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Walter WD, Fameli A, Russo‐Petrick K, Edson JE, Rosenberry CS, Schuler KL, Tonkovich MJ. Large-scale assessment of genetic structure to assess risk of populations of a large herbivore to disease. Ecol Evol 2024; 14:e11347. [PMID: 38774134 PMCID: PMC11106048 DOI: 10.1002/ece3.11347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 03/28/2024] [Accepted: 04/12/2024] [Indexed: 05/24/2024] Open
Abstract
Chronic wasting disease (CWD) can spread among cervids by direct and indirect transmission, the former being more likely in emerging areas. Identifying subpopulations allows the delineation of focal areas to target for intervention. We aimed to assess the population structure of white-tailed deer (Odocoileus virginianus) in the northeastern United States at a regional scale to inform managers regarding gene flow throughout the region. We genotyped 10 microsatellites in 5701 wild deer samples from Maryland, New York, Ohio, Pennsylvania, and Virginia. We evaluated the distribution of genetic variability through spatial principal component analysis and inferred genetic structure using non-spatial and spatial Bayesian clustering algorithms (BCAs). We simulated populations representing each inferred wild cluster, wild deer in each state and each physiographic province, total wild population, and a captive population. We conducted genetic assignment tests using these potential sources, calculating the probability of samples being correctly assigned to their origin. Non-spatial BCA identified two clusters across the region, while spatial BCA suggested a maximum of nine clusters. Assignment tests correctly placed deer into captive or wild origin in most cases (94%), as previously reported, but performance varied when assigning wild deer to more specific origins. Assignments to clusters inferred via non-spatial BCA performed well, but efficiency was greatly reduced when assigning samples to clusters inferred via spatial BCA. Differences between spatial BCA clusters are not strong enough to make assignment tests a reliable method for inferring the geographic origin of deer using 10 microsatellites. However, the genetic distinction between clusters may indicate natural and anthropogenic barriers of interest for management.
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Affiliation(s)
- W. David Walter
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Alberto Fameli
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Kelly Russo‐Petrick
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Jessie E. Edson
- Pennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | | | - Krysten L. Schuler
- Cornell Wildlife Health Lab, New York State Wildlife Health ProgramIthacaNew YorkUSA
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De R, Nigam P, Williams AC, Goyal SP. Beyond consensus genotyping: a case study on the Asian elephant Elephas maximus. CONSERV GENET RESOUR 2022. [DOI: 10.1007/s12686-022-01287-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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3
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Assessing tiger corridor functionality with landscape genetics and modelling across Terai-Arc landscape, India. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01460-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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4
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Araguas RM, Vidal O, García S, Sanz N. Genetic diversity and population structure of the Western European hedgehog, Erinaceus europaeus: conservation status of populations in the Iberian Peninsula. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00235-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractAnthropogenic habitat fragmentation and roadkill mortality are considered important threats to European hedgehogs. Habitat fragmentation isolates hedgehog populations and, as a consequence, reduces their genetic diversity and leads the populations to vulnerable situations. The hedgehog populations in the Iberian Peninsula represent the southern limit of the species. We used microsatellite markers to estimate the genetic diversity and population structure of Erinaceus europaeus on the Iberian Peninsula. The obtained results indicated the presence of two differentiated groups, north-western and north-eastern, which coincided with the distribution of the two phylogeographic mitochondrial lineages described in the Peninsula. Moreover, in the north-eastern group, three genetically different clusters (Girona, Central Catalonia and Zoo) were identified. The highest genetic diversity (Hs = 0.696) was detected in the north-western region. Significant genetic differentiation (FST range = 0.072–0.224) was found among the clusters, indicating that these groups are well differentiated and present low gene flow. We concluded that the north-western group is genetically stable, whereas in the north-eastern region, despite some contact among groups, some populations are isolated and vulnerable.
