1
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Beer MA, Proft KM, Veillet A, Kozakiewicz CP, Hamilton DG, Hamede R, McCallum H, Hohenlohe PA, Burridge CP, Margres MJ, Jones ME, Storfer A. Disease-driven top predator decline affects mesopredator population genomic structure. Nat Ecol Evol 2024; 8:293-303. [PMID: 38191839 DOI: 10.1038/s41559-023-02265-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/02/2023] [Indexed: 01/10/2024]
Abstract
Top predator declines are pervasive and often have dramatic effects on ecological communities via changes in food web dynamics, but their evolutionary consequences are virtually unknown. Tasmania's top terrestrial predator, the Tasmanian devil, is declining due to a lethal transmissible cancer. Spotted-tailed quolls benefit via mesopredator release, and they alter their behaviour and resource use concomitant with devil declines and increased disease duration. Here, using a landscape community genomics framework to identify environmental drivers of population genomic structure and signatures of selection, we show that these biotic factors are consistently among the top variables explaining genomic structure of the quoll. Landscape resistance negatively correlates with devil density, suggesting that devil declines will increase quoll genetic subdivision over time, despite no change in quoll densities detected by camera trap studies. Devil density also contributes to signatures of selection in the quoll genome, including genes associated with muscle development and locomotion. Our results provide some of the first evidence of the evolutionary impacts of competition between a top predator and a mesopredator species in the context of a trophic cascade. As top predator declines are increasing globally, our framework can serve as a model for future studies of evolutionary impacts of altered ecological interactions.
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Affiliation(s)
- Marc A Beer
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Kirstin M Proft
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Anne Veillet
- Hilo Core Genomics Facility, University of Hawaii at Hilo, Hilo, HI, USA
| | - Christopher P Kozakiewicz
- Department of Integrative Biology, Michigan State University, W.K. Kellogg Biological Station, Hickory Corners, MI, USA
| | - David G Hamilton
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Rodrigo Hamede
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le Cancer, Montpellier, France
| | - Hamish McCallum
- Environmental Futures Research Institute, Griffith University, Nathan, Queensland, Australia
| | - Paul A Hohenlohe
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID, USA
| | | | - Mark J Margres
- Department of Integrative Biology, University of South Florida, Tampa, FL, USA
| | - Menna E Jones
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, USA.
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2
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Effective dispersal and genetic structure of a small mammal in an intensively managed agricultural landscape: is there any barrier to movement? Evol Ecol 2023. [DOI: 10.1007/s10682-023-10233-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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3
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Cordonnier M, Felten D, Trindl A, Heinze J, Bernadou A. Absence of genetic isolation across highly fragmented landscape in the ant Temnothorax nigriceps. BMC Ecol Evol 2022; 22:91. [PMID: 35840881 PMCID: PMC9284864 DOI: 10.1186/s12862-022-02044-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Human activities, including changes in agricultural landscapes, often impact biodiversity through habitat fragmentation. This potentially reduces genetic exchange between previously connected populations. Using a combination of nuclear and mitochondrial markers, we investigated (i) genetic diversity and population structure at multiple spatial scales and (ii) colony genetic structure and queen mating frequency in the ant species Temnothorax nigriceps in a highly anthropized environment.
Results
Although the results highlighted genetic structure on a European spatial scale, they did not reveal an impact of fragmentation on a regional scale, and we did not observe any genetic population structure on a regional scale. Across all populations, regardless of their geographical location, colony structure suggested monogyny (a single queen per colony) and monandry (single mating). However, nestmates were more related than expected, indicating that large-scale dispersal does not fully prevent genetic isolation.
Conclusions
Despite living in fragmented patches of habitat, populations of Temnothorax nigriceps are apparently genetically not isolated at a regional scale. However, large-scale dispersal alone does not prevent genetic isolation. The ecological requirements of T. nigriceps may explain their resilience to habitat fragmentation by allowing them to survive in very small patches of suitable habitat. The deeper investigation of the diversity of functional habitats for this species should allow to appreciate better the mechanisms permitting this species to overcome the negative impacts of fragmentation.
