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Day CC, Alò D, Simmons RK, Cotey SR, Zarn KE, Gazeley IF, Small M, Fortin MJ, Bearlin AR, Smith SR, Landguth EL. Disentangling effects of dispersal, environment and anthropogenic barriers on functional connectivity in aquatic systems. Mol Ecol 2024:e17500. [PMID: 39188095 DOI: 10.1111/mec.17500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 07/24/2024] [Accepted: 08/07/2024] [Indexed: 08/28/2024]
Abstract
Disentangling the roles of structural landscape factors and animal movement behaviour can present challenges for practitioners managing landscapes to maintain functional connectivity and achieve conservation goals. We used a landscape genetics approach to combine robust demographic, behavioural and genetic datasets with spatially explicit simulations to evaluate the effects of anthropogenic barriers (dams, culverts) and natural landscape resistance (gradient, elevation) affecting dispersal behaviour, genetic connectivity and genetic structure in a resident population of Westslope Cutthroat Trout (Oncorhynchus clarkii lewisi). Analyses based on 10 years of sampling effort revealed a pattern of restricted dispersal, and population genetics identified discrete population clusters between distal tributaries and the mainstem stream and no structure within the mainstem stream. Demogenetic simulations demonstrated that, for this population, the effects of existing anthropogenic barriers on population structure are redundant with effects of restricted dispersal associated with the underlying environmental resistance. Our approach provides an example of how extensive field sampling combined with landscape genetics can be incorporated into spatially explicit simulation modelling to explore how, together, movement ecology and landscape resistance can be used to inform decisions around restoration and connectivity.
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Affiliation(s)
- Casey C Day
- Computational Ecology Lab, University of Montana, Missoula, Montana, USA
| | - Dominique Alò
- Departamento de Sistemas Acuáticos. Facultad de Ciencias Ambientales y Centro de Ciencias Ambientales EULA-Chile, Universidad de Concepción, Concepción, Chile
| | - Ryan K Simmons
- Environment, Land, and Licensing, Seattle City Light, Seattle, Washington, USA
| | - Stacy R Cotey
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan, USA
| | - Katherine E Zarn
- National Technology and Development Program, USDA Forest Service, Flagstaff, Arizona, USA
| | - Ian F Gazeley
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Maureen Small
- Washington Department of Fish and Wildlife, Olympia, Washington, USA
| | - Marie-Josee Fortin
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Andrew R Bearlin
- Environment, Land, and Licensing, Seattle City Light, Seattle, Washington, USA
| | - Seth R Smith
- Washington Department of Fish and Wildlife, Olympia, Washington, USA
| | - Erin L Landguth
- Computational Ecology Lab, University of Montana, Missoula, Montana, USA
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2
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Carroll SL, Schmidt GM, Waller JS, Graves TA. Evaluating density-weighted connectivity of black bears (Ursus americanus) in Glacier National Park with spatial capture-recapture models. MOVEMENT ECOLOGY 2024; 12:8. [PMID: 38263096 PMCID: PMC11334611 DOI: 10.1186/s40462-023-00445-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/19/2023] [Indexed: 01/25/2024]
Abstract
BACKGROUND Improved understanding of wildlife population connectivity among protected area networks can support effective planning for the persistence of wildlife populations in the face of land use and climate change. Common approaches to estimating connectivity often rely on small samples of individuals without considering the spatial structure of populations, leading to limited understanding of how individual movement links to demography and population connectivity. Recently developed spatial capture-recapture (SCR) models provide a framework to formally connect inference about individual movement, connectivity, and population density, but few studies have applied this approach to empirical data to support connectivity planning. METHODS We used mark-recapture data collected from 924 genetic detections of 598 American black bears (Ursus americanus) in 2004 with SCR ecological distance models to simultaneously estimate density, landscape resistance to movement, and population connectivity in Glacier National Park northwest Montana, USA. We estimated density and movement parameters separately for males and females and used model estimates to calculate predicted density-weighted connectivity surfaces. RESULTS Model results indicated that landscape structure influences black bear density and space use in Glacier. The mean density estimate was 16.08 bears/100 km2 (95% CI 12.52-20.6) for females and 9.27 bears/100 km2 (95% CI 7.70-11.14) for males. Density increased with forest cover for both sexes. For male black bears, density decreased at higher grizzly bear (Ursus arctos) densities. Drainages, valley bottoms, and riparian vegetation decreased estimates of landscape resistance to movement for male and female bears. For males, forest cover also decreased estimated resistance to movement, but a transportation corridor bisecting the study area strongly increased resistance to movement presenting a barrier to connectivity. CONCLUSIONS Density-weighed connectivity surfaces highlighted areas important for population connectivity that were distinct from areas with high potential connectivity. For black bears in Glacier and surrounding landscapes, consideration of both vegetation and valley topography could inform the placement of underpasses along the transportation corridor in areas characterized by both high population density and potential connectivity. Our study demonstrates that the SCR ecological distance model can provide biologically realistic, spatially explicit predictions to support movement connectivity planning across large landscapes.
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Affiliation(s)
- Sarah L Carroll
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Greta M Schmidt
- Department of Biology, San Diego State University, San Diego, CA, 92182, USA
| | - John S Waller
- Glacier National Park, P.O. Box 128, West Glacier, MT, 59936, USA
| | - Tabitha A Graves
- U.S. Geological Survey, Northern Rocky Mountain Science Center, PO Box 169, West Glacier, MT, 59936, USA
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Asadi Aghbolaghi M, Keyghobadi N, Azarakhsh Z, Dadizadeh M, Asadi Aghbolaghi S, Zamani N. An evaluation of isolation by distance and isolation by resistance on genetic structure of the Persian squirrel ( Sciurus anomalus) in the Zagros forests of Iran. Ecol Evol 2023; 13:e10225. [PMID: 37408621 PMCID: PMC10318582 DOI: 10.1002/ece3.10225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 05/27/2023] [Accepted: 06/11/2023] [Indexed: 07/07/2023] Open
Abstract
For the conservation of wild species, it is important to understand how landscape change and land management can affect gene flow and movement. Landscape genetic analyses provide a powerful approach to infer effects of various landscape factors on gene flow, thereby informing conservation actions. The Persian squirrel is a keystone species in the woodlands and oak forests of Western Asia, where it has experienced recent habitat loss and fragmentation. We conducted landscape genetic analyses of individuals sampled in the northern Zagros Mountains of Iran (provinces of Kurdistan, Kermanshah, and Ilam), focusing on the evaluation of isolation by distance (IBD) and isolation by resistance (IBR), using 16 microsatellite markers. The roles of geographical distance and landscape features including roads, rivers, developed areas, farming and agriculture, forests, lakes, plantation forests, rangelands, shrublands, and rocky areas of varying canopy cover, and swamp margins on genetic structure were quantified using individual-based approaches and resistance surface modeling. We found a significant pattern of IBD but only weak support for an effect of forest cover on genetic structure and gene flow. It seems that geographical distance is an important factor limiting the dispersal of the Persian squirrel in this region. The results of the current study inform ongoing conservation programs for the Persian squirrel in the Zagros oak forest.
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Affiliation(s)
- Marzieh Asadi Aghbolaghi
- Department of Biodiversity and Ecosystem Management, Environmental Sciences Research InstituteShahid Beheshti UniversityTehranIran
| | - Nusha Keyghobadi
- Department of BiologyThe University of Western OntarioLondonCanada
| | - Zeinab Azarakhsh
- Center of Remote Sensing and GIS Research, Faculty of Earth SciencesShahid Beheshti UniversityTehranIran
| | - Marzieh Dadizadeh
- Center of Remote Sensing and GIS Research, Faculty of Earth SciencesShahid Beheshti UniversityTehranIran
| | - Shahab Asadi Aghbolaghi
- Department of Education of Chaharmahal and Bakhtiari Province (Ministry of Education)ShahrekordIran
| | - Navid Zamani
- Department of Environmental Science, Faculty of Natural ResourceUniversity of KurdistanSanandajIran
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4
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Delheimer MS, Moriarty KM, Munro HL, Early DA, Hamm KA, Green RE. Structural complexity characterizes fine‐scale forest conditions used by Pacific martens. J Wildl Manage 2023. [DOI: 10.1002/jwmg.22388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Affiliation(s)
- Matthew S. Delheimer
- USDA Forest Service Pacific Southwest Research Station 2480 Carson Road Placerville CA 95667 USA
| | - Katie M. Moriarty
- National Council for Air and Stream Improvement, Inc. 2438 NW Professional Drive Corvallis OR 97330 USA
| | - Holly L. Munro
- National Council for Air and Stream Improvement, Inc. 180 E Green Street Athens GA 30602 USA
| | | | - Keith A. Hamm
- Green Diamond Resource Company PO Box 68 Korbel CA 95550 USA
| | - Rebecca E. Green
- USDA Forest Service Pacific Southwest Research Station 2081 E. Sierra Avenue Fresno CA 93710 USA
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Martin SA, Peterman WE, Lipps GJ, Gibbs HL. Inferring population connectivity in eastern massasauga rattlesnakes (Sistrurus catenatus) using landscape genetics. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2793. [PMID: 36482809 DOI: 10.1002/eap.2793] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 10/18/2022] [Accepted: 10/25/2022] [Indexed: 06/17/2023]
Abstract
Assessing the environmental factors that influence the ability of a threatened species to move through a landscape can be used to identify conservation actions that connect isolated populations. However, direct observations of species' movement are often limited, making the development of alternate approaches necessary. Here we use landscape genetic analyses to assess the impact of landscape features on the movement of individuals between local populations of a threatened snake, the eastern massasauga rattlesnake (Sistrurus catenatus). We linked connectivity data with habitat information from two landscapes of similar size: a large region of unfragmented habitat and a previously studied fragmented landscape consisting of isolated patches of habitat. We used this analysis to identify features of the landscape where modification or acquisition would enhance population connectivity in the fragmented region. We found evidence that current connectivity was impacted by both contemporary land-cover features, especially roads, and inherent landscape features such as elevation. Next, we derived estimates of expected movement ability using a recently developed pedigree-based approach and least-cost paths through the unfragmented landscape. We then used our pedigree and resistance map to estimate resistance polygons of the potential extent for S. catenatus movement in the fragmented landscape. These polygons identify possible sites for future corridors connecting currently isolated populations in this landscape by linking the impact of future habitat modification or land acquisition to dispersal ability in this species. Overall, our study shows how modeling landscape resistance across differently fragmented landscapes can identify habitat features that affect contemporary movement in threatened species in fragmented landscapes and how this information can be used to guide mitigation actions whose goal is to connect isolated populations.