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De R, Sharma R, Davidar P, Arumugam N, Sedhupathy A, Puyravaud JP, Selvan KM, Rahim PA, Udayraj S, Parida J, Digal DK, Kanagaraj R, Kakati K, Nigam P, Williams AC, Habib B, Goyal SP. Pan-India population genetics signifies the importance of habitat connectivity for wild Asian elephant conservation. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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Kudla N, McCluskey EM, Lulla V, Grundel R, Moore JA. Intact landscape promotes gene flow and low genetic structuring in the threatened Eastern Massasauga Rattlesnake. Ecol Evol 2021; 11:6276-6288. [PMID: 34141217 PMCID: PMC8207425 DOI: 10.1002/ece3.7480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/07/2020] [Accepted: 02/01/2021] [Indexed: 11/07/2022] Open
Abstract
Genetic structuring of wild populations is dependent on environmental, ecological, and life-history factors. The specific role environmental context plays in genetic structuring is important to conservation practitioners working with rare species across areas with varying degrees of fragmentation. We investigated fine-scale genetic patterns of the federally threatened Eastern Massasauga Rattlesnake (Sistrurus catenatus) on a relatively undisturbed island in northern Michigan, USA. This species often persists in habitat islands throughout much of its distribution due to extensive habitat loss and distance-limited dispersal. We found that the entire island population exhibited weak genetic structuring with spatially segregated variation in effective migration and genetic diversity. The low level of genetic structuring contrasts with previous studies in the southern part of the species' range at comparable fine scales (~7 km), in which much higher levels of structuring were documented. The island population's genetic structuring more closely resembles that of populations from Ontario, Canada, that occupy similarly intact habitats. Intrapopulation variation in effective migration and genetic diversity likely corresponds to the presence of large inland lakes acting as barriers and more human activity in the southern portion of the island. The observed genetic structuring in this intact landscape suggests that the Eastern Massasauga is capable of sufficient interpatch movements to reduce overall genetic structuring and colonize new habitats. Landscape mosaics with multiple habitat patches and localized barriers (e.g., large water bodies or roads) will promote gene flow and natural colonization for this declining species.
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Affiliation(s)
- Nathan Kudla
- Biology DepartmentGrand Valley State UniversityAllendaleMIUSA
| | | | - Vijay Lulla
- Department of GeographyIUPUIIndianapolis, INUSA
| | - Ralph Grundel
- Great Lakes Science CenterU.S. Geological SurveyChestertonINUSA
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7
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Spatial ecology of the stone marten in an Alpine area: combining camera-trapping and genetic surveys. MAMMAL RES 2021. [DOI: 10.1007/s13364-021-00564-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
AbstractA species’ potential distribution can be modelled adequately only if no factor other than habitat availability affects its occurrences. Space use by stone marten Martes foina is likely to be affected by interspecific competition with the strictly related pine marten Martes martes, the latter being able to outcompete the first species in forested habitats. Hence, to point out the environmental factors which determine the distribution and density of the stone marten, a relatively understudied mesocarnivore, we applied two non-invasive survey methods, camera-trapping and faecal-DNA based genetic analysis, in an Alpine area where the pine marten was deemed to be absent (Val Grande National Park N Italy). Camera trapping was conducted from October 2014 to November 2015, using up to 27 cameras. Marten scats were searched for between July and November 2015 and, to assess density, in spring 2017. Species identification was accomplished by a PCR-RFLP method, while 17 autosomal microsatellites were used for individual identification. The stone marten occurred in all available habitats (83% of trapping sites and 73.2% of scats); nonetheless, habitat suitability, as assessed using MaxEnt, depended on four major land cover variables—rocky grasslands, rocks and debris, beech forests and chestnut forests—, martens selecting forests and avoiding open rocky areas. Sixteen individuals were identified, of which 14 related to each other, possibly forming six different groups. Using capwire estimators, density was assessed as 0.95 (0.7–1.3) ind/km2. In the study area, the widespread stone marten selected forested areas, attaining density values like those reported for the pine marten in northern Europe and suggesting that patterns of habitat selection may depend on the relative abundance of the two competing martens.