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4
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Tsuchiya MTN, Dikow RB, Cassin-Sackett L. First Genome Sequence of the Gunnison's Prairie Dog (Cynomys gunnisoni), a Keystone Species and Player in the Transmission of Sylvatic Plague. Genome Biol Evol 2021; 12:618-625. [PMID: 32277812 PMCID: PMC7250503 DOI: 10.1093/gbe/evaa069] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2020] [Indexed: 12/30/2022] Open
Abstract
Prairie dogs (genus Cynomys) are a charismatic symbol of the American West. Their large social aggregations and complex vocalizations have been the subject of scientific and popular interest for decades. A large body of literature has documented their role as keystone species of western North America's grasslands: They generate habitat for other vertebrates, increase nutrient availability for plants, and act as a food source for mammalian, squamate, and avian predators. An additional keystone role lies in their extreme susceptibility to sylvatic plague (caused by Yersinia pestis), which results in periodic population extinctions, thereby generating spatiotemporal heterogeneity in both biotic communities and ecological processes. Here, we report the first Cynomys genome for a Gunnison's prairie dog (C. gunnisoni gunnisoni) from Telluride, Colorado (USA). The genome was constructed using a hybrid assembly of PacBio and Illumina reads and assembled with MaSuRCA and PBJelly, which resulted in a scaffold N50 of 824 kb. Total genome size was 2.67 Gb, with 32.46% of the bases occurring in repeat regions. We recovered 94.9% (91% complete) of the single copy orthologs using the mammalian Benchmarking Universal Single-Copy Orthologs database and detected 49,377 gene models (332,141 coding regions). Pairwise Sequentially Markovian Coalescent showed support for long-term stable population size followed by a steady decline beginning near the end of the Pleistocene, as well as a recent population reduction. The genome will aid in studies of mammalian evolution, disease resistance, and the genomic basis of life history traits in ground squirrels.
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Affiliation(s)
- Mirian T N Tsuchiya
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia
| | - Rebecca B Dikow
- Data Science Lab, Office of the Chief Information Officer, Smithsonian Institution, Washington, District of Columbia
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5
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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] [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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Reding DM, Castañeda-Rico S, Shirazi S, Hofman CA, Cancellare IA, Lance SL, Beringer J, Clark WR, Maldonado JE. Mitochondrial Genomes of the United States Distribution of Gray Fox (Urocyon cinereoargenteus) Reveal a Major Phylogeographic Break at the Great Plains Suture Zone. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.666800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We examined phylogeographic structure in gray fox (Urocyon cinereoargenteus) across the United States to identify the location of secondary contact zone(s) between eastern and western lineages and investigate the possibility of additional cryptic intraspecific divergences. We generated and analyzed complete mitochondrial genome sequence data from 75 samples and partial control region mitochondrial DNA sequences from 378 samples to investigate levels of genetic diversity and structure through population- and individual-based analyses including estimates of divergence (FST and SAMOVA), median joining networks, and phylogenies. We used complete mitochondrial genomes to infer phylogenetic relationships and date divergence times of major lineages of Urocyon in the United States. Despite broad-scale sampling, we did not recover additional major lineages of Urocyon within the United States, but identified a deep east-west split (∼0.8 million years) with secondary contact at the Great Plains Suture Zone and confirmed the Channel Island fox (Urocyon littoralis) is nested within U. cinereoargenteus. Genetic diversity declined at northern latitudes in the eastern United States, a pattern concordant with post-glacial recolonization and range expansion. Beyond the east-west divergence, morphologically-based subspecies did not form monophyletic groups, though unique haplotypes were often geographically limited. Gray foxes in the United States displayed a deep, cryptic divergence suggesting taxonomic revision is needed. Secondary contact at a common phylogeographic break, the Great Plains Suture Zone, where environmental variables show a sharp cline, suggests ongoing evolutionary processes may reinforce this divergence. Follow-up study with nuclear markers should investigate whether hybridization is occurring along the suture zone and characterize contemporary population structure to help identify conservation units. Comparative work on other wide-ranging carnivores in the region should test whether similar evolutionary patterns and processes are occurring.