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Affiliation(s)
- Scott A Martin
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| | - William E Peterman
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
- School of Environmental and Natural Resources, The Ohio State University, Columbus, Ohio, USA
| | - Gregory J Lipps
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
| | - H Lisle Gibbs
- Department of Evolution, Ecology, and Organismal Biology, The Ohio State University, Columbus, Ohio, USA
- Ohio Biodiversity Conservation Partnership, The Ohio State University, Columbus, Ohio, USA
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Wishingrad V, Thomson RC. Biogeographic inferences across spatial and evolutionary scales. Mol Ecol 2023; 32:2055-2070. [PMID: 36695049 DOI: 10.1111/mec.16861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 01/05/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023]
Abstract
The field of biogeography unites landscape genetics and phylogeography under a common conceptual framework. Landscape genetics traditionally focuses on recent-time, population-based, spatial genetics processes at small geographical scales, while phylogeography typically investigates deep past, lineage- and species-based processes at large geographical scales. Here, we evaluate the link between landscape genetics and phylogeographical methods using the western fence lizard (Sceloporus occidentalis) as a model species. First, we conducted replicated landscape genetics studies across several geographical scales to investigate how population genetics inferences change depending on the spatial extent of the study area. Then, we carried out a phylogeographical study of population structure at two evolutionary scales informed by inferences derived from landscape genetics results to identify concordance and conflict between these sets of methods. We found significant concordance in landscape genetics processes at all but the largest geographical scale. Phylogeographical results indicate major clades are restricted to distinct river drainages or distinct hydrological regions. At a more recent timescale, we find minor clades are restricted to single river canyons in the majority of cases, while the remainder of river canyons include samples from at most two clades. Overall, the broad-scale pattern implicating stream and river valleys as key features linking populations in the landscape genetics results, and high degree of clade specificity within major topographic subdivisions in the phylogeographical results, is consistent. As landscape genetics and phylogeography share many of the same objectives, synthesizing theory, models and methods between these fields will help bring about a better understanding of ecological and evolutionary processes structuring genetic variation across space and time.
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Affiliation(s)
- Van Wishingrad
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA.,Hawai'i, Institute of Marine Biology, Kāne'ohe, Hawai'i, USA
| | - Robert C Thomson
- School of Life Sciences, University of Hawai'i at Mānoa, Honolulu, Hawaii, USA
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Hsiao C, Ju YT, Chang CH, Chen SW, Tsai HW, Wang L, Lin WC, Hwang MH. Genetic status and conservation implications of endangered Formosan black bears. URSUS 2022. [DOI: 10.2192/ursus-d-21-00011.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Chen Hsiao
- Department of Animal Science and Technology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
| | - Yu-Ten Ju
- Department of Animal Science and Technology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
| | - Chun-Hao Chang
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Sec. 1, Hsech-Fu Road, Pingtung, 912301 Taiwan
| | - Sheng-Wei Chen
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Sec. 1, Hsech-Fu Road, Pingtung, 912301 Taiwan
| | - Hui-Wen Tsai
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Sec. 1, Hsech-Fu Road, Pingtung, 912301 Taiwan
| | - Ling Wang
- Department of Animal Science and Technology, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei, 10617 Taiwan
| | - Wan-Ching Lin
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Sec. 1, Hsech-Fu Road, Pingtung, 912301 Taiwan
| | - Mei-Hsiu Hwang
- Institute of Wildlife Conservation, College of Veterinary Medicine, National Pingtung University of Science and Technology, Sec. 1, Hsech-Fu Road, Pingtung, 912301 Taiwan
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Schmidt GM, Graves TA, Pederson JC, Carroll SL. Precision and bias of spatial capture-recapture estimates: A multi-site, multi-year Utah black bear case study. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2022; 32:e2618. [PMID: 35368131 PMCID: PMC9287071 DOI: 10.1002/eap.2618] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 01/13/2022] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Spatial capture-recapture (SCR) models are powerful analytical tools that have become the standard for estimating abundance and density of wild animal populations. When sampling populations to implement SCR, the number of unique individuals detected, total recaptures, and unique spatial relocations can be highly variable. These sample sizes influence the precision and accuracy of model parameter estimates. Testing the performance of SCR models with sparse empirical data sets typical of low-density, wide-ranging species can inform the threshold at which a more integrated modeling approach with additional data sources or additional years of monitoring may be required to achieve reliable, precise parameter estimates. Using a multi-site, multi-year Utah black bear (Ursus americanus) capture-recapture data set, we evaluated factors influencing the uncertainty of SCR structural parameter estimates, specifically density, detection, and the spatial scale parameter, sigma. We also provided some of the first SCR density estimates for Utah black bear populations, which ranged from 3.85 to 74.33 bears/100 km2 . Increasing total detections decreased the uncertainty of density estimates, whereas an increasing number of total recaptures and individuals with recaptures decreased the uncertainty of detection and sigma estimates, respectively. In most cases, multiple years of data were required for precise density estimates (<0.2 coefficient of variation [CV]). Across study areas there was an average decline in CV of 0.07 with the addition of another year of data. One sampled population with very high estimated bear density had an atypically low number of spatial recaptures relative to total recaptures, apparently inflating density estimates. A complementary simulation study used to assess estimate bias suggested that when <30% of recaptured individuals were spatially recaptured, density estimates were unreliable and ranged widely, in some cases to >3 times the simulated density. Additional research could evaluate these requirements for other density scenarios. Large numbers of individuals detected, numbers of spatial recaptures, and precision alone may not be sufficient indicators of parameter estimate reliability. We provide an evaluation of simple summary statistics of capture-recapture data sets that can provide an early signal of the need to alter sampling design or collect auxiliary data before model implementation to improve estimate precision and accuracy.
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Affiliation(s)
- Greta M. Schmidt
- Department of BiologySan Diego State UniversitySan DiegoCaliforniaUSA
| | - Tabitha A. Graves
- U.S. Geological Survey, Northern Rocky Mountain Science CenterWest GlacierMontanaUSA
| | | | - Sarah L. Carroll
- Graduate Degree Program in EcologyColorado State UniversityFort CollinsColoradoUSA
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Landscape genetics of an endangered salt marsh endemic: Identifying population continuity and barriers to dispersal. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01446-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractPreserving the genetic diversity of endangered species is fundamental to their conservation and requires an understanding of genetic structure. In turn, identification of landscape features that impede gene flow can facilitate management to mitigate such obstacles and help with identifying isolated populations. We conducted a landscape genetic study of the endangered salt marsh harvest mouse (Reithrodontomys raviventris), a species endemic to the coastal marshes of the San Francisco Estuary of California. We collected and genotyped > 500 samples from across the marshes of Suisun Bay which contain the largest remaining tracts of habitat for the species. Cluster analyses and a population tree identified three geographically discrete populations. Next, we conducted landscape genetic analyses at two scales (the entire study area and across the Northern Marshes) where we tested 65 univariate models of landscape features and used the best supported to test multivariable analyses. Our analysis of the entire study area indicated that open water and elevation (> 2 m) constrained gene flow. Analysis of the Northern Marshes, where low elevation marsh habitat is more continuous, indicated that geographic distance was the only significant predictor of genetic distance at this scale. The identification of a large, connected population across Northern Marshes achieves a number of recovery targets for this stronghold of the species. The identification of landscape features that act as barriers to dispersal enables the identification of isolated and vulnerable populations more broadly across the species range, thus aiding conservation prioritization.
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10
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Zimmerman SJ, Aldridge CL, Hooten MB, Oyler-McCance SJ. Scale-dependent influence of the sagebrush community on genetic connectivity of the sagebrush obligate Gunnison sage-grouse. Mol Ecol 2022; 31:3267-3285. [PMID: 35501946 PMCID: PMC9325045 DOI: 10.1111/mec.16470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/23/2022] [Accepted: 04/01/2022] [Indexed: 11/30/2022]
Abstract
Habitat fragmentation and degradation impacts an organism's ability to navigate the landscape, ultimately resulting in decreased gene flow and increased extinction risk. Understanding how landscape composition impacts gene flow (i.e., connectivity) and interacts with scale is essential to conservation decision‐making. We used a landscape genetics approach implementing a recently developed statistical model based on the generalized Wishart probability distribution to identify the primary landscape features affecting gene flow and estimate the degree to which each component influences connectivity for Gunnison sage‐grouse (Centrocercus minimus). We were interested in two spatial scales: among distinct populations rangewide and among leks (i.e., breeding grounds) within the largest population, Gunnison Basin. Populations and leks are nested within a landscape fragmented by rough terrain and anthropogenic features, although requisite sagebrush habitat is more contiguous within populations. Our best fit models for each scale confirm the importance of sagebrush habitat in connectivity, although the important sagebrush characteristics differ. For Gunnison Basin, taller shrubs and higher quality nesting habitat were the primary drivers of connectivity, while more sagebrush cover and less conifer cover facilitated connectivity rangewide. Our findings support previous assumptions that Gunnison sage‐grouse range contraction is largely the result of habitat loss and degradation. Importantly, we report direct estimates of resistance for landscape components that can be used to create resistance surfaces for prioritization of specific locations for conservation or management (i.e., habitat preservation, restoration, or development) or as we demonstrated, can be combined with simulation techniques to predict impacts to connectivity from potential management actions.
