has disproportionate potential in educating the public about ecological principles and their application to wise management. Mammals have been central to many computational and statistical developments in recent years, including refinements to traditional approaches and metrics (e.g., capture-recapture) as well as advancements of novel and developing fields (e.g., spatial capture-recapture, occupancy modeling, integrated population models). The study of mammals also poses challenges in terms of fully characterizing dynamics in natural conditions. Ongoing climate change threatens to affect global ecosystems, and mammals provide visible and charismatic subjects for research on local and regional effects of such change as well as predictive modeling of the long-term effects on ecosystem function and stability. Although much remains to be done, the population ecology of mammals continues to be a vibrant and rapidly developing field. We anticipate that the next quarter century will prove as exciting and productive for the study of mammals as has the recent one.
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Affiliation(s)
- Douglas A Kelt
- Department of Wildlife, Fish, & Conservation Biology, University of California, Davis, CA, USA
| | - Edward J Heske
- Museum of Southwestern Biology, University of New Mexico, Albuquerque, NM, USA
| | - Xavier Lambin
- School of Biological Sciences, University of Aberdeen, Aberdeen, United Kingdom
| | - Madan K Oli
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA
| | - John L Orrock
- Department of Integrative Biology, University of Wisconsin, Madison, WI, USA
| | - Arpat Ozgul
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Jonathan N Pauli
- Department of Forest and Wildlife Ecology, University of Wisconsin, Madison, WI, USA
| | - Laura R Prugh
- School of Environmental and Forest Sciences, University of Washington, Seattle, WA, USA
| | - Rahel Sollmann
- Department of Wildlife, Fish, & Conservation Biology, University of California, Davis, CA, USA
| | - Stefan Sommer
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
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Genetic structure and environmental niche modeling confirm two evolutionary and conservation units within the western spadefoot (Spea hammondii). CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1066-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Zero VH, Barocas A, Jochimsen DM, Pelletier A, Giroux-Bougard X, Trumbo DR, Castillo JA, Evans Mack D, Linnell MA, Pigg RM, Hoisington-Lopez J, Spear SF, Murphy MA, Waits LP. Complementary Network-Based Approaches for Exploring Genetic Structure and Functional Connectivity in Two Vulnerable, Endemic Ground Squirrels. Front Genet 2017; 8:81. [PMID: 28659969 PMCID: PMC5469978 DOI: 10.3389/fgene.2017.00081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 05/29/2017] [Indexed: 11/18/2022] Open
Abstract
The persistence of small populations is influenced by genetic structure and functional connectivity. We used two network-based approaches to understand the persistence of the northern Idaho ground squirrel (Urocitellus brunneus) and the southern Idaho ground squirrel (U. endemicus), two congeners of conservation concern. These graph theoretic approaches are conventionally applied to social or transportation networks, but here are used to study population persistence and connectivity. Population graph analyses revealed that local extinction rapidly reduced connectivity for the southern species, while connectivity for the northern species could be maintained following local extinction. Results from gravity models complemented those of population graph analyses, and indicated that potential vegetation productivity and topography drove connectivity in the northern species. For the southern species, development (roads) and small-scale topography reduced connectivity, while greater potential vegetation productivity increased connectivity. Taken together, the results of the two network-based methods (population graph analyses and gravity models) suggest the need for increased conservation action for the southern species, and that management efforts have been effective at maintaining habitat quality throughout the current range of the northern species. To prevent further declines, we encourage the continuation of management efforts for the northern species, whereas conservation of the southern species requires active management and additional measures to curtail habitat fragmentation. Our combination of population graph analyses and gravity models can inform conservation strategies of other species exhibiting patchy distributions.