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7
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Watt C, Kierepka E, Ferreira C, Koen E, Row J, Bowman J, Wilson P, Murray D. Canada lynx ( Lynx canadensis) gene flow across a mountain transition zone in western North America. CAN J ZOOL 2021. [DOI: 10.1139/cjz-2019-0247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Mountain ecotones have the potential to cause multiple patterns in divergence, from simple barrier effects to more fundamental ecological divergence. Most work in mountain ecotones in North America has focused on reinforcement between refugial populations, making prediction of how mountains impact species that are not restricted to separate glacial refugia remains difficult. This study focused on the Canada lynx (Lynx canadensis Kerr, 1792), a highly mobile felid considered to be a habitat and dietary specialist. Specifically, we used 14 microsatellite loci and landscape genetic tools to investigate if the Rocky Mountains and associated climatic transitions influence lynx genetic differentiation in western North America. Although lynx exhibited high gene flow across the region, analyses detected structuring of neutral genetic variation across our study area. Gene flow for lynx most strongly related to temperature and elevation compared with other landscape variables (terrain roughness, percent forest cover, and habitat suitability index) and geographic distance alone. Overall, genetic structure in lynx is most consistent with barrier effects created by the Rocky Mountains rather than ecological divergence. Furthermore, warmer temperatures had a measurable impact on gene flow, which suggests connectivity may further decrease in peripheral or fragmented populations as climate warms.
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Affiliation(s)
- C.M. Watt
- Biology Department, Trent University, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - E.M. Kierepka
- North Carolina Museum of Natural Sciences, North Carolina State University, Department of Forestry and Environmental Resources, Raleigh, NC 27601, USA
| | - C.C. Ferreira
- Biology Department, Trent University, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
- UFZ-Helmholtz Centre for Environmental Research, Department of Conservation Biology, Permoserstr, 15, 04318 Leipzig, Germany
| | - E.L. Koen
- Ontario Ministry of Natural Resources, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - J.R. Row
- Minnow Environmental Inc., Queen’s University, Georgetown, ON L7G 3M9, Canada
| | - J. Bowman
- Ontario Ministry of Natural Resources, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - P.J. Wilson
- Biology Department, Trent University, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - D.L. Murray
- Biology Department, Trent University, Trent University DNA Building, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
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8
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Liu T, Zhang K, Dai W, Jin L, Sun K, Feng J. Evolutionary insights into
Rhinolophus episcopus
(Chiroptera, Rhinolophidae) in China: Isolation by distance, environment, or sensory system? J ZOOL SYST EVOL RES 2020. [DOI: 10.1111/jzs.12394] [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)
- Tong Liu
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Kangkang Zhang
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- Key Laboratory of Vegetation Ecology Ministry of Education Changchun China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization Northeast Normal University Changchun China
- College of Life Science Jilin Agricultural University Changchun China
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9
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Jacquier M, Vandel JM, Léger F, Duhayer J, Pardonnet S, Queney G, Kaerle C, Say L, Ruette S, Devillard S. Population genetic structures at multiple spatial scales: importance of social groups in European badgers. J Mammal 2020. [DOI: 10.1093/jmammal/gyaa090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AbstractPopulation viability and metapopulation dynamics are strongly affected by gene flow. Identifying ecological correlates of genetic structure and gene flow in wild populations is therefore a major issue both in evolutionary ecology and species management. Studying the genetic structure of populations also enables identification of the spatial scale at which most gene flow occurs, hence the scale of the functional connectivity, which is of paramount importance for species ecology. In this study, we examined the genetic structure of a social, continuously distributed mammal, the European badger (Meles meles), both at large spatial scales (among populations) and fine (within populations) spatial scales. The study was carried out in 11 sites across France utilizing a noninvasive hair trapping protocol at 206 monitored setts. We identified 264 badgers genotyped at 24 microsatellite DNA loci. At the large scale, we observed high and significant genetic differentiation among populations (global Fst = 0.139; range of pairwise Fst [0.046–0.231]) that was not related to the geographic distance among sites, suggesting few large-scale dispersal events. Within populations, we detected a threshold value below which badgers were genetically close (< 400 m), highlighting that sociality is the major structuring process within badger populations at the fine scale.