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Affiliation(s)
- Shawna J Zimmerman
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Cameron L Aldridge
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
| | - Mevin B Hooten
- Department of Statistics and Data Sciences, The University of Texas at Austin, Austin, Texas, USA
| | - Sara J Oyler-McCance
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, USA
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11
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Landscape genetic connectivity in European wildcat (Felis silvestris silvestris): a matter of food, shelters and demographic status of populations. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01443-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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12
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Larroque J, Wittische J, James PMA. Quantifying and predicting population connectivity of an outbreaking forest insect pest. LANDSCAPE ECOLOGY 2021; 37:763-778. [PMID: 35273428 PMCID: PMC8897358 DOI: 10.1007/s10980-021-01382-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Context Dispersal has a key role in the population dynamics of outbreaking species such as the spruce budworm (Choristoneura fumiferana) as it can synchronize the demography of distant populations and favor the transition from endemic to epidemic states. However, we know very little about how landscape structure influences dispersal in such systems while such knowledge is essential for better forecasting of spatially synchronous population dynamics and to guide management strategies. Objectives We aimed to characterize the spatial environmental determinants of spruce budworm dispersal to determine how these features affect outbreak spread in Quebec (Canada). We then apply our findings to predict expected future landscape connectivity and explore its potential consequences on future outbreaks. Methods We used a machine-learning landscape genetics approach on 447 larvae covering most of the outbreak area and genotyped at 3562 SNP loci to identify the main variables affecting connectivity. Results We found that the connectivity between outbreak populations was driven by the combination of precipitation and host cover. Our forecasting suggests that between the current and next outbreaks, connectivity may increase between Ontario and Quebec, and might decrease in the eastern part, which could have the effect of limiting outbreak spread from Ontario and Quebec to the eastern provinces. Conclusions Although we did not identify any discrete barriers, low connectivity areas might constrain dispersal in the current and future outbreaks and should in turn, be intensively monitored. However, continued sampling as the outbreak progresses is needed to confirm the temporal stability of the observed patterns. Supplementary Information The online version contains supplementary material available at 10.1007/s10980-021-01382-9.
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Affiliation(s)
- Jeremy Larroque
- Department of Wildlife Sciences, University of Göttingen, Buesgenweg 3, 37077 Göttingen, Germany
| | - Julian Wittische
- Department of Biological Sciences, Pavillon Marie-Victorin, Université de Montréal, 90 Vincent-d’Indy Avenue, Montreal, QC H2V 2S9 Canada
| | - Patrick M. A. James
- Institute of Forestry and Conservation, John H. Daniels Faculty of Architecture, Landscape, and Design, University of Toronto, 33 Willcocks Street, Toronto, ON M5S 3E8 Canada
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Atzeni L, Cushman SA, Wang J, Riordan P, Shi K, Bauman D. Evidence of spatial genetic structure in a snow leopard population from Gansu, China. Heredity (Edinb) 2021; 127:522-534. [PMID: 34743188 PMCID: PMC8626472 DOI: 10.1038/s41437-021-00483-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 11/09/2022] Open
Abstract
Understanding the spatial structure of genetic diversity provides insights into a populations' genetic status and enables assessment of its capacity to counteract the effects of genetic drift. Such knowledge is particularly scarce for the snow leopard, a conservation flagship species of Central Asia mountains. Focusing on a snow leopard population in the Qilian mountains of Gansu Province, China, we characterised the spatial genetic patterns by incorporating spatially explicit indices of diversity and multivariate analyses, based on different inertia levels of Principal Component Analysis (PCA). We compared two datasets differing in the number of loci and individuals. We found that genetic patterns were significantly spatially structured and were characterised by a broad geographical division coupled with a fine-scale cline of differentiation. Genetic admixture was detected in two adjoining core areas characterised by higher effective population size and allelic diversity, compared to peripheral localities. The power to detect significant spatial relationships depended primarily on the number of loci, and secondarily on the number of PCA axes. Spatial patterns and indices of diversity highlighted the cryptic structure of snow leopard genetic diversity, likely driven by its ability to disperse over large distances. In combination, the species' low allelic richness and large dispersal ability result in weak genetic differentiation related to major geographical features and isolation by distance. This study illustrates how cryptic genetic patterns can be investigated and analysed at a fine spatial scale, providing insights into the spatially variable isolation effects of both geographic distance and landscape resistance.
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Affiliation(s)
- Luciano Atzeni
- Wildlife Institute, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
| | - Samuel A Cushman
- US Forest Service, Rocky Mountain Research Station, Flagstaff, AZ, USA
| | - Jun Wang
- Wildlife Institute, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | - Philip Riordan
- Wildlife Institute, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China
- Marwell Wildlife, Winchester, UK
- Department of Biological Sciences, University of Southampton, Southampton, UK
| | - Kun Shi
- Wildlife Institute, School of Ecology and Nature Conservation, Beijing Forestry University, Beijing, China.
- Eco-Bridge Continental, Beijing, China.
| | - David Bauman
- Smithsonian Environmental Research Center, Edgewater, MD, USA
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
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Thom G, Gehara M, Smith BT, Miyaki CY, do Amaral FR. Microevolutionary dynamics show tropical valleys are deeper for montane birds of the Atlantic Forest. Nat Commun 2021; 12:6269. [PMID: 34725329 PMCID: PMC8560783 DOI: 10.1038/s41467-021-26537-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/08/2021] [Indexed: 11/18/2022] Open
Abstract
Tropical mountains hold more biodiversity than their temperate counterparts, and this disparity is often associated with the latitudinal climatic gradient. However, distinguishing the impact of latitude versus the background effects of species history and traits is challenging due to the evolutionary distance between tropical and temperate assemblages. Here, we test whether microevolutionary processes are linked to environmental variation across a sharp latitudinal transition in 21 montane birds of the southern Atlantic Forest in Brazil. We find that effective dispersal within populations in the tropical mountains is lower and genomic differentiation is better predicted by the current environmental complexity of the region than within the subtropical populations. The concordant response of multiple co-occurring populations is consistent with spatial climatic variability as a major process driving population differentiation. Our results provide evidence for how a narrow latitudinal gradient can shape microevolutionary processes and contribute to broader scale biodiversity patterns. There are many hypotheses for why the tropics are more biodiverse than higher latitudes. Phylogenomic analyses of 21 montane birds finds that tropical birds disperse less and have more genetically structured populations than their counterparts at higher latitudes, possibly due to a larger elevational climate gradient in the tropics
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Affiliation(s)
- Gregory Thom
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA. .,Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP, 05508-090, Brazil.
| | - Marcelo Gehara
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.,Department of Earth and Environmental Sciences, Rutgers University Newark, 195 University Ave, Newark, NJ, 07102, USA
| | - Brian Tilston Smith
- Department of Ornithology, American Museum of Natural History, Central Park West at 79th Street, New York, NY, 10024, USA
| | - Cristina Y Miyaki
- Departamento de Genética e Biologia Evolutiva, Universidade de São Paulo, Rua do Matão, 277, Cidade Universitária, São Paulo, SP, 05508-090, Brazil
| | - Fábio Raposo do Amaral
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo, Rua Prof. Artur Riedel, 275, Jardim Eldorado, Diadema, SP, CEP 09972-270, Brazil
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15
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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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16
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Bauder JM, Peterman WE, Spear SF, Jenkins CL, Whiteley AR, McGarigal K. Multiscale assessment of functional connectivity: Landscape genetics of eastern indigo snakes in an anthropogenically fragmented landscape in central Florida. Mol Ecol 2021; 30:3422-3438. [PMID: 33978288 DOI: 10.1111/mec.15979] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/04/2021] [Accepted: 05/05/2021] [Indexed: 01/08/2023]
Abstract
Landscape features can strongly influence gene flow and the strength and direction of these effects may vary across spatial scales. However, few studies have evaluated methodological approaches for selecting spatial scales in landscape genetics analyses, in part because of computational challenges associated with optimizing landscape resistance surfaces (LRS). We used the federally threatened eastern indigo snake (Drymarchon couperi) in central Florida as a case study with which to compare the importance of landscape features and their scales of effect in influencing gene flow. We used genetic algorithms (ResistanceGA) to empirically optimize LRS using categorical land cover surfaces, multiscale resource selection surfaces (RSS), and four combinations of landscape covariates measured at multiple spatial scales (multisurface multiscale LRS). We compared LRS where scale was selected using pseudo- and full optimization. Multisurface multiscale LRS received more empirical support than LRS optimized from categorical land cover surfaces or RSS. Multiscale LRS with scale selected using full optimization generally outperformed those with scale selected using pseudo-optimization. Multiscale LRS with large spatial scales (1200-1800 m) received the most empirical support. Our results highlight the importance of considering landscape features across multiple spatial scales in landscape genetic analyses, particularly broad scales relative to species movement potential. Different effects of scale on home range-level movements and dispersal could explain weak associations between habitat suitability and gene flow in other studies. Our results also demonstrate the importance of large tracts of undeveloped upland habitat with heterogenous vegetation communities and low urbanization for promoting indigo snake connectivity.