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Sanz N, Vidal O, García S, Molina R, Araguas RM. Molecular characterization of spiny hedgehogs of the Iberian Peninsula: the missing link in the postglacial colonization of the western European hedgehog. MAMMAL RES 2021. [DOI: 10.1007/s13364-020-00550-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Pichlmueller F, Murphy EC, MacKay JWB, Henderson J, Fewster RM, Russell JC. Island invasion and reinvasion: Informing invasive species management with genetic measures of connectivity. J Appl Ecol 2020. [DOI: 10.1111/1365-2664.13727] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Florian Pichlmueller
- School of Biological Sciences University of Auckland Auckland New Zealand
- School of Biomedical Sciences University of Otago Dunedin New Zealand
| | | | - Jamie W. B. MacKay
- School of Biological Sciences University of Auckland Auckland New Zealand
- Wildland Consultants Ltd Auckland New Zealand
| | | | - Rachel M. Fewster
- Department of Statistics University of Auckland Auckland New Zealand
| | - James C. Russell
- School of Biological Sciences University of Auckland Auckland New Zealand
- Department of Statistics University of Auckland Auckland New Zealand
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Dalui S, Khatri H, Singh SK, Basu S, Ghosh A, Mukherjee T, Sharma LK, Singh R, Chandra K, Thakur M. Fine-scale landscape genetics unveiling contemporary asymmetric movement of red panda (Ailurus fulgens) in Kangchenjunga landscape, India. Sci Rep 2020; 10:15446. [PMID: 32963325 PMCID: PMC7508845 DOI: 10.1038/s41598-020-72427-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/31/2020] [Indexed: 11/09/2022] Open
Abstract
Wildlife management in rapid changing landscapes requires critical planning through cross cutting networks, and understanding of landscape features, often affected by the anthropogenic activities. The present study demonstrates fine-scale spatial patterns of genetic variation and contemporary gene flow of red panda (Ailurus fulgens) populations with respect to landscape connectivity in Kangchenjunga Landscape (KL), India. The study found about 1,309.54 km2 area suitable for red panda in KL-India, of which 62.21% area fell under the Protected Area network. We identified 24 unique individuals from 234 feces collected at nine microsatellite loci. The spatially explicit and non-explicit Bayesian clustering algorithms evident to exhibit population structuring and supported red panda populations to exist in meta-population frame work. In concurrence to the habitat suitability and landscape connectivity models, gene flow results supported a contemporary asymmetric movement of red panda by connecting KL-India in a crescent arc. We demonstrate the structural-operational connectivity of corridors in KL-India that facilitated red panda movement in the past. We also seek for cooperation in Nepal, Bhutan and China to aid in preparing for a comprehensive monitoring plan for the long-term conservation and management of red panda in trans-boundary landscapes.
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Affiliation(s)
- Supriyo Dalui
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, 700019, India
| | - Hiren Khatri
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
- Amity Institute of Forestry and Wildlife, Amity University Campus, Sector-125, Noida, UP, 201303, India
| | - Sujeet Kumar Singh
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
| | - Shambadeb Basu
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
| | - Avijit Ghosh
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, 700019, India
| | - Tanoy Mukherjee
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
- Department of Zoology, University of Calcutta, Kolkata, West Bengal, 700019, India
| | - Lalit Kumar Sharma
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
| | - Randeep Singh
- Amity Institute of Forestry and Wildlife, Amity University Campus, Sector-125, Noida, UP, 201303, India
| | - Kailash Chandra
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India
| | - Mukesh Thakur
- Zoological Survey of India, New Alipore, Kolkata, West Bengal, 700053, India.