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Affiliation(s)
- Mickaël Jacquier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558 LBBE, Villeurbanne, France
- Office Français de la Biodiversité, Unité-PAD, Montfort, Birieux, France
| | - Jean-Michel Vandel
- Office Français de la Biodiversité, Unité-PAD, Montfort, Birieux, France
| | - François Léger
- Office Français de la Biodiversité, Unité-PAD, Gerstheim, France
| | - Jeanne Duhayer
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558 LBBE, Villeurbanne, France
| | - Sylvia Pardonnet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558 LBBE, Villeurbanne, France
| | | | | | - Ludovic Say
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558 LBBE, Villeurbanne, France
| | - Sandrine Ruette
- Office Français de la Biodiversité, Unité-PAD, Montfort, Birieux, France
| | - Sébastien Devillard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, UMR5558 LBBE, Villeurbanne, France
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10
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Ford BM, Cornellas A, Leonard JA, Weir RD, Russello MA. Spatiotemporal analyses suggest the role of glacial history and the ice-free corridor in shaping American badger population genetic variation. Ecol Evol 2020; 10:8345-8357. [PMID: 32788984 PMCID: PMC7417222 DOI: 10.1002/ece3.6541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 06/03/2020] [Accepted: 06/10/2020] [Indexed: 11/07/2022] Open
Abstract
Recurring glacial cycles through the Quaternary period drastically altered the size and distribution of natural populations of North American flora and fauna. The "southerly refugia model" has been the longstanding framework for testing the effects of glaciation on contemporary genetic patterns; however, insights from ancient DNA have contributed to the reconstruction of more complex histories for some species. The American badger, Taxidea taxus, provides an interesting species for exploring the genetic legacy of glacial history, having been hypothesized to have postglacially emerged from a single, southerly refugium to recolonize northern latitudes. However, previous studies have lacked genetic sampling from areas where distinct glacial refugia have been hypothesized, including the Pacific Northwest and American Far North (Yukon, Alaska). In order to further investigate the phylogeographic history of American badgers, we collected mitochondrial DNA sequence data from ancient subfossil material collected within the historical range (Alaska, Yukon) and combined them with new and previously published data from across the species' contemporary distribution (n = 1,207). We reconstructed a mostly unresolved phylogenetic tree and star-like haplotype network indicative of emergence from a largely panmictic glacial refugium and recent population expansion, the latter further punctuated by significantly negative Tajima's D and Fu's Fs values. Although directionality of migration cannot be unequivocally inferred, the moderate to high levels of genetic variation exhibited by American badgers, alongside the low frequency of haplotypes with indels in the Midwest, suggest a potential recolonization into central North America after the hypothesized ice-free corridor reopened ~13,000 years ago. Overall, the expanded reconstruction of phylogeographic history of American badgers offers a broader understanding of contemporary range-wide patterns and identifies unique genetic units that can likely be used to inform conservation of at-risk populations at the northern periphery.