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Affiliation(s)
- Javan M Bauder
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA.,Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, IL, USA
| | - William E Peterman
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, USA
| | - Stephen F Spear
- The Orianne Society, Tiger, GA, USA.,Department of Fish and Wildlife Resources, University of Idaho, Moscow, ID, USA.,The Wilds, Cumberland, OH, USA.,Upper Midwest Environmental Sciences Center, U.S. Geological Survey, La Crosse, WI, USA
| | | | - Andrew R Whiteley
- Department of Ecosystems and Conservation Sciences and Wildlife Biology Program, University of Montana, Missoula, MT, USA
| | - Kevin McGarigal
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA, USA
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17
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Burgess SM, Garrick RC. The effect of sampling density and study area size on landscape genetics inferences for the Mississippi slimy salamander ( Plethodon mississippi). Ecol Evol 2021; 11:6289-6304. [PMID: 34141218 PMCID: PMC8207395 DOI: 10.1002/ece3.7481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 02/27/2021] [Accepted: 03/08/2021] [Indexed: 11/30/2022] Open
Abstract
In landscape genetics, it is largely unknown how choices regarding sampling density and study area size impact inferences upon which habitat features impede vs. facilitate gene flow. While it is recommended that sampling locations be spaced no further apart than the average individual's dispersal distance, for low-mobility species, this could lead to a challenging number of sampling locations, or an unrepresentative study area. We assessed the effects of sampling density and study area size on landscape genetic inferences for a dispersal-limited amphibian, Plethodon mississippi, via analysis of nested datasets. Microsatellite-based genetic distances among individuals were divided into three datasets representing sparse sampling across a large study area, dense sampling across a small study area, or sparse sampling across the same small study area. These datasets were a proxy for gene flow (i.e., the response variable) in maximum-likelihood population effects models that assessed the nature and strength of their relationship with each of five land-use classes (i.e., potential predictor variables). Comparisons of outcomes were based on the rank order of effect, sign of effect (i.e., gene flow resistance vs. facilitation), spatial scale of effect, and functional relationship with gene flow. The best-fit model for each dataset had the same sign of effect for hardwood forests, manmade structures, and pine forests, indicating the impacts of these land-use classes on dispersal and gene flow in P. mississippi are robust to sampling scheme. Contrasting sampling densities led to a different inferred functional relationship between agricultural areas and gene flow. Study area size appeared to influence the scale of effect of manmade structures and the sign of effect of pine forests. Our findings provided evidence for an influence of sampling density, study area size, and sampling effort upon inferences. Accordingly, we recommend iterative subsampling of empirical datasets and continued investigation into the sensitivities of landscape genetic analyses using simulations.
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18
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Chafin TK, Zbinden ZD, Douglas MR, Martin BT, Middaugh CR, Gray MC, Ballard JR, Douglas ME. Spatial population genetics in heavily managed species: Separating patterns of historical translocation from contemporary gene flow in white-tailed deer. Evol Appl 2021; 14:1673-1689. [PMID: 34178112 PMCID: PMC8210790 DOI: 10.1111/eva.13233] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 03/10/2021] [Indexed: 01/16/2023] Open
Abstract
Approximately 100 years ago, unregulated harvest nearly eliminated white-tailed deer (Odocoileus virginianus) from eastern North America, which subsequently served to catalyze wildlife management as a national priority. An extensive stock-replenishment effort soon followed, with deer broadly translocated among states as a means of re-establishment. However, an unintended consequence was that natural patterns of gene flow became obscured and pretranslocation signatures of population structure were replaced. We applied cutting-edge molecular and biogeographic tools to disentangle genetic signatures of historical management from those reflecting spatially heterogeneous dispersal by evaluating 35,099 single nucleotide polymorphisms (SNPs) derived via reduced-representation genomic sequencing from 1143 deer sampled statewide in Arkansas. We then employed Simpson's diversity index to summarize ancestry assignments and visualize spatial genetic transitions. Using sub-sampled transects across these transitions, we tested clinal patterns across loci against theoretical expectations of their response under scenarios of re-colonization and restricted dispersal. Two salient results emerged: (A) Genetic signatures from historic translocations are demonstrably apparent; and (B) Geographic filters (major rivers; urban centers; highways) now act as inflection points for the distribution of this contemporary ancestry. These results yielded a statewide assessment of contemporary population structure in deer as driven by historic translocations as well as ongoing processes. In addition, the analytical framework employed herein to effectively decipher extant/historic drivers of deer distribution in Arkansas is also applicable for other biodiversity elements with similarly complex demographic histories.
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Affiliation(s)
- Tyler K. Chafin
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
- Present address:
Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderCOUSA
| | - Zachery D. Zbinden
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Marlis R. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | - Bradley T. Martin
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
| | | | - M. Cory Gray
- Research DivisionArkansas Game and Fish CommissionLittle RockARUSA
| | | | - Michael E. Douglas
- Department of Biological SciencesUniversity of ArkansasFayettevilleARUSA
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19
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Ribeiro SE, de Almeida-Rocha JM, Weber MM, Kajin M, Lorini ML, Cerqueira R. Do anthropogenic matrix and life-history traits structure small mammal populations? A meta-analytical approach. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01352-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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20
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Dar SA, Singh SK, Wan HY, Kumar V, Cushman SA, Sathyakumar S. Projected climate change threatens Himalayan brown bear habitat more than human land use. Anim Conserv 2021. [DOI: 10.1111/acv.12671] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- S. A. Dar
- Wildlife Institute of India Dehradun India
| | | | - H. Y. Wan
- Department of Wildlife Humboldt State University Arcata CA USA
| | - V. Kumar
- Wildlife Institute of India Dehradun India
| | - S. A. Cushman
- USDA Forest Service Rocky Mountain Research Station Flagstaff AZ USA
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21
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Draheim HM, Moore JA, Winterstein SR, Scribner KT. Spatial genetic structure and landscape connectivity in black bears: Investigating the significance of using different land cover datasets and classifications in landscape genetics analyses. Ecol Evol 2021; 11:978-989. [PMID: 33520180 PMCID: PMC7820153 DOI: 10.1002/ece3.7111] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2019] [Revised: 11/03/2020] [Accepted: 11/06/2020] [Indexed: 11/13/2022] Open
Abstract
Landscape genetic analyses allow detection of fine-scale spatial genetic structure (SGS) and quantification of effects of landscape features on gene flow and connectivity. Typically, analyses require generation of resistance surfaces. These surfaces characteristically take the form of a grid with cells that are coded to represent the degree to which landscape or environmental features promote or inhibit animal movement. How accurately resistance surfaces predict association between the landscape and movement is determined in large part by (a) the landscape features used, (b) the resistance values assigned to features, and (c) how accurately resistance surfaces represent landscape permeability. Our objective was to evaluate the performance of resistance surfaces generated using two publicly available land cover datasets that varied in how accurately they represent the actual landscape. We genotyped 365 individuals from a large black bear population (Ursus americanus) in the Northern Lower Peninsula (NLP) of Michigan, USA at 12 microsatellite loci, and evaluated the relationship between gene flow and landscape features using two different land cover datasets. We investigated the relative importance of land cover classification and accuracy on landscape resistance model performance. We detected local spatial genetic structure in Michigan's NLP black bears and found roads and land cover were significantly correlated with genetic distance. We observed similarities in model performance when different land cover datasets were used despite 21% dissimilarity in classification between the two land cover datasets. However, we did find the performance of land cover models to predict genetic distance was dependent on the way the land cover was defined. Models in which land cover was finely defined (i.e., eight land cover classes) outperformed models where land cover was defined more coarsely (i.e., habitat/non-habitat or forest/non-forest). Our results show that landscape genetic researchers should carefully consider how land cover classification changes inference in landscape genetic studies.
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Affiliation(s)
- Hope M. Draheim
- Department of ZoologyMichigan State UniversityEast LansingMichiganUSA
| | | | - Scott R. Winterstein
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
| | - Kim T. Scribner
- Department of ZoologyMichigan State UniversityEast LansingMichiganUSA
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMichiganUSA
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22
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Hidden Markov Models reveal a clear human footprint on the movements of highly mobile African wild dogs. Sci Rep 2020; 10:17908. [PMID: 33087737 PMCID: PMC7578658 DOI: 10.1038/s41598-020-74329-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/29/2020] [Indexed: 02/04/2023] Open
Abstract
Large carnivores have experienced considerable range contraction, increasing the importance of movement across human-altered landscapes between small, isolated populations. African wild dogs (Lycaon pictus) are exceptionally wide-ranging, and recolonization is an important element of their persistence at broad scales. The competition-movement-connection hypothesis suggests that adaptations to move through areas that are unfavorable due to dominant competitors might promote the ability of subordinate competitors (like wild dogs) to move through areas that are unfavorable due to humans. Here, we used hidden Markov models to test how wild dog movements were affected by the Human Footprint Index in areas inside and outside of South Luangwa National Park. Movements were faster and more directed when outside the National Park, but slowed where the human footprint was stronger. Our results can be directly and quantitatively applied to connectivity planning, and we use them to identify ways to better understand differences between species in recent loss of connectivity.