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11
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Genetic structure of regional water vole populations and footprints of reintroductions: a case study from southeast England. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01268-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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12
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Miller WL, Miller‐Butterworth CM, Diefenbach DR, Walter WD. Assessment of spatial genetic structure to identify populations at risk for infection of an emerging epizootic disease. Ecol Evol 2020; 10:3977-3990. [PMID: 32489625 PMCID: PMC7244803 DOI: 10.1002/ece3.6161] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/04/2020] [Accepted: 01/24/2020] [Indexed: 12/19/2022] Open
Abstract
Understanding the geographic extent and connectivity of wildlife populations can provide important insights into the management of disease outbreaks but defining patterns of population structure is difficult for widely distributed species. Landscape genetic analyses are powerful methods for identifying cryptic structure and movement patterns that may be associated with spatial epizootic patterns in such cases.We characterized patterns of population substructure and connectivity using microsatellite genotypes from 2,222 white-tailed deer (Odocoileus virginianus) in the Mid-Atlantic region of the United States, a region where chronic wasting disease was first detected in 2009. The goal of this study was to evaluate the juxtaposition between population structure, landscape features that influence gene flow, and current disease management units.Clustering analyses identified four to five subpopulations in this region, the edges of which corresponded to ecophysiographic provinces. Subpopulations were further partitioned into 11 clusters with subtle (F ST ≤ 0.041), but significant genetic differentiation. Genetic differentiation was lower and migration rates were higher among neighboring genetic clusters, indicating an underlying genetic cline. Genetic discontinuities were associated with topographic barriers, however.Resistance surface modeling indicated that gene flow was diffuse in homogenous landscapes, but the direction and extent of gene flow were influenced by forest cover, traffic volume, and elevational relief in subregions heterogeneous for these landscape features. Chronic wasting disease primarily occurred among genetic clusters within a single subpopulation and along corridors of high landscape connectivity.These results may suggest a possible correlation between population substructure, landscape connectivity, and the occurrence of diseases for widespread species. Considering these factors may be useful in delineating effective management units, although only the largest features produced appreciable differences in subpopulation structure. Disease mitigation strategies implemented at the scale of ecophysiographic provinces are likely to be more effective than those implemented at finer scales.
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Affiliation(s)
- William L. Miller
- Pennsylvania Cooperative Fish and Wildlife Research UnitDepartment of Ecosystem Science and ManagementIntercollege Graduate Degree Program in EcologyThe Pennsylvania State UniversityUniversity ParkPAUSA
| | | | - Duane R. Diefenbach
- U.S. Geological SurveyPennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - W. David Walter
- U.S. Geological SurveyPennsylvania Cooperative Fish and Wildlife Research UnitThe Pennsylvania State UniversityUniversity ParkPAUSA
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Moore JA, McCluskey EM, Gould B, Laarman P, Sapak J. Nest-Site Fidelity and Sex-Biased Dispersal Affect Spatial Genetic Structure of Eastern Box Turtles (Terrapene carolina carolina) at Their Northern Range Edge. COPEIA 2020. [DOI: 10.1643/ce-19-206] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Jennifer A. Moore
- Biology Department, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401; (JAM) ; (EMM) ; and (PL) . Send reprint requests to JAM
| | - Eric M. McCluskey
- Biology Department, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401; (JAM) ; (EMM) ; and (PL) . Send reprint requests to JAM
| | - Breanna Gould
- Luna College, 366 Luna Drive, Las Vegas, New Mexico 87701;
| | - Patrick Laarman
- Biology Department, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401; (JAM) ; (EMM) ; and (PL) . Send reprint requests to JAM
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Arslan Y, Demi̇rtaş S, Herman JS, Pustilnik JD, Searle JB, Gündüz İ. The Anatolian glacial refugium and human-mediated colonization: a phylogeographical study of the stone marten (Martes foina) in Turkey. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
AbstractThe Anatolian Peninsula, comprising most of modern Turkey, is situated at the junction of Europe, the Middle East and Asia. Together with its complex geomorphological and climatic history, this has given rise to a rich fauna and flora, which exhibits a wide range of historical biogeographical patterns. The stone marten (Martes foina) is a small carnivore that is found across the temperate Palaearctic region including Anatolia, where it is often associated with habitats modified by humans, but few genetic data exist for this species. We sequenced a 1840-bp region of the mitochondrial genome from 97 martens sampled across the peninsula and intron 7 of the nuclear β-fibrinogen gene from 53 of these. Two mitochondrial lineages were recovered, with overlapping eastern and western distributions, but there was no geographical structure for the autosomal marker. Coalescent analyses indicated that both of the lineages originated during the Last Glacial Maximum, one of them within an eastern Anatolian refugium and the other in a western Anatolian or Balkan refugium. The western lineage colonized most of Europe in the Holocene, while the eastern lineage may be endemic to Anatolia, from where it colonized the Iberian Peninsula via human translocation. The presence of at least one refugial stone marten population highlights the importance of Anatolia to the preservation of genetic variation and biodiversity.