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Affiliation(s)
- Brett M. Ford
- Department of BiologyUniversity of British ColumbiaKelownaBCCanada
| | - Anna Cornellas
- Conservation and Evolutionary Genetics GroupEstación Biológica de Doñana (EBD‐CSIC)SevilleSpain
| | - Jennifer A. Leonard
- Conservation and Evolutionary Genetics GroupEstación Biológica de Doñana (EBD‐CSIC)SevilleSpain
| | - Richard D. Weir
- British Columbia Ministry of Environment and Climate Change StrategyVictoriaBCCanada
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11
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Cullingham CI, Moehrenschlager A. Genetics of a reintroduced swift fox population highlights the need for integrated conservation between neighbouring countries. Anim Conserv 2019. [DOI: 10.1111/acv.12508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- C. I. Cullingham
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - A. Moehrenschlager
- Centre for Conservation Research Calgary Zoological Society Calgary Alberta Canada
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12
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Doyle JC, Sample DW, Long L, Van Deelen TR. Space Use and Habitat Selection of American Badgers (Taxidea Taxus) in Southwestern Wisconsin. AMERICAN MIDLAND NATURALIST 2019. [DOI: 10.1674/0003-0031-182.1.63] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- James C. Doyle
- Department of Forest and Wildlife Ecology, University of Wisconsin – Madison 53706
| | - David W. Sample
- Science Services, Wisconsin Department of Natural Resources, Madison 53716
| | - Lindsey Long
- Wildlife Management, Wisconsin Department of Natural Resources, Madison, 53716
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13
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Fine-scale genetic structure and conservation status of American badgers at their northwestern range periphery. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01192-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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14
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Evaluating the Hypothesis of Pleistocene Refugia for Mammals in the Cuatro Ciénegas Basin. ANIMAL DIVERSITY AND BIOGEOGRAPHY OF THE CUATRO CIÉNEGAS BASIN 2019. [DOI: 10.1007/978-3-030-11262-2_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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15
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Priadka P, Manseau M, Trottier T, Hervieux D, Galpern P, McLoughlin PD, Wilson PJ. Partitioning drivers of spatial genetic variation for a continuously distributed population of boreal caribou: Implications for management unit delineation. Ecol Evol 2019; 9:141-153. [PMID: 30680102 PMCID: PMC6342118 DOI: 10.1002/ece3.4682] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/25/2018] [Accepted: 10/14/2018] [Indexed: 12/31/2022] Open
Abstract
Isolation by distance (IBD) is a natural pattern not readily incorporated into theoretical models nor traditional metrics for differentiating populations, although clinal genetic differentiation can be characteristic of many wildlife species. Landscape features can also drive population structure additive to baseline IBD resulting in differentiation through isolation-by-resistance (IBR). We assessed the population genetic structure of boreal caribou across western Canada using nonspatial (STRUCTURE) and spatial (MEMGENE) clustering methods and investigated the relative contribution of IBD and IBR on genetic variation of 1,221 boreal caribou multilocus genotypes across western Canada. We further introduced a novel approach to compare the partitioning of individuals into management units (MU) and assessed levels of genetic connectivity under different MU scenarios. STRUCTURE delineated five genetic clusters while MEMGENE identified finer-scale differentiation across the study area. IBD was significant and did not differ for males and females both across and among detected genetic clusters. MEMGENE landscape analysis further quantified the proportion of genetic variation contributed by IBD and IBR patterns, allowing for the relative importance of spatial drivers, including roads, water bodies, and wildfires, to be assessed and incorporated into the characterization of population structure for the delineation of MUs. Local population units, as currently delineated in the boreal caribou recovery strategy, do not capture the genetic variation and connectivity of the ecotype across the study area. Here, we provide the tools to assess fine-scale spatial patterns of genetic variation, partition drivers of genetic variation, and evaluate the best management options for maintaining genetic connectivity. Our approach is highly relevant to vagile wildlife species that are of management and conservation concern and demonstrate varying degrees of IBD and IBR with clinal spatial genetic structure that challenges the delineation of discrete population boundaries.
