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Preckler-Quisquater S, Kierepka EM, Reding DM, Piaggio AJ, Sacks BN. Can demographic histories explain long-term isolation and recent pulses of asymmetric gene flow between highly divergent grey fox lineages? Mol Ecol 2023; 32:5323-5337. [PMID: 37632719 DOI: 10.1111/mec.17105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/28/2023]
Abstract
Secondary contact zones between deeply divergent, yet interfertile, lineages provide windows into the speciation process. North American grey foxes (Urocyon cinereoargenteus) are divided into western and eastern lineages that diverged approximately 1 million years ago. These ancient lineages currently hybridize in a relatively narrow zone of contact in the southern Great Plains, a pattern more commonly observed in smaller-bodied taxa, which suggests relatively recent contact after a long period of allopatry. Based on local ancestry inference with whole-genome sequencing (n = 43), we identified two distinct Holocene pulses of admixture. The older pulse (500-3500 YBP) reflected unidirectional gene flow from east to west, whereas the more recent pulse (70-200 YBP) of admixture was bi-directional. Augmented with genotyping-by-sequencing data from 216 additional foxes, demographic analyses indicated that the eastern lineage declined precipitously after divergence, remaining small throughout most of the late Pleistocene, and expanding only during the Holocene. Genetic diversity in the eastern lineage was highest in the southeast and lowest near the contact zone, consistent with a westward expansion. Concordantly, distribution modelling indicated that during their isolation, the most suitable habitat occurred far east of today's contact zone or west of the Great Plains. Thus, long-term isolation was likely caused by the small, distant location of the eastern refugium, with recent contact reflecting a large increase in suitable habitat and corresponding demographic expansion from the eastern refugium. Ultimately, long-term isolation in grey foxes may reflect their specialized bio-climatic niche. This system presents an opportunity for future investigation of potential pre- and post-zygotic isolating mechanisms.
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Affiliation(s)
- Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
| | - Elizabeth M Kierepka
- North Carolina Museum of Natural Sciences, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, North Carolina, USA
| | - Dawn M Reding
- Department of Biology, Luther College, Decorah, Iowa, USA
| | - Antoinette J Piaggio
- USDA, Wildlife Services, National Wildlife Research Center, Wildlife Genetics Lab, Fort Collins, Colorado, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, California, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, California, USA
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Kierepka EM, Preckler-Quisquater S, Reding DM, Piaggio AJ, Riley SPD, Sacks BN. Genomic analyses of gray fox lineages suggest ancient divergence and secondary contact in the Southern Great Plains. J Hered 2022; 114:110-119. [PMID: 36326769 DOI: 10.1093/jhered/esac060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022] Open
Abstract
Abstract
The gray fox (Urocyon cinereoargenteus) lineage diverged from all other extant canids at their most basal node and is restricted to the Americas. Previous mitochondrial analysis from coastal populations identified deeply divergent (up to 1 Mya) eastern and western lineages that predate most intraspecific splits in carnivores. We conducted genotyping by sequencing (GBS) and mitochondrial analysis on gray foxes sampled across North America to determine geographic concordance between nuclear and mitochondrial contact zones and divergence times. We also estimated the admixture within the contact zone between eastern and western gray foxes based on nuclear DNA. Both datasets confirmed that eastern and western lineages met in the southern Great Plains (i.e, Texas and Oklahoma), where they maintained high differentiation. Admixture was generally low, with the majority of admixed individuals carrying <10% ancestry from the other lineage. Divergence times confirmed a mid-Pleistocene split, similar to the mitochondrial estimates. Taken together, findings suggest gray fox lineages represent an ancient divergence event, far older than most intraspecific divergences in North American carnivores. Low admixture may reflect a relatively recent time since secondary contact (e.g., post-Pleistocene) or, alternatively, ecological or reproductive barriers between lineages. Though further research is needed to disentangle these factors, our genomic investigation suggests species-level divergence exists between eastern and western gray fox lineages.