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Affiliation(s)
- Yağmur Arslan
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Sadik Demi̇rtaş
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
| | - Jeremy S Herman
- Department of Natural Sciences, National Museums Scotland, Edinburgh, UK
| | - Jeremy D Pustilnik
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - Jeremy B Searle
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, USA
| | - İslam Gündüz
- Department of Biology, Faculty of Arts and Sciences, Ondokuz Mayis University, Samsun, Turkey
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Jensen AM, O'Neil NP, Iwaniuk AN, Burg TM. Landscape effects on the contemporary genetic structure of Ruffed Grouse ( Bonasa umbellus) populations. Ecol Evol 2019; 9:5572-5592. [PMID: 31160983 PMCID: PMC6540679 DOI: 10.1002/ece3.5112] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 01/28/2019] [Accepted: 02/08/2019] [Indexed: 01/01/2023] Open
Abstract
The amount of dispersal that occurs among populations can be limited by landscape heterogeneity, which is often due to both natural processes and anthropogenic activity leading to habitat loss or fragmentation. Understanding how populations are structured and mapping existing dispersal corridors among populations is imperative to both determining contemporary forces mediating population connectivity, and informing proper management of species with fragmented populations. Furthermore, the contemporary processes mediating gene flow across heterogeneous landscapes on a large scale are understudied, particularly with respect to widespread species. This study focuses on a widespread game bird, the Ruffed Grouse (Bonasa umbellus), for which we analyzed samples from the western extent of the range. Using three types of genetic markers, we uncovered multiple factors acting in concert that are responsible for mediating contemporary population connectivity in this species. Multiple genetically distinct groups were detected; microsatellite markers revealed six groups, and a mitochondrial marker revealed four. Many populations of Ruffed Grouse are genetically isolated, likely by macrogeographic barriers. Furthermore, the addition of landscape genetic methods not only corroborated genetic structure results, but also uncovered compelling evidence that dispersal resistance created by areas of unsuitable habitat is the most important factor mediating population connectivity among the sampled populations. This research has important implications for both our study species and other inhabitants of the early successional forest habitat preferred by Ruffed Grouse. Moreover, it adds to a growing body of evidence that isolation by resistance is more prevalent in shaping population structure of widespread species than previously thought.
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Affiliation(s)
- Ashley M. Jensen
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
| | - Nicholas P. O'Neil
- Canadian Centre for Behavioural NeuroscienceUniversity of LethbridgeLethbridgeAlbertaCanada
| | - Andrew N. Iwaniuk
- Canadian Centre for Behavioural NeuroscienceUniversity of LethbridgeLethbridgeAlbertaCanada
| | - Theresa M. Burg
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
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Tsoupas A, Andreadou M, Papakosta MA, Karaiskou N, Bakaloudis DE, Chatzinikos E, Sakoulis A, Triantafyllidis A, Vlachos CG. Phylogeography of Martes foina in Greece. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.02.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Bhattacharyya S, Ishtiaq F. Noninvasive sampling reveals population genetic structure in the Royle's pika, Ochotona roylei, in the western Himalaya. Ecol Evol 2019; 9:180-191. [PMID: 30680105 PMCID: PMC6342111 DOI: 10.1002/ece3.4707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 10/11/2018] [Accepted: 10/22/2018] [Indexed: 11/09/2022] Open
Abstract
Understanding population genetic structure of climate-sensitive herbivore species is important as it provides useful insights on how shifts in environmental conditions can alter their distribution and abundance. Herbivore responses to the environment can have a strong indirect cascading effect on community structure. This is particularly important for Royle's pika (Lagomorpha: Ochotona roylei), a herbivorous talus-dwelling species in alpine ecosystem, which forms a major prey base for many carnivores in the Himalayan arc. In this study, we used seven polymorphic microsatellite loci to detect evidence for recent changes in genetic diversity and population structure in Royle's pika across five locations sampled between 8 and 160 km apart in the western Himalaya. Using four clustering approaches, we found the presence of significant contemporary genetic structure in Royle's pika populations. The detected genetic structure could be primarily attributed to the landscape features in alpine habitat (e.g., wide lowland valleys, rivers) that may act as semipermeable barriers to gene flow and distribution of food plants, which are key determinants in spatial distribution of herbivores. Pika showed low inbreeding coefficients (F IS) and a high level of pairwise relatedness for individuals within 1 km suggesting low dispersal abilities of talus-dwelling pikas. We have found evidence of a recent population bottleneck, possibly due to effects of environmental disturbances (e.g., snow melting patterns or thermal stress). Our results reveal significant evidence of isolation by distance in genetic differentiation (F ST range = 0.04-0.19). This is the first population genetics study on Royle's pika, which helps to address evolutionary consequences of climate change which are expected to significantly affect the distribution and population dynamics in this talus-dwelling species.