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Affiliation(s)
- Pauline Priadka
- Natural Resources InstituteUniversity of ManitobaWinnipegManitobaCanada
| | - Micheline Manseau
- Natural Resources InstituteUniversity of ManitobaWinnipegManitobaCanada
- Landscape Science and Technology DivisionEnvironment and Climate Change CanadaOttawaOntarioCanada
- Biology DepartmentTrent UniversityPeterboroughOntarioCanada
| | - Tim Trottier
- Ministry of EnvironmentSaskatchewan GovernmentLa RongeSaskatchewanCanada
| | - Dave Hervieux
- Department of Environment and ParksAlberta GovernmentGrande Prairie, AlbertaCanada
| | - Paul Galpern
- Faculty of Environmental Design and Department of Biological SciencesUniversity of CalgaryCalgaryAlbertaCanada
| | | | - Paul J. Wilson
- Natural Resources InstituteUniversity of ManitobaWinnipegManitobaCanada
- Biology DepartmentTrent UniversityPeterboroughOntarioCanada
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16
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Guerrero J, Byrne AW, Lavery J, Presho E, Kelly G, Courcier EA, O'Keeffe J, Fogarty U, O'Meara DB, Ensing D, McCormick C, Biek R, Skuce RA, Allen AR. The population and landscape genetics of the European badger ( Meles meles) in Ireland. Ecol Evol 2018; 8:10233-10246. [PMID: 30397461 PMCID: PMC6206220 DOI: 10.1002/ece3.4498] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/20/2018] [Accepted: 07/27/2018] [Indexed: 01/06/2023] Open
Abstract
The population genetic structure of free-ranging species is expected to reflect landscape-level effects. Quantifying the role of these factors and their relative contribution often has important implications for wildlife management. The population genetics of the European badger (Meles meles) have received considerable attention, not least because the species acts as a potential wildlife reservoir for bovine tuberculosis (bTB) in Britain and Ireland. Herein, we detail the most comprehensive population and landscape genetic study of the badger in Ireland to date-comprised of 454 Irish badger samples, genotyped at 14 microsatellite loci. Bayesian and multivariate clustering methods demonstrated continuous clinal variation across the island, with potentially distinct differentiation observed in Northern Ireland. Landscape genetic analyses identified geographic distance and elevation as the primary drivers of genetic differentiation, in keeping with badgers exhibiting high levels of philopatry. Other factors hypothesized to affect gene flow, including earth worm habitat suitability, land cover type, and the River Shannon, had little to no detectable effect. By providing a more accurate picture of badger population structure and the factors effecting it, these data can guide current efforts to manage the species in Ireland and to better understand its role in bTB.
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Affiliation(s)
- Jimena Guerrero
- Centre D'Ecologie Fonctionelle et EvolutiveCEFE‐CNRSMontpellierFrance
| | - Andrew W. Byrne
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - John Lavery
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Eleanor Presho
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Gavin Kelly
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Emily A. Courcier
- Department of Agriculture, Environment and Rural Affairs Northern Ireland (DAERA‐NI)Veterinary Epidemiology UnitBelfastUK
| | - James O'Keeffe
- Department of Agriculture Food and the Marine (DAFM)DublinIreland
| | | | - Denise B. O'Meara
- Department of Chemical and Life SciencesWaterford Institute of TechnologyWaterfordIreland
| | - Dennis Ensing
- Agriculture, Sustainable Agri‐Food Sciences DivisionAgri‐Food and Biosciences InstituteBelfastUK
| | - Carl McCormick
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Roman Biek
- Institute of Biodiversity Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - Robin A. Skuce
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
| | - Adrian R. Allen
- Veterinary Sciences DivisionAgri‐Food and Biosciences Institute (AFBI)BelfastUK
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17
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Robertson EP, Fletcher RJ, Austin JD. Microsatellite polymorphism in the endangered snail kite reveals a panmictic, low diversity population. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-1003-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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