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Affiliation(s)
- Victoria H. Zero
- Haub School of Environment and Natural Resources, University of WyomingLaramie, WY, United States
| | - Adi Barocas
- Department of Zoology and Physiology, University of WyomingLaramie, WY, United States
- Program in Ecology, University of WyomingLaramie, WY, United States
| | - Denim M. Jochimsen
- Department of Biological Sciences, University of IdahoMoscow, ID, United States
| | - Agnès Pelletier
- Department of Environmental Studies and Sciences, University of WinnipegWinnipeg, MB, Canada
| | | | - Daryl R. Trumbo
- School of Biological Sciences, Washington State UniversityPullman, WA, United States
| | - Jessica A. Castillo
- Department of Fisheries and Wildlife, Oregon State UniversityCorvallis, OR, United States
| | - Diane Evans Mack
- Idaho Department of Fish and Game, McCall SubregionMcCall, ID, United States
| | - Mark A. Linnell
- Department of Fisheries and Wildlife, Oregon State UniversityCorvallis, OR, United States
| | - Rachel M. Pigg
- Division of Biology, Kansas State UniversityManhattan, KS, United States
| | - Jessica Hoisington-Lopez
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of MedicineSt. Louis, MO, United States
| | | | - Melanie A. Murphy
- Program in Ecology, University of WyomingLaramie, WY, United States
- Department of Ecosystem Science and Management, University of WyomingLaramie, WY, United States
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of IdahoMoscow, ID, United States
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Brown NL, Peacock MM, Ritchie ME. Genetic variation and population structure in a threatened species, the Utah prairie dog Cynomys parvidens: the use of genetic data to inform conservation actions. Ecol Evol 2016; 6:426-46. [PMID: 26843928 PMCID: PMC4729250 DOI: 10.1002/ece3.1874] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 11/23/2015] [Indexed: 11/11/2022] Open
Abstract
The Utah prairie dog (Cynomys parvidens), listed as threatened under the United States Endangered Species Act, was the subject of an extensive eradication program throughout its range during the 20th century. Eradication campaigns, habitat destruction/fragmentation/conversion, and epizootic outbreaks (e.g., sylvatic plague) have reduced prairie dog numbers from an estimated 95,000 individuals in the 1920s to approximately 14,000 (estimated adult spring count) today. As a result of these anthropogenic actions, the species is now found in small isolated sets of subpopulations. We characterized the levels of genetic diversity and population genetic structure using 10 neutral nuclear microsatellite loci for twelve populations (native and transplanted) representative of the three management designated "recovery units," found in three distinct biogeographic regions, sampled across the species' range. The results indicate (1) low levels of genetic diversity within colonies (H e = 0.109-0.357; H o = 0.106- 0.313), (2) high levels of genetic differentiation among colonies (global F ST = 0.296), (3) very small genetic effective population sizes, and (4) evidence of genetic bottlenecks. The genetic data reveal additional subdivision such that colonies within recovery units do not form single genotype clusters consistent with recovery unit boundaries. Genotype cluster membership support historical gene flow among colonies in the easternmost West Desert Recovery Unit with the westernmost Pausaugunt colonies and among the eastern Pausaugunt colonies and the Awapa Recovery unit to the north. In order to maintain the long-term viability of the species, there needs to be an increased focus on maintaining suitable habitat between groups of existing populations that can act as connective corridors. The location of future translocation sites should be located in areas that will maximize connectivity, leading to maintenance of genetic variation and evolutionary potential.
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Affiliation(s)
- Nathanael L. Brown
- Department of BiologySyracuse University107 College Place, LSCSyracuseNew York13224 Mark Ritchie
- Utah Field OfficeUnited States Fish and Wildlife Service1789 N. Wedgewood LaneCedar CityUtah84721
| | - Mary M. Peacock
- Department of Biology MS314University of Nevada Reno1664 North Virginia StreetReno89557Nevada
| | - Mark E. Ritchie
- Department of BiologySyracuse University107 College Place, LSCSyracuseNew York13224 Mark Ritchie
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Castellanos-Morales G, Ortega J, Castillo-Gámez RA, Sackett LC, Eguiarte LE. Genetic Variation and Structure in Contrasting Geographic Distributions: Widespread Versus Restricted Black-Tailed Prairie Dogs (SubgenusCynomys). J Hered 2015; 106 Suppl 1:478-90. [DOI: 10.1093/jhered/esv021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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Lohr K, Yensen E, Munger JC, Novak SJ. Relationship between habitat characteristics and densities of southern Idaho ground squirrels. J Wildl Manage 2013. [DOI: 10.1002/jwmg.541] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Kristin Lohr
- Department of Biological Sciences; Boise State University; 1910 University Drive; Boise ID 83725 USA
| | - Eric Yensen
- Department of Biology; The College of Idaho, 2112 Cleveland Boulevard; Caldwell ID 83605 USA
| | - James C. Munger
- Department of Biological Sciences; Boise State University; 1910 University Drive; Boise ID 83725 USA
| | - Stephen J. Novak
- Department of Biological Sciences; Boise State University; 1910 University Drive; Boise ID 83725 USA
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Suronen EF, Newingham BA. A Starting Point: An Ecosystem of Reference for Habitat Restoration of the Northern Idaho Ground Squirrel, Urocitellus brunneus brunneus. ACTA ACUST UNITED AC 2013. [DOI: 10.1898/12-28.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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