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Affiliation(s)
| | - Farah Ishtiaq
- Centre for Ecological SciencesIndian Institute of ScienceBangaloreIndia
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İbiş O, Koepfli KP, Özcan S, Tez C. Genetic analysis of Turkish martens: Do two species of the genusMartesoccur in Anatolia? ZOOL SCR 2018. [DOI: 10.1111/zsc.12289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Osman İbiş
- Department of Agricultural Biotechnology; Faculty of Agriculture; Erciyes University; Kayseri Turkey
- Genome and Stem Cell Center (GENKOK); Erciyes University; Kayseri Turkey
| | - Klaus-Peter Koepfli
- National Zoological Park; Smithsonian Conservation Biology Institute; Washington District of Columbia
- Theodosius Dobzhansky Center for Genome Bioinformatics; Saint Petersburg State University; Saint Petersburg Russia
| | - Servet Özcan
- Genome and Stem Cell Center (GENKOK); Erciyes University; Kayseri Turkey
- Department of Biology; Faculty of Sciences; Erciyes University; Kayseri Turkey
| | - Coşkun Tez
- Department of Biology; Faculty of Sciences; Erciyes University; Kayseri Turkey
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Jenkins DA, Yannic G, Schaefer JA, Conolly J, Lecomte N. Population structure of caribou in an ice-bound archipelago. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12748] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Deborah. A. Jenkins
- Environmental and Life Sciences Graduate Program; Trent University; Peterborough ON Canada
- Canada Research Chair in Polar and Boreal Ecology and Centre d'Études Nordiques; University of Moncton; Moncton NB Canada
| | - Glenn Yannic
- University of Grenoble Alpes; University of Savoie Mont Blanc; CNRS; LECA (Laboratoire d'Ecologie Alpine); Le Bourget-du-Lac France
| | | | - James Conolly
- Department of Anthropology; Trent University; Peterborough ON Canada
| | - Nicolas Lecomte
- Canada Research Chair in Polar and Boreal Ecology and Centre d'Études Nordiques; University of Moncton; Moncton NB Canada
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Wereszczuk A, Leblois R, Zalewski A. Genetic diversity and structure related to expansion history and habitat isolation: stone marten populating rural-urban habitats. BMC Ecol 2017; 17:46. [PMID: 29273026 PMCID: PMC5741947 DOI: 10.1186/s12898-017-0156-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 12/13/2017] [Indexed: 11/10/2022] Open
Abstract
Background Population genetic diversity and structure are determined by past and current evolutionary processes, among which spatially limited dispersal, genetic drift, and shifts in species distribution boundaries have major effects. In most wildlife species, environmental modifications by humans often lead to contraction of species’ ranges and/or limit their dispersal by acting as environmental barriers. However, in species well adapted to anthropogenic habitat or open landscapes, human induced environmental changes may facilitate dispersal and range expansions. In this study, we analysed whether isolation by distance and deforestation, among other environmental features, promotes or restricts dispersal and expansion in stone marten (Martes foina) populations. Results We genotyped 298 martens from eight sites at twenty-two microsatellite loci to characterize the genetic variability, population structure and demographic history of stone martens in Poland. At the landscape scale, limited genetic differentiation between sites in a mosaic of urban, rural and forest habitats was mostly influenced by isolation by distance. Statistical clustering and multivariate analyses showed weak genetic structuring with two to four clusters and a high rate of gene flow between them. Stronger genetic differentiation was detected for one stone marten population (NE1) located inside a large forest complex. Genetic differentiation between this site and all others was 20% higher than between other sites separated by similar distances. The genetic uniqueness index of NE1 was also twofold higher than in other sites. Past demographic history analyses showed recent expansion of this species in north-eastern Poland. A decrease in genetic diversity from south to north, and MIGRAINE analyses indicated the direction of expansion of stone marten. Conclusions Our results showed that two processes, changes in species distribution boundaries and limited dispersal associated with landscape barriers, affect genetic diversity and structure in stone marten. Analysis of local barriers that reduced dispersal and large scale analyses of genetic structure and demographic history highlight the importance of isolation by distance and forest cover for the past colonization of central Europe by stone marten. This confirmed the hypothesis that human-landscape changes (deforestation) accelerated stone marten expansion, to which climate warming probably has also been contributing over the last few decades. Electronic supplementary material The online version of this article (10.1186/s12898-017-0156-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anna Wereszczuk
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland.