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23
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Dupuis JR, Judge KA, Brunet BMT, Ohlmann Chan S, Sperling FAH. Does hunger lead to hybridization in a genus of sexually cannibalistic insects (Orthoptera: Prophalangopsidae)? Biol J Linn Soc Lond 2020. [DOI: 10.1093/biolinnean/blaa094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Allochronic isolation can be a strong mechanism for reproductive isolation and speciation. However, imperfect allochrony and the expression of phenological plasticity can erode temporal barriers to gene flow and result in hybridization between divergent lineages. Here, we combine behavioural ecology and genomics to investigate this scenario in two closely related species of grigs in the genus Cyphoderris. These species exhibit a unique mating system whereby females feed on the fleshy hind wings of the male during copulation, and copulation with conspecific males is more likely in food-restricted females than in well-fed females. In western Canada, Cyphoderris buckelli and Cyphoderris monstrosa are sympatric but largely allochronically separated, with C. buckelli breeding earlier. However, their breeding seasons can overlap, leading to potential for older C. buckelli females to mate with young C. monstrosa males to obtain resources via sexual cannibalism. We used behavioural assays to test whether female feeding status affects the propensity for interspecific mating between C. buckelli females and C. monstrosa males. We then tested for hybridization and gene exchange in wild populations of both species, using morphology, mitochondrial DNA and genome-wide nuclear markers. We found that interspecific courtship and mating can occur, but the relationship between food restriction and increased propensity for hybridization was not significant. Although we observed intraspecific population genetic structure in both species, we found no signatures of hybridization in the morphological or genetic datasets, which suggests that postmating reproductive barriers might be preventing successful hybridization in the wild.
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Affiliation(s)
- Julian R Dupuis
- Department of Entomology, University of Kentucky, Lexington, KY, USA
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Kevin A Judge
- Department of Biological Sciences, MacEwan University, Edmonton, Alberta, Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada
| | - Bryan M T Brunet
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Shawna Ohlmann Chan
- Department of Biological Sciences, MacEwan University, Edmonton, Alberta, Canada
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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24
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Atzeni L, Cushman SA, Bai D, Wang J, Chen P, Shi K, Riordan P. Meta-replication, sampling bias, and multi-scale model selection: A case study on snow leopard ( Panthera uncia) in western China. Ecol Evol 2020; 10:7686-7712. [PMID: 32760557 PMCID: PMC7391562 DOI: 10.1002/ece3.6492] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/04/2022] Open
Abstract
Replicated multiple scale species distribution models (SDMs) have become increasingly important to identify the correct variables determining species distribution and their influences on ecological responses. This study explores multi-scale habitat relationships of the snow leopard (Panthera uncia) in two study areas on the Qinghai-Tibetan Plateau of western China. Our primary objectives were to evaluate the degree to which snow leopard habitat relationships, expressed by predictors, scales of response, and magnitude of effects, were consistent across study areas or locally landcape-specific. We coupled univariate scale optimization and the maximum entropy algorithm to produce multivariate SDMs, inferring the relative suitability for the species by ensembling top performing models. We optimized the SDMs based on average omission rate across the top models and ensembles' overlap with a simulated reference model. Comparison of SDMs in the two study areas highlighted landscape-specific responses to limiting factors. These were dependent on the effects of the hydrological network, anthropogenic features, topographic complexity, and the heterogeneity of the landcover patch mosaic. Overall, even accounting for specific local differences, we found general landscape attributes associated with snow leopard ecological requirements, consisting of a positive association with uplands and ridges, aggregated low-contrast landscapes, and large extents of grassy and herbaceous vegetation. As a means to evaluate the performance of two bias correction methods, we explored their effects on three datasets showing a range of bias intensities. The performance of corrections depends on the bias intensity; however, density kernels offered a reliable correction strategy under all circumstances. This study reveals the multi-scale response of snow leopards to environmental attributes and confirms the role of meta-replicated study designs for the identification of spatially varying limiting factors. Furthermore, this study makes important contributions to the ongoing discussion about the best approaches for sampling bias correction.
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Affiliation(s)
- Luciano Atzeni
- Wildlife InstituteSchool of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | | | - Defeng Bai
- Wildlife InstituteSchool of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Jun Wang
- Wildlife InstituteSchool of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
- Faculty of Science and EngineeringManchester Metropolitan UniversityManchesterUK
| | - Pengju Chen
- Wildlife InstituteSchool of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
| | - Kun Shi
- Wildlife InstituteSchool of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
- Eco‐Bridge ContinentalBeijingChina
| | - Philip Riordan
- Wildlife InstituteSchool of Ecology and Nature ConservationBeijing Forestry UniversityBeijingChina
- Marwell WildlifeWinchesterUK
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25
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Marrec R, Abdel Moniem HE, Iravani M, Hricko B, Kariyeva J, Wagner HH. Conceptual framework and uncertainty analysis for large-scale, species-agnostic modelling of landscape connectivity across Alberta, Canada. Sci Rep 2020; 10:6798. [PMID: 32321948 PMCID: PMC7176682 DOI: 10.1038/s41598-020-63545-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/30/2020] [Indexed: 11/08/2022] Open
Abstract
Sustainable land-use planning should consider large-scale landscape connectivity. Commonly-used species-specific connectivity models are difficult to generalize for a wide range of taxa. In the context of multi-functional land-use planning, there is growing interest in species-agnostic approaches, modelling connectivity as a function of human landscape modification. We propose a conceptual framework, apply it to model connectivity as current density across Alberta, Canada, and assess map sensitivity to modelling decisions. We directly compared the uncertainty related to (1) the definition of the degree of human modification, (2) the decision whether water bodies are considered barriers to movement, and (3) the scaling function used to translate degree of human modification into resistance values. Connectivity maps were most sensitive to the consideration of water as barrier to movement, followed by the choice of scaling function, whereas maps were more robust to different conceptualizations of the degree of human modification. We observed higher concordance among cells with high (standardized) current density values than among cells with low values, which supports the identification of cells contributing to larger-scale connectivity based on a cut-off value. We conclude that every parameter in species-agnostic connectivity modelling requires attention, not only the definition of often-criticized expert-based degrees of human modification.
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Affiliation(s)
- Ronan Marrec
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
- EDYSAN (Ecologie et Dynamique des Systèmes Anthropisés) UMR 7058 CNRS-Université de Picardie Jules Verne, 33 rue Saint Leu, F-80039, Amiens, France.
| | - Hossam E Abdel Moniem
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Centre for Urban Environments, University of Toronto Mississauga, Mississauga, Ontario, Canada
- Department of Zoology, Faculty of Science, Suez Canal University, Ismailia, Egypt
| | - Majid Iravani
- Alberta Biodiversity Monitoring Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Branko Hricko
- Alberta Biodiversity Monitoring Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Jahan Kariyeva
- Alberta Biodiversity Monitoring Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Helene H Wagner
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
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26
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Proctor MF, Kasworm WF, Teisberg JE, Servheen C, Radandt TG, Lamb CT, Kendall KC, Mace RD, Paetkau D, Boyce MS. American black bear population fragmentation detected with pedigrees in the transborder Canada–United States region. URSUS 2020. [DOI: 10.2192/ursus-d-18-00003r2] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | - Wayne F. Kasworm
- U.S. Fish and Wildlife Service, 385 Fish Hatchery Road, Libby, MT 59923, USA
| | - Justin E. Teisberg
- U.S. Fish and Wildlife Service, 385 Fish Hatchery Road, Libby, MT 59923, USA
| | - Chris Servheen
- U.S. Fish and Wildlife Service, College of Forestry and Conservation, 309 University Hall, University of Montana, Missoula, MT 59812, USA
| | - Thomas G. Radandt
- U.S. Fish and Wildlife Service, 385 Fish Hatchery Road, Libby, MT 59923, USA
| | - Clayton T. Lamb
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Katherine C. Kendall
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Glacier National Park, West Glacier, MT 59936, USA
| | - Richard D. Mace
- Montana Fish, Wildlife and Parks, 490 N Meridian Road, Kalispel, MT 59417, USA
| | - David Paetkau
- Wildlife Genetics International, P.O. Box 274, Nelson, BC V1L 5P9, Canada
| | - Mark S. Boyce
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
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27
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Maigret TA, Cox JJ, Weisrock DW. A spatial genomic approach identifies time lags and historical barriers to gene flow in a rapidly fragmenting Appalachian landscape. Mol Ecol 2020; 29:673-685. [PMID: 31981245 DOI: 10.1111/mec.15362] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 01/03/2020] [Accepted: 01/13/2020] [Indexed: 12/15/2022]
Abstract
The resolution offered by genomic data sets coupled with recently developed spatially informed analyses are allowing researchers to quantify population structure at increasingly fine temporal and spatial scales. However, both empirical research and conservation measures have been limited by questions regarding the impacts of data set size, data quality thresholds and the timescale at which barriers to gene flow become detectable. Here, we used restriction site associated DNA sequencing to generate a 2,140 single nucleotide polymorphism (SNP) data set for the copperhead snake (Agkistrodon contortrix) and address the population genomic impacts of recent and widespread landscape modification across an ~1,000-km2 region of eastern Kentucky, USA. Nonspatial population-based assignment and clustering methods supported little to no population structure. However, using individual-based spatial autocorrelation approaches we found evidence for genetic structuring which closely follows the path of a historically important highway which experienced high traffic volumes from c. 1920 to 1970 before losing most traffic to a newly constructed alternative route. We found no similar spatial genomic signatures associated with more recently constructed highways or surface mining activity, although a time lag effect may be responsible for the lack of any emergent spatial genetic patterns. Subsampling of our SNP data set suggested that similar results could be obtained with as few as 250 SNPs, and a range of thresholds for missing data exhibited limited impacts on the spatial patterns we detected. While we were not able to estimate relative effects of land uses or precise time lags, our findings highlight the importance of temporal factors in landscape genetics approaches, and suggest the potential advantages of genomic data sets and fine-scale, spatially informed approaches for quantifying subtle genetic patterns in temporally complex landscapes.
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Affiliation(s)
- Thomas A Maigret
- Department of Biology, University of Kentucky, Lexington, KY, USA.,Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY, USA
| | - John J Cox
- Department of Forestry and Natural Resources, University of Kentucky, Lexington, KY, USA
| | - David W Weisrock
- Department of Biology, University of Kentucky, Lexington, KY, USA
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28
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Multiscale landscape genetics of American marten at their southern range periphery. Heredity (Edinb) 2020; 124:550-561. [PMID: 31992842 PMCID: PMC7080830 DOI: 10.1038/s41437-020-0295-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 11/10/2019] [Accepted: 11/11/2019] [Indexed: 11/08/2022] Open
Abstract
American marten (Martes americana) are a conservation priority in many forested regions of North America. Populations are fragmented at the southern edge of their distribution due to suboptimal habitat conditions. Facilitating gene flow may improve population resilience through genetic and demographic rescue. We used a multiscale approach to estimate the relationship between genetic connectivity and landscape characteristics among individuals at three scales in the northeastern United States: regional, subregional, and local. We integrated multiple modeling techniques and identified top models based on consensus. Top models were used to parameterize resistance surfaces at each scale, and circuit theory was used to identify potential movement corridors. Regional gene flow was affected by forest cover, elevation, developed land cover, and slope. At subregional and local scales, the effects were site specific and included subsets of temperature, elevation, developed land cover, and slope. Developed land cover significantly affected gene flow at each scale. At finer scales, lack of variance in forest cover may have limited the ability to detect a relationship with gene flow. The effect of slope on gene flow was positive or negative, depending on the site examined. Occupancy probability was a relatively poor predictor, and we caution its use as a proxy for landscape resistance. Our results underscore the importance of replication and multiscale approaches in landscape genetics. Climate warming and landscape conversion may reduce the genetic connectivity of marten populations in the northeastern United States, and represent the primary challenges to marten conservation at the southern periphery of their range.
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29
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Differing, multiscale landscape effects on genetic diversity and differentiation in eastern chipmunks. Heredity (Edinb) 2020; 124:457-468. [PMID: 31919481 DOI: 10.1038/s41437-020-0293-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 11/04/2019] [Accepted: 11/08/2019] [Indexed: 11/08/2022] Open
Abstract
Understanding how habitat loss and fragmentation impact genetic variation is a major goal in landscape genetics, but to date, most studies have focused solely on the correlation between intervening matrix and genetic differentiation at a single spatial scale. Several caveats exist in these study designs, among them is the inability to include measures of genetic diversity in addition to differentiation. Both genetic metrics help predict population persistence, but are expected to function at differing spatial scales, which requires a multiscale investigation. In this study, we sampled two distinct spatial scales in 31 independent landscapes along a gradient of landscape context (i.e., forest amount, configuration, and types of intervening matrix) to investigate how landscape heterogeneity influences genetic diversity and differentiation in the forest-associated eastern chipmunk (Tamias striatus). Overall, quality of intervening matrix was correlated with genetic differentiation at multiple spatial scales, whereas only configuration was associated with regional scale genetic diversity. Habitat amount, in contrast, did not influence genetic differentiation or diversity at either spatial scale. Based on our findings, landscape effects on genetic variation appears to differ based on spatial scale, the type of genetic response variable, and random variation among landscapes, making extrapolation of results from single scale, unreplicated studies difficult. We encourage landscape geneticists to utilize multiscale, replicated landscapes with both genetic diversity, and differentiation to gain a more comprehensive understanding of how habitat loss and fragmentation influence genetic variation.
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30
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Kozakiewicz CP, Burridge CP, Funk WC, Salerno PE, Trumbo DR, Gagne RB, Boydston EE, Fisher RN, Lyren LM, Jennings MK, Riley SPD, Serieys LEK, VandeWoude S, Crooks KR, Carver S. Urbanization reduces genetic connectivity in bobcats (Lynx rufus) at both intra- and interpopulation spatial scales. Mol Ecol 2019; 28:5068-5085. [PMID: 31613411 DOI: 10.1111/mec.15274] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 10/07/2019] [Accepted: 10/14/2019] [Indexed: 01/02/2023]
Abstract
Urbanization is a major factor driving habitat fragmentation and connectivity loss in wildlife. However, the impacts of urbanization on connectivity can vary among species and even populations due to differences in local landscape characteristics, and our ability to detect these relationships may depend on the spatial scale at which they are measured. Bobcats (Lynx rufus) are relatively sensitive to urbanization and the status of bobcat populations is an important indicator of connectivity in urban coastal southern California. We genotyped 271 bobcats at 13,520 SNP loci to conduct a replicated landscape resistance analysis in five genetically distinct populations. We tested urban and natural factors potentially influencing individual connectivity in each population separately, as well as study-wide. Overall, landscape genomic effects were most frequently detected at the study-wide spatial scale, with urban land cover (measured as impervious surface) having negative effects and topographic roughness having positive effects on gene flow. The negative effect of urban land cover on connectivity was also evident when populations were analyzed separately despite varying substantially in spatial area and the proportion of urban development, confirming a pervasive impact of urbanization largely independent of spatial scale. The effect of urban development was strongest in one population where stream habitat had been lost to development, suggesting that riparian corridors may help mitigate reduced connectivity in urbanizing areas. Our results demonstrate the importance of replicating landscape genetic analyses across populations and considering how landscape genetic effects may vary with spatial scale and local landscape structure.
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Affiliation(s)
| | | | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | | | - Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | - Roderick B Gagne
- Wildlife Genomics and Disease Ecology Laboratory, Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA.,Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Erin E Boydston
- Western Ecological Research Center, U.S. Geological Survey, Thousand Oaks, CA, USA
| | - Robert N Fisher
- Western Ecological Research Center, U.S. Geological Survey, San Diego, CA, USA
| | - Lisa M Lyren
- Western Ecological Research Center, U.S. Geological Survey, Thousand Oaks, CA, USA
| | - Megan K Jennings
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Seth P D Riley
- National Park Service, Santa Monica Mountains National Recreation Area, Thousand Oaks, CA, USA
| | - Laurel E K Serieys
- Department of Environmental Studies, University of California Santa Cruz, Santa Cruz, CA, USA.,Institute for Communities and Wildlife in Africa, Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Kevin R Crooks
- Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA.,Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, USA
| | - Scott Carver
- School of Natural Sciences, University of Tasmania, Hobart, Tasmania, Australia
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31
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Trumbo DR, Salerno PE, Logan KA, Alldredge MW, Gagne RB, Kozakiewicz CP, Kraberger S, Fountain-Jones NM, Craft ME, Carver S, Ernest HB, Crooks KR, VandeWoude S, Funk WC. Urbanization impacts apex predator gene flow but not genetic diversity across an urban-rural divide. Mol Ecol 2019; 28:4926-4940. [PMID: 31587398 DOI: 10.1111/mec.15261] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 08/11/2019] [Accepted: 09/20/2019] [Indexed: 02/06/2023]
Abstract
Apex predators are important indicators of intact natural ecosystems. They are also sensitive to urbanization because they require broad home ranges and extensive contiguous habitat to support their prey base. Pumas (Puma concolor) can persist near human developed areas, but urbanization may be detrimental to their movement ecology, population structure, and genetic diversity. To investigate potential effects of urbanization in population connectivity of pumas, we performed a landscape genomics study of 130 pumas on the rural Western Slope and more urbanized Front Range of Colorado, USA. Over 12,000 single nucleotide polymorphisms (SNPs) were genotyped using double-digest, restriction site-associated DNA sequencing (ddRADseq). We investigated patterns of gene flow and genetic diversity, and tested for correlations between key landscape variables and genetic distance to assess the effects of urbanization and other landscape factors on gene flow. Levels of genetic diversity were similar for the Western Slope and Front Range, but effective population sizes were smaller, genetic distances were higher, and there was more admixture in the more urbanized Front Range. Forest cover was strongly positively associated with puma gene flow on the Western Slope, while impervious surfaces restricted gene flow and more open, natural habitats enhanced gene flow on the Front Range. Landscape genomic analyses revealed differences in puma movement and gene flow patterns in rural versus urban settings. Our results highlight the utility of dense, genome-scale markers to document subtle impacts of urbanization on a wide-ranging carnivore living near a large urban center.
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Affiliation(s)
- Daryl R Trumbo
- Department of Biology, Colorado State University, Fort Collins, CO, USA
| | | | | | | | - Roderick B Gagne
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | | | - Simona Kraberger
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | | | - Meggan E Craft
- Department of Veterinary Population Medicine, University of Minnesota, Saint Paul, MN, USA
| | - Scott Carver
- Department of Biological Sciences, University of Tasmania, Hobart, TAS., Australia
| | - Holly B Ernest
- Department of Veterinary Sciences, University of Wyoming, Laramie, WY, USA
| | - Kevin R Crooks
- Department of Fish, Wildlife, and Conservation Biology, Colorado State University, Fort Collins, CO, USA
| | - Sue VandeWoude
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, CO, USA.,Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
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32
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A Wandering Black Bear (Ursus americanus, Pallas 1780) in the Sierra Gorda Biosphere Reserve, Queretaro. AMERICAN MIDLAND NATURALIST 2019. [DOI: 10.1674/0003-0031-182.2.252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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33
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Homola JJ, Loftin CS, Kinnison MT. Landscape genetics reveals unique and shared effects of urbanization for two sympatric pool-breeding amphibians. Ecol Evol 2019; 9:11799-11823. [PMID: 31695889 PMCID: PMC6822048 DOI: 10.1002/ece3.5685] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/26/2019] [Accepted: 08/30/2019] [Indexed: 01/05/2023] Open
Abstract
Metapopulation-structured species can be negatively affected when landscape fragmentation impairs connectivity. We investigated the effects of urbanization on genetic diversity and gene flow for two sympatric amphibian species, spotted salamanders (Ambystoma maculatum) and wood frogs (Lithobates sylvaticus), across a large (>35,000 km2) landscape in Maine, USA, containing numerous natural and anthropogenic gradients. Isolation-by-distance (IBD) patterns differed between the species. Spotted salamanders showed a linear and relatively high variance relationship between genetic and geographic distances (r = .057, p < .001), whereas wood frogs exhibited a strongly nonlinear and lower variance relationship (r = 0.429, p < .001). Scale dependence analysis of IBD found gene flow has its most predictable influence (strongest IBD correlations) at distances up to 9 km for spotted salamanders and up to 6 km for wood frogs. Estimated effective migration surfaces revealed contrasting patterns of high and low genetic diversity and gene flow between the two species. Population isolation, quantified as the mean IBD residuals for each population, was associated with local urbanization and less genetic diversity in both species. The influence of geographic proximity and urbanization on population connectivity was further supported by distance-based redundancy analysis and multiple matrix regression with randomization. Resistance surface modeling found interpopulation connectivity to be influenced by developed land cover, light roads, interstates, and topography for both species, plus secondary roads and rivers for wood frogs. Our results highlight the influence of anthropogenic landscape features within the context of natural features and broad spatial genetic patterns, in turn supporting the premise that while urbanization significantly restricts interpopulation connectivity for wood frogs and spotted salamanders, specific landscape elements have unique effects on these two sympatric species.
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Affiliation(s)
| | - Cynthia S. Loftin
- Maine Cooperative Fish and Wildlife Research UnitU.S. Geological SurveyOronoMEUSA
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34
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Fedorca A, Russo IRM, Ionescu O, Ionescu G, Popa M, Fedorca M, Curtu AL, Sofletea N, Tabor GM, Bruford MW. Inferring fine-scale spatial structure of the brown bear (Ursus arctos) population in the Carpathians prior to infrastructure development. Sci Rep 2019; 9:9494. [PMID: 31263171 PMCID: PMC6602936 DOI: 10.1038/s41598-019-45999-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/20/2019] [Indexed: 12/05/2022] Open
Abstract
Landscape genetics is increasingly being used in landscape planning for biodiversity conservation by assessing habitat connectivity and identifying landscape barriers, using intraspecific genetic data and quantification of landscape heterogeneity to statistically test the link between genetic variation and landscape variability. In this study we used genetic data to understand how landscape features and environmental factors influence demographic connectedness in Europe’s largest brown bear population and to assist in mitigating planned infrastructure development in Romania. Model-based clustering inferred one large and continuous bear population across the Carpathians suggesting that suitable bear habitat has not become sufficiently fragmented to restrict movement of individuals. However, at a finer scale, large rivers, often located alongside large roads with heavy traffic, were found to restrict gene flow significantly, while eastern facing slopes promoted genetic exchange. Since the proposed highway infrastructure development threatens to fragment regions of the Carpathians where brown bears occur, we develop a decision support tool based on models that assess the landscape configuration needed for brown bear conservation using wildlife corridor parameters. Critical brown bear corridors were identified through spatial mapping and connectivity models, which may be negatively influenced by infrastructure development and which therefore require mitigation. We recommend that current and proposed infrastructure developments incorporate these findings into their design and where possible avoid construction measures that may further fragment Romania’s brown bear population or include mitigation measures where alternative routes are not feasible.
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Affiliation(s)
- Ancuta Fedorca
- National Institute for Research and Development in Forestry Marin Dracea, Brasov, 500040, Closca Street 13, Romania. .,Faculty of Silviculture and Forest Engineering, Transilvania University of Brasov, Brasov, 500123, Beethoven Lane 1, Romania.
| | - Isa-Rita M Russo
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
| | - Ovidiu Ionescu
- National Institute for Research and Development in Forestry Marin Dracea, Brasov, 500040, Closca Street 13, Romania.,Faculty of Silviculture and Forest Engineering, Transilvania University of Brasov, Brasov, 500123, Beethoven Lane 1, Romania
| | - Georgeta Ionescu
- National Institute for Research and Development in Forestry Marin Dracea, Brasov, 500040, Closca Street 13, Romania.,Faculty of Silviculture and Forest Engineering, Transilvania University of Brasov, Brasov, 500123, Beethoven Lane 1, Romania
| | - Marius Popa
- National Institute for Research and Development in Forestry Marin Dracea, Brasov, 500040, Closca Street 13, Romania.,Faculty of Silviculture and Forest Engineering, Transilvania University of Brasov, Brasov, 500123, Beethoven Lane 1, Romania
| | - Mihai Fedorca
- National Institute for Research and Development in Forestry Marin Dracea, Brasov, 500040, Closca Street 13, Romania.,Faculty of Silviculture and Forest Engineering, Transilvania University of Brasov, Brasov, 500123, Beethoven Lane 1, Romania
| | - Alexandru Lucian Curtu
- Faculty of Silviculture and Forest Engineering, Transilvania University of Brasov, Brasov, 500123, Beethoven Lane 1, Romania
| | - Neculae Sofletea
- Faculty of Silviculture and Forest Engineering, Transilvania University of Brasov, Brasov, 500123, Beethoven Lane 1, Romania
| | - Gary M Tabor
- Center for Large Landscape Conservation, 303 W Mendenhall St #4, Bozeman, MT, 59715, USA
| | - Michael W Bruford
- Cardiff School of Biosciences, Sir Martin Evans Building, Cardiff University, Museum Avenue, Cardiff, CF10 3AX, United Kingdom
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Seaborn T, Hauser SS, Konrade L, Waits LP, Goldberg CS. Landscape genetic inferences vary with sampling scenario for a pond-breeding amphibian. Ecol Evol 2019; 9:5063-5078. [PMID: 31110662 PMCID: PMC6509389 DOI: 10.1002/ece3.5023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 11/25/2022] Open
Abstract
A critical decision in landscape genetic studies is whether to use individuals or populations as the sampling unit. This decision affects the time and cost of sampling and may affect ecological inference. We analyzed 334 Columbia spotted frogs at 8 microsatellite loci across 40 sites in northern Idaho to determine how inferences from landscape genetic analyses would vary with sampling design. At all sites, we compared a proportion available sampling scheme (PASS), in which all samples were used, to resampled datasets of 2-11 individuals. Additionally, we compared a population sampling scheme (PSS) to an individual sampling scheme (ISS) at 18 sites with sufficient sample size. We applied an information theoretic approach with both restricted maximum likelihood and maximum likelihood estimation to evaluate competing landscape resistance hypotheses. We found that PSS supported low-density forest when restricted maximum likelihood was used, but a combination model of most variables when maximum likelihood was used. We also saw variations when AIC was used compared to BIC. ISS supported this model as well as additional models when testing hypotheses of land cover types that create the greatest resistance to gene flow for Columbia spotted frogs. Increased sampling density and study extent, seen by comparing PSS to PASS, showed a change in model support. As number of individuals increased, model support converged at 7-9 individuals for ISS to PSS. ISS may be useful to increase study extent and sampling density, but may lack power to provide strong support for the correct model with microsatellite datasets. Our results highlight the importance of additional research on sampling design effects on landscape genetics inference.
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Affiliation(s)
- Travis Seaborn
- School of Biological SciencesWashington State UniversityPullmanWashington
| | | | - Lauren Konrade
- Department of Biological SciencesWichita State UniversityWichitaKansas
| | - Lisette P. Waits
- Department of Fish and Wildlife SciencesUniversity of IdahoMoscowIdaho
| | - Caren S. Goldberg
- School of the EnvironmentWashington State UniversityPullmanWashington
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36
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Dupuis JR, Cullingham CI, Nielsen SE, Sperling FAH. Environmental effects on gene flow in a species complex of vagile, hilltopping butterflies. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Julian R Dupuis
- Department of Plant and Environmental Protection Services, University of Hawai’i at Mānoa, Honolulu, HI, USA
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Scott E Nielsen
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta Canada
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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37
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Emel SL, Olson DH, Knowles LL, Storfer A. Comparative landscape genetics of two endemic torrent salamander species, Rhyacotriton kezeri and R. variegatus: implications for forest management and species conservation. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01172-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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38
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Ohnishi N, Osawa T, Yamamoto T, Uno R. Landscape heterogeneity in landform and land use provides functional resistance to gene flow in continuous Asian black bear populations. Ecol Evol 2019; 9:4958-4968. [PMID: 31031957 PMCID: PMC6476753 DOI: 10.1002/ece3.5102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 03/03/2019] [Accepted: 03/05/2019] [Indexed: 11/29/2022] Open
Abstract
CONTEXT Genetic diversity is one of the most important facets of biological diversity, and changes in the spatial pattern of habitats, often modified by human activity, are believed to have affected the genetic diversity of resident natural populations. OBJECTIVES We undertook a landscape genetic analysis in order to determine which landscape features influence gene flow within Asian black bear populations and to identify the underlying processes. METHODS In our evaluation of gene flow, we estimated four parameters of resistance with regard to landscape elevation: the mean, the difference between the highest and lowest, the standard deviation, and the coefficient of variation of elevation among individuals. We then examined the resistance effect of different land use types. RESULTS With the exception of mean elevation, we found that all parameters showed a significant relationship with genetic distance, indicating that unevenness in elevation provides functional resistance to gene flow. Although we found no evidence of landscape barriers (isolation-by-barrier), there was an indication of landscape resistance (isolation-by-resistance). Urban area and farmland are suggested to be the strong factors contributing to the resistance to gene flow, even though isolation-by-distance was also detected. When we examined gene flow for pairs of males and pairs of females, both isolation-by-distance and isolation-by-resistance were stronger in order of female pairs, male pairs, all individual pairs. CONCLUSIONS We conclude that landscape resistance was detectable with a high contrast in landscape heterogeneity and they are more influential on females than males. OPEN PRACTICES This article has been awarded Open Data badge. All materials and data are publicly accessible via the Open Science Framework at https://doi.org/10.5061/dryad.gn0qf16. Learn more about the Open Practices badges from the Center for Open Science: https://osf.io/tvyxz/wiki.
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Affiliation(s)
- Naoki Ohnishi
- Tohoku Research CenterForestry and Forest Products Research InstituteMoriokaJapan
| | - Takeshi Osawa
- Graduate School of Urban Environmental SciencesTokyo Metropolitan UniversityHachioujiTokyoJapan
| | - Toshiaki Yamamoto
- Department of Veterinary Nursing and TechnologyNippon Veterinary and Life Science UniversityMusashinoTokyoJapan
| | - Reina Uno
- Institute for Advanced BiosciencesKeio UniversityTsuruokaYamagataJapan
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39
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Reddy PA, Puyravaud J, Cushman SA, Segu H. Spatial variation in the response of tiger gene flow to landscape features and limiting factors. Anim Conserv 2019. [DOI: 10.1111/acv.12488] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- P. A. Reddy
- CSIR‐Centre for Cellular and Molecular Biology Hyderabad India
- Academy of Scientific and Innovative Research (AcSIR) Ghaziabad India
| | - J.‐P. Puyravaud
- Sigur Nature Trust, Mavinhalla Masinagudi P.O. Nilgiris India
| | - S. A. Cushman
- US Forest Service Rocky Mountain Research Station Flagstaff AZ USA
| | - H. Segu
- CSIR‐Centre for Cellular and Molecular Biology Hyderabad India
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40
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DiLeo MF, Husby A, Saastamoinen M. Landscape permeability and individual variation in a dispersal-linked gene jointly determine genetic structure in the Glanville fritillary butterfly. Evol Lett 2018; 2:544-556. [PMID: 30564438 PMCID: PMC6292703 DOI: 10.1002/evl3.90] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 10/22/2018] [Accepted: 10/29/2018] [Indexed: 12/14/2022] Open
Abstract
There is now clear evidence that species across a broad range of taxa harbor extensive heritable variation in dispersal. While studies suggest that this variation can facilitate demographic outcomes such as range expansion and invasions, few have considered the consequences of intraspecific variation in dispersal for the maintenance and distribution of genetic variation across fragmented landscapes. Here, we examine how landscape characteristics and individual variation in dispersal combine to predict genetic structure using genomic and spatial data from the Glanville fritillary butterfly. We used linear and latent factor mixed models to identify the landscape features that best predict spatial sorting of alleles in the dispersal-related gene phosphoglucose isomerase (Pgi). We next used structural equation modeling to test if variation in Pgi mediated gene flow as measured by Fst at putatively neutral loci. In a year when the population was recovering following a large decline, individuals with a genotype associated with greater dispersal ability were found at significantly higher frequencies in populations isolated by water and forest, and these populations showed lower levels of genetic differentiation at neutral loci. These relationships disappeared in the next year when metapopulation density was high, suggesting that the effects of individual variation are context dependent. Together our results highlight that (1) more complex aspects of landscape structure beyond just the configuration of habitat can be important for maintaining spatial variation in dispersal traits and (2) that individual variation in dispersal plays a key role in maintaining genetic variation across fragmented landscapes.
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Affiliation(s)
- Michelle F. DiLeo
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiPO Box 6500014Finland
| | - Arild Husby
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiPO Box 6500014Finland
- Department of Evolutionary Biology, EBCUppsala UniversityNorbyvägen 18D75236UppsalaSweden
| | - Marjo Saastamoinen
- Organismal and Evolutionary Biology Research ProgrammeUniversity of HelsinkiPO Box 6500014Finland
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41
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Ashrafzadeh MR, Khosravi R, Ahmadi M, Kaboli M. Landscape heterogeneity and ecological niche isolation shape the distribution of spatial genetic variation in Iranian brown bears, Ursus arctos (Carnivora: Ursidae). Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.08.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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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43
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Macdonald EA, Cushman SA, Landguth EL, Hearn AJ, Malhi Y, Macdonald DW. Simulating impacts of rapid forest loss on population size, connectivity and genetic diversity of Sunda clouded leopards (Neofelis diardi) in Borneo. PLoS One 2018; 13:e0196974. [PMID: 30208031 PMCID: PMC6135353 DOI: 10.1371/journal.pone.0196974] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/18/2018] [Indexed: 11/18/2022] Open
Abstract
Habitat loss is the greatest threat to biodiversity in Borneo, and to anticipate and combat its effects it is important to predict the pattern of loss and its consequences. Borneo is a region of extremely high biodiversity from which forest is being lost faster than in any other. The little-known Sunda clouded leopard (Neofelis diardi) is the top predator in Borneo and is likely to depend critically on habitat connectivity that is currently being rapidly lost to deforestation. We modeled the effects of landscape fragmentation on population size, genetic diversity and population connectivity for the Sunda clouded leopard across the entirety of Borneo. We modelled the impacts of land use change between the years 2000, 2010 and projected forwards to 2020. We found substantial reductions across all metrics between 2000 and 2010: the proportion of landscape connected by dispersal fell by approximately 12.5% and the largest patch size declined by around 15.1%, leading to a predicted 11.4% decline in clouded leopard numbers. We also predict that these trends will accelerate greatly towards 2020, with the percentage of the landscape being connected by dispersal falling by about 57.8%, the largest patch size falling by around 62.8% and the predicted clouded leopard population falling by 62.5% between 2010 and 2020. We predicted that these large declines in clouded leopard population size and connectivity will also substantially reduce the genetic diversity of the remaining clouded leopard population.
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Affiliation(s)
- Ewan A. Macdonald
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
- Wildlife Conservation Research Unit, Zoology Department, University of Oxford, The Recanati-Kaplan Centre, Tubney, Abingdon, United Kingdom
| | - Samuel A. Cushman
- Rocky Mountain Research Station, United States Forest Service, Flagstaff, Arizona, United States of America
| | - Erin L. Landguth
- Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - Andrew J. Hearn
- Wildlife Conservation Research Unit, Zoology Department, University of Oxford, The Recanati-Kaplan Centre, Tubney, Abingdon, United Kingdom
| | - Yadvinder Malhi
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, United Kingdom
| | - David W. Macdonald
- Wildlife Conservation Research Unit, Zoology Department, University of Oxford, The Recanati-Kaplan Centre, Tubney, Abingdon, United Kingdom
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44
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Draheim HM, Moore JA, Fortin M, Scribner KT. Beyond the snapshot: Landscape genetic analysis of time series data reveal responses of American black bears to landscape change. Evol Appl 2018; 11:1219-1230. [PMID: 30151035 PMCID: PMC6100183 DOI: 10.1111/eva.12617] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 02/08/2018] [Indexed: 01/18/2023] Open
Abstract
Landscape genetic studies typically focus on the evolutionary processes that give rise to spatial patterns that are quantified at a single point in time. Although landscape change is widely recognized as a strong driver of microevolutionary processes, few landscape genetic studies have directly evaluated the change in spatial genetic structure (SGS) over time with concurrent changes in landscape pattern. We introduce a novel approach to analyze landscape genetic data through time. We demonstrate this approach using genotyped samples (n = 569) from a large black bear (Ursus americanus) population in Michigan (USA) that were harvested during 3 years (2002, 2006, and 2010). We identified areas that were consistently occupied over this 9-year period and quantified temporal variation in SGS. Then, we evaluated alternative hypotheses about effects of changes in landscape features (e.g., deforestation or crop conversion) on fine-scale SGS among years using spatial autoregressive modeling and model selection. Relative measures of landscape change such as magnitude of landscape change (i.e., number of patches changing from suitable to unsuitable states or vice versa), and during later periods, measures of fragmentation (i.e., patch aggregation and cohesion) were associated with change in SGS. Our results stress the importance of conducting time series studies for the conservation and management of wildlife inhabiting rapidly changing landscapes.
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Affiliation(s)
- Hope M. Draheim
- Department of ZoologyMichigan State UniversityEast LansingMIUSA
| | | | - Marie‐Josée Fortin
- Department of Ecology & Evolutionary BiologyUniversity of TorontoTorontoONCanada
| | - Kim T. Scribner
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMIUSA
- Department of Integrative BiologyMichigan State UniversityEast LansingMIUSA
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45
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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46
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Robertson JM, Murphy MA, Pearl CA, Adams MJ, Páez-Vacas MI, Haig SM, Pilliod DS, Storfer A, Funk WC. Regional variation in drivers of connectivity for two frog species (Rana pretiosa and R. luteiventris) from the U.S. Pacific Northwest. Mol Ecol 2018; 27:3242-3256. [PMID: 30010212 DOI: 10.1111/mec.14798] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 06/29/2018] [Accepted: 07/05/2018] [Indexed: 01/17/2023]
Abstract
Comparative landscape genetics has uncovered high levels of variability in which landscape factors affect connectivity among species and regions. However, the relative importance of species traits versus environmental variation for predicting landscape patterns of connectivity is unresolved. We provide evidence from a landscape genetics study of two sister taxa of frogs, the Oregon spotted frog (Rana pretiosa) and the Columbia spotted frog (Rana luteiventris) in Oregon and Idaho, USA. Rana pretiosa is relatively more dependent on moisture for dispersal than R. luteiventris, so if species traits influence connectivity, we predicted that connectivity among R. pretiosa populations would be more positively associated with moisture than R. luteiventris. However, if environmental