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Affiliation(s)
- Elizabeth M Kierepka
- North Carolina Museum of Natural Sciences, Department of Forestry and Environmental Resources, North Carolina State University , Raleigh, NC, USA
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine , University of California-Davis, Davis, CA, USA
| | - Sophie Preckler-Quisquater
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine , University of California-Davis, Davis, CA, USA
| | - Dawn M Reding
- Department of Biology, Luther College, Decorah , IA, USA
| | - Antoinette J Piaggio
- USDA, Wildlife Services, National Wildlife Research Center, Wildlife Genetics Lab, Fort Collins , CO, USA
| | - Seth P D Riley
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, CA, USA; Department of Ecology and Evolutionary Biology, University of California, Los Angeles, Los Angeles , CA, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, School of Veterinary Medicine , University of California-Davis, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis , Davis, CA, USA
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3
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Cancellare IA, Kierepka EM, Janecka J, Weckworth B, Kazmaier RT, Ward R. Multiscale patterns of isolation by ecology and fine-scale population structure in Texas bobcats. PeerJ 2021; 9:e11498. [PMID: 34141475 PMCID: PMC8180196 DOI: 10.7717/peerj.11498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 05/01/2021] [Indexed: 12/03/2022] Open
Abstract
Patterns of spatial genetic variation can be generated by a variety of ecological processes, including individual preferences based on habitat. These ecological processes act at multiple spatial and temporal scales, generating scale-dependent effects on gene flow. In this study, we focused on bobcats (Lynx rufus), a highly mobile, generalist felid that exhibits ecological and behavioral plasticity, high abundance, and broad connectivity across much of their range. However, bobcats also show genetic differentiation along habitat breaks, a pattern typically observed in cases of isolation-by-ecology (IBE). The IBE observed in bobcats is hypothesized to occur due to habitat-biased dispersal, but it is unknown if this occurs at other habitat breaks across their range or at what spatial scale IBE becomes most apparent. Thus, we used a multiscale approach to examine isolation by ecology (IBE) patterns in bobcats (Lynx rufus) at both fine and broad spatial scales in western Texas. We genotyped 102 individuals at nine microsatellite loci and used partial redundancy analysis (pRDA) to test if a suite of landscape variables influenced genetic variation in bobcats. Bobcats exhibited a latitudinal cline in population structure with a spatial signature of male-biased dispersal, and no clear barriers to gene flow. Our pRDA tests revealed high genetic similarity in similar habitats, and results differed by spatial scale. At the fine spatial scale, herbaceous rangeland was an important influence on gene flow whereas mixed rangeland and agriculture were significant at the broad spatial scale. Taken together, our results suggests that complex interactions between spatial-use behavior and landscape heterogeneity can create non-random gene flow in highly mobile species like bobcats. Furthermore, our results add to the growing body of data highlighting the importance of multiscale study designs when assessing spatial genetic structure.
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Affiliation(s)
- Imogene A Cancellare
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA.,Department of Entomology and Wildlife Ecology, University of Delaware, Newark, DE, USA
| | - Elizabeth M Kierepka
- Department of Forestry and Environmental Resources, North Carolina Museum of Natural Sciences, Raleigh, North Carolina, USA
| | - Jan Janecka
- Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania, USA
| | | | - Richard T Kazmaier
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA
| | - Rocky Ward
- Department of Life, Earth, and Environmental Sciences, West Texas A&M University, Canyon, Texas, USA
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Davis AJ, Keiter DA, Kierepka EM, Slootmaker C, Piaggio AJ, Beasley JC, Pepin KM. A comparison of cost and quality of three methods for estimating density for wild pig (Sus scrofa). Sci Rep 2020; 10:2047. [PMID: 32029837 PMCID: PMC7004977 DOI: 10.1038/s41598-020-58937-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/13/2020] [Indexed: 12/02/2022] Open
Abstract
A critical element in effective wildlife management is monitoring the status of wildlife populations; however, resources to monitor wildlife populations are typically limited. We compared cost effectiveness of three common population estimation methods (i.e. non-invasive DNA sampling, camera sampling, and sampling from trapping) by applying them to wild pigs (Sus scrofa) across three habitats in South Carolina, U.S.A where they are invasive. We used mark-recapture analyses for fecal DNA sampling data, spatially-explicit capture-recapture analyses for camera sampling data, and a removal analysis for removal sampling from trap data. Density estimates were similar across methods. Camera sampling was the least expensive, but had large variances. Fecal DNA sampling was the most expensive, although this technique generally performed well. We examined how reductions in effort by method related to increases in relative bias or imprecision. For removal sampling, the largest cost savings while maintaining unbiased density estimates was from reducing the number of traps. For fecal DNA sampling, a reduction in effort only minimally reduced costs due to the need for increased lab replicates while maintaining high quality estimates. For camera sampling, effort could only be marginally reduced before inducing bias. We provide a decision tree for researchers to help make monitoring decisions.
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Affiliation(s)
- Amy J Davis
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 Laporte Avenue, Fort Collins, CO, 80521, USA.
| | - David A Keiter
- University of Georgia, Savannah River Ecology Laboratory, D. B. Warnell School of Forestry and Natural Resources, PO Drawer E, Aiken, SC, 29802, USA
- University of Nebraska, School of Natural Resources, Hardin Hall, 3310 Holdrege St., Lincoln, NE, 68583-0961, USA
| | - Elizabeth M Kierepka
- University of Georgia, Savannah River Ecology Laboratory, D. B. Warnell School of Forestry and Natural Resources, PO Drawer E, Aiken, SC, 29802, USA
- Trent University, Peterborough, Ontario, K9L 0G2, Canada
| | - Chris Slootmaker
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 Laporte Avenue, Fort Collins, CO, 80521, USA
- Mountain Data Group, 115 N. College Ave. Suite 220, Fort Collins, CO, 80524, USA
| | - Antoinette J Piaggio
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 Laporte Avenue, Fort Collins, CO, 80521, USA
| | - James C Beasley
- University of Georgia, Savannah River Ecology Laboratory, D. B. Warnell School of Forestry and Natural Resources, PO Drawer E, Aiken, SC, 29802, USA
| | - Kim M Pepin
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, 4101 Laporte Avenue, Fort Collins, CO, 80521, USA
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Kierepka EM, Juarez R, Turner K, Smith J, Hamilton M, Lyons P, Hall MA, Beasley JC, Rhodes OE. Population Genetics of Invasive Brown Tree Snakes (Boiga irregularis) on Guam, USA. HERPETOLOGICA 2019. [DOI: 10.1655/d-18-00057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Elizabeth M. Kierepka
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29802, USA
| | - Rebeca Juarez
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29802, USA
| | - Kelsey Turner
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29802, USA
| | - Joshua Smith
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29802, USA
| | - Matthew Hamilton
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29802, USA
| | - Phillip Lyons
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29802, USA
| | - Marc A. Hall
- NAVFAC MAR, PSC 455, Box 195, Honolulu, HI 96540-2937, USA
| | - James C. Beasley
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29802, USA
| | - Olin E. Rhodes
- Savannah River Ecology Laboratory, University of Georgia, PO Drawer E, Aiken, SC 29802, USA
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Milligan BG, Archer FI, Ferchaud A, Hand BK, Kierepka EM, Waples RS. Disentangling genetic structure for genetic monitoring of complex populations. Evol Appl 2018; 11:1149-1161. [PMID: 30026803 PMCID: PMC6050185 DOI: 10.1111/eva.12622] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 02/14/2018] [Indexed: 12/25/2022] Open
Abstract
Genetic monitoring estimates temporal changes in population parameters from molecular marker information. Most populations are complex in structure and change through time by expanding or contracting their geographic range, becoming fragmented or coalescing, or increasing or decreasing density. Traditional approaches to genetic monitoring rely on quantifying temporal shifts of specific population metrics-heterozygosity, numbers of alleles, effective population size-or measures of geographic differentiation such as FST. However, the accuracy and precision of the results can be heavily influenced by the type of genetic marker used and how closely they adhere to analytical assumptions. Care must be taken to ensure that inferences reflect actual population processes rather than changing molecular techniques or incorrect assumptions of an underlying model of population structure. In many species of conservation concern, true population structure is unknown, or structure might shift over time. In these cases, metrics based on inappropriate assumptions of population structure may not provide quality information regarding the monitored population. Thus, we need an inference model that decouples the complex elements that define population structure from estimation of population parameters of interest and reveals, rather than assumes, fine details of population structure. Encompassing a broad range of possible population structures would enable comparable inferences across biological systems, even in the face of range expansion or contraction, fragmentation, or changes in density. Currently, the best candidate is the spatial Λ-Fleming-Viot (SLFV) model, a spatially explicit individually based coalescent model that allows independent inference of two of the most important elements of population structure: local population density and local dispersal. We support increased use of the SLFV model for genetic monitoring by highlighting its benefits over traditional approaches. We also discuss necessary future directions for model development to support large genomic datasets informing real-world management and conservation issues.
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Affiliation(s)
| | | | - Anne‐Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Brian K. Hand
- Flathead Lake Biological StationUniversity of MontanaPolsonMTUSA
| | | | - Robin S. Waples
- NOAA FisheriesNorthwest Fisheries Science CenterSeattleWAUSA
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7
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Kanine JM, Kierepka EM, Castleberry SB, Mengak MT, Nibbelink NP, Glenn TC. Influence of landscape heterogeneity on the functional connectivity of Allegheny woodrats (Neotoma magister) in Virginia. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1093-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Affiliation(s)
| | - John C. Kilgo
- USDA Forest ServiceSouthern Research StationP.O. Box 700New EllentonSC29809USA
| | - Olin E. Rhodes
- University of GeorgiaSavannah River Ecology LaboratoryAikenSC29802USA
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9
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Kierepka EM, Latch EK. High gene flow in the American badger overrides habitat preferences and limits broadscale genetic structure. Mol Ecol 2016; 25:6055-6076. [PMID: 27862522 DOI: 10.1111/mec.13915] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 10/13/2016] [Accepted: 11/01/2016] [Indexed: 01/05/2023]
Abstract
Habitat associations are a function of habitat preferences and dispersal capabilities, both of which can influence how species responded to Quaternary climatic changes and contemporary habitat heterogeneity. Predicting resultant genetic structure is not always straightforward, especially in species where high dispersal potential and habitat preferences yield opposing predictions. The American badger has high dispersal capabilities that predict widespread panmixia, but avoids closed-canopy forests and clay soils, which could restrict gene flow and create ecologically based population genetic structure. We used mitochondrial sequence and microsatellite data sets to characterize how these opposing forces contribute to genetic structure in badgers at a continent-wide scale. Our data revealed an overall lack of ecologically based population genetic structure, suggesting that high dispersal capabilities were sufficiently realized to overcome most habitat-based genetic structure. At a broadscale, badger gene flow is limited only by geographic distance (isolation by distance) and large water barriers (Lake Michigan and the Mississippi River). The absence of genetic structure in a species with strong avoidance of unsuitable habitats advances our understanding of when and how genetic structure emerges in widespread, highly mobile species.
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Affiliation(s)
- E M Kierepka
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
| | - E K Latch
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, 53211, USA
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10
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Kierepka EM, Anderson SJ, Swihart RK, Rhodes OE. Evaluating the influence of life-history characteristics on genetic structure: a comparison of small mammals inhabiting complex agricultural landscapes. Ecol Evol 2016; 6:6376-96. [PMID: 27648250 PMCID: PMC5016657 DOI: 10.1002/ece3.2269] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 05/15/2016] [Accepted: 05/31/2016] [Indexed: 01/16/2023] Open
Abstract
Conversion of formerly continuous native habitats into highly fragmented landscapes can lead to numerous negative demographic and genetic impacts on native taxa that ultimately reduce population viability. In response to concerns over biodiversity loss, numerous investigators have proposed that traits such as body size and ecological specialization influence the sensitivity of species to habitat fragmentation. In this study, we examined how differences in body size and ecological specialization of two rodents (eastern chipmunk; Tamias striatus and white‐footed mouse; Peromyscus leucopus) impact their genetic connectivity within the highly fragmented landscape of the Upper Wabash River Basin (UWB), Indiana, and evaluated whether landscape configuration and complexity influenced patterns of genetic structure similarly between these two species. The more specialized chipmunk exhibited dramatically more genetic structure across the UWB than white‐footed mice, with genetic differentiation being correlated with geographic distance, configuration of intervening habitats, and complexity of forested habitats within sampling sites. In contrast, the generalist white‐footed mouse resembled a panmictic population across the UWB, and no landscape factors were found to influence gene flow. Despite the extensive previous work in abundance and occupancy within the UWB, no landscape factor that influenced occupancy or abundance was correlated with genetic differentiation in either species. The difference in predictors of occupancy, abundance, and gene flow suggests that species‐specific responses to fragmentation are scale dependent.
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Affiliation(s)
- Elizabeth M Kierepka
- Savannah River Ecology Laboratory University of Georgia PO Drawer E Aiken South Carolina 29802
| | - Sara J Anderson
- Biosciences Department Minnesota State University Moorhead 1104 7th Ave Moorhead Minnesota 56563
| | - Robert K Swihart
- Department of Forestry and Natural Resources Purdue University 715 W. State Street West Lafayette Indiana 47907
| | - Olin E Rhodes
- Savannah River Ecology Laboratory University of Georgia PO Drawer E Aiken South Carolina 29802
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Kierepka EM, Unger SD, Keiter DA, Beasley JC, Rhodes OE, Cunningham FL, Piaggio AJ. Identification of robust microsatellite markers for wild pig fecal DNA. J Wildl Manage 2016. [DOI: 10.1002/jwmg.21102] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Shem D. Unger
- University of GeorgiaSavannah River Ecology LaboratoryAikenSC29802USA
| | - David A. Keiter
- University of Georgia, Savannah River Ecology LaboratoryWarnell School of Forestry and Natural ResourcesAikenSC29802USA
| | - James C. Beasley
- University of Georgia, Savannah River Ecology LaboratoryWarnell School of Forestry and Natural ResourcesAikenSC29802USA
| | - Olin E. Rhodes
- University of GeorgiaSavannah River Ecology LaboratoryAikenSC29802USA
| | - Fred L. Cunningham
- U.S. Department of Agriculture, Mississippi Field Station, National Wildlife Research CenterWildlife ServicesPO Box 6099Mississippi StateMS39762USA
| | - Antoinette J. Piaggio
- U.S. Department of Agriculture, National Wildlife Research CenterWildlife Services4101 LaPorte AvenueFort CollinsCO80521USA
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12
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Kierepka EM, Latch EK. Fine-scale landscape genetics of the American badger (Taxidea taxus): disentangling landscape effects and sampling artifacts in a poorly understood species. Heredity (Edinb) 2016; 116:33-43. [PMID: 26243136 PMCID: PMC4675871 DOI: 10.1038/hdy.2015.67] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 06/05/2015] [Accepted: 06/12/2015] [Indexed: 11/09/2022] Open
Abstract
Landscape genetics is a powerful tool for conservation because it identifies landscape features that are important for maintaining genetic connectivity between populations within heterogeneous landscapes. However, using landscape genetics in poorly understood species presents a number of challenges, namely, limited life history information for the focal population and spatially biased sampling. Both obstacles can reduce power in statistics, particularly in individual-based studies. In this study, we genotyped 233 American badgers in Wisconsin at 12 microsatellite loci to identify alternative statistical approaches that can be applied to poorly understood species in an individual-based framework. Badgers are protected in Wisconsin owing to an overall lack in life history information, so our study utilized partial redundancy analysis (RDA) and spatially lagged regressions to quantify how three landscape factors (Wisconsin River, Ecoregions and land cover) impacted gene flow. We also performed simulations to quantify errors created by spatially biased sampling. Statistical analyses first found that geographic distance was an important influence on gene flow, mainly driven by fine-scale positive spatial autocorrelations. After controlling for geographic distance, both RDA and regressions found that Wisconsin River and Agriculture were correlated with genetic differentiation. However, only Agriculture had an acceptable type I error rate (3-5%) to be considered biologically relevant. Collectively, this study highlights the benefits of combining robust statistics and error assessment via simulations and provides a method for hypothesis testing in individual-based landscape genetics.
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Affiliation(s)
- E M Kierepka
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - E K Latch
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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13
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Anderson SJ, Kierepka EM, Swihart RK, Latch EK, Rhodes OE. Assessing the permeability of landscape features to animal movement: using genetic structure to infer functional connectivity. PLoS One 2015; 10:e0117500. [PMID: 25719366 PMCID: PMC4342345 DOI: 10.1371/journal.pone.0117500] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/26/2014] [Indexed: 11/19/2022] Open
Abstract
Human-altered environments often challenge native species with a complex spatial distribution of resources. Hostile landscape features can inhibit animal movement (i.e., genetic exchange), while other landscape attributes facilitate gene flow. The genetic attributes of organisms inhabiting such complex environments can reveal the legacy of their movements through the landscape. Thus, by evaluating landscape attributes within the context of genetic connectivity of organisms within the landscape, we can elucidate how a species has coped with the enhanced complexity of human altered environments. In this research, we utilized genetic data from eastern chipmunks (Tamias striatus) in conjunction with spatially explicit habitat attribute data to evaluate the realized permeability of various landscape elements in a fragmented agricultural ecosystem. To accomplish this we 1) used logistic regression to evaluate whether land cover attributes were most often associated with the matrix between or habitat within genetically identified populations across the landscape, and 2) utilized spatially explicit habitat attribute data to predict genetically-derived Bayesian probabilities of population membership of individual chipmunks in an agricultural ecosystem. Consistency between the results of the two approaches with regard to facilitators and inhibitors of gene flow in the landscape indicate that this is a promising new way to utilize both landscape and genetic data to gain a deeper understanding of human-altered ecosystems.
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Affiliation(s)
- Sara J. Anderson
- Biosciences Department, Minnesota State University Moorhead, 1104 7 Ave, Moorhead, MN, 56563, United States of America
- Department of Forestry and Natural Resources, 715 W. State Street, Purdue University, West Lafayette, IN, 47907, United States of America
| | - Elizabeth M. Kierepka
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Ave., Milwaukee, WI, 53024, United States of America
| | - Robert K. Swihart
- Department of Forestry and Natural Resources, 715 W. State Street, Purdue University, West Lafayette, IN, 47907, United States of America
| | - Emily K. Latch
- Behavioral and Molecular Ecology Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N. Maryland Ave., Milwaukee, WI, 53024, United States of America
| | - Olin E. Rhodes
- Department of Forestry and Natural Resources, 715 W. State Street, Purdue University, West Lafayette, IN, 47907, United States of America
- Savannah River Ecology Laboratory, PO Drawer E, Aiken, SC, 29802, United States of America
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Abstract
Studies of hybrid zones have revealed an array of evolutionary outcomes, yet the underlying structure is typically characterized as one of three types: a hybrid zone, a hybrid swarm or a hybrid taxon. Our primary objective was to determine which of these three structures best characterizes a zone of hybridization between two divergent lineages of mule deer (Odocoileus hemionus), mule deer and black-tailed deer. These lineages are morphologically, ecologically and genetically distinct, yet hybridize readily along a zone of secondary contact between the east and west slopes of the Cascade Mountains (Washington and Oregon, USA). Using microsatellite and mitochondrial DNA, we found clear evidence for extensive hybridization and introgression between lineages, with varying degrees of admixture across the zone of contact. The pattern of hybridization in this region closely resembles a hybrid swarm; based on data from 10 microsatellite loci, we detected hybrids that extend well beyond the F1 generation, did not detect linkage disequilibrium at the centre of the zone and found that genotypes were associated randomly within the zone of contact. Introgression was characterized as bidirectional and symmetric, which is surprising given that the zone of contact occurs along a sharp ecotone and that lineages are characterized by large differences in body size (a key component of mating success). Regardless of the underlying mechanisms promoting hybrid swarm maintenance, it is clear that the persistence of a hybrid swarm presents unique challenges for management in this region.
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Affiliation(s)
- Emily K Latch
- Behavioral and Molecular Ecology Research Group, Department of Biological Sciences, University of Wisconsin-Milwaukee, 3209 N Maryland Ave, Milwaukee, WI 53211, USA.
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