| | - Raphaël Leblois
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, University Montpellier, Montpellier, France.,Institut de Biologie Computationnelle, University Montpellier, Montpellier, France
| | - Andrzej Zalewski
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
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Larroque J, Ruette S, Vandel JM, Queney G, Devillard S. Age and sex-dependent effects of landscape cover and trapping on the spatial genetic structure of the stone marten (Martes foina). CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0862-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Basto MP, Santos-Reis M, Simões L, Grilo C, Cardoso L, Cortes H, Bruford MW, Fernandes C. Assessing Genetic Structure in Common but Ecologically Distinct Carnivores: The Stone Marten and Red Fox. PLoS One 2016; 11:e0145165. [PMID: 26727497 PMCID: PMC4699814 DOI: 10.1371/journal.pone.0145165] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 11/30/2015] [Indexed: 11/23/2022] Open
Abstract
The identification of populations and spatial genetic patterns is important for ecological and conservation research, and spatially explicit individual-based methods have been recognised as powerful tools in this context. Mammalian carnivores are intrinsically vulnerable to habitat fragmentation but not much is known about the genetic consequences of fragmentation in common species. Stone martens (Martes foina) and red foxes (Vulpes vulpes) share a widespread Palearctic distribution and are considered habitat generalists, but in the Iberian Peninsula stone martens tend to occur in higher quality habitats. We compared their genetic structure in Portugal to see if they are consistent with their differences in ecological plasticity, and also to illustrate an approach to explicitly delineate the spatial boundaries of consistently identified genetic units. We analysed microsatellite data using spatial Bayesian clustering methods (implemented in the software BAPS, GENELAND and TESS), a progressive partitioning approach and a multivariate technique (Spatial Principal Components Analysis-sPCA). Three consensus Bayesian clusters were identified for the stone marten. No consensus was achieved for the red fox, but one cluster was the most probable clustering solution. Progressive partitioning and sPCA suggested additional clusters in the stone marten but they were not consistent among methods and were geographically incoherent. The contrasting results between the two species are consistent with the literature reporting stricter ecological requirements of the stone marten in the Iberian Peninsula. The observed genetic structure in the stone marten may have been influenced by landscape features, particularly rivers, and fragmentation. We suggest that an approach based on a consensus clustering solution of multiple different algorithms may provide an objective and effective means to delineate potential boundaries of inferred subpopulations. sPCA and progressive partitioning offer further verification of possible population structure and may be useful for revealing cryptic spatial genetic patterns worth further investigation.
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Affiliation(s)
- Mafalda P. Basto
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
- * E-mail:
| | - Margarida Santos-Reis
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Luciana Simões
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Clara Grilo
- Centro Brasileiro de Estudos em Ecologia de Estradas/Programa de Pós-graduação em Ecologia Aplicada, Universidade Federal de Lavras, Lavras, Minas Gerais, Brasil
| | - Luís Cardoso
- Departamento de Ciências Veterinárias, Escola de Ciências Agrárias e Veterinárias, Universidade de Trás-os-Montes e Alto Douro (UTAD), Vila Real, Portugal
| | - Helder Cortes
- Laboratório de Parasitologia Victor Caeiro, Instituto de Ciências Agrárias e Ambientais Mediterrânicas (ICAAM), Universidade de Évora, Évora, Portugal
| | - Michael W. Bruford
- Cardiff School of Biosciences, Cardiff University, Cardiff, United Kingdom
| | - Carlos Fernandes
- Ce3C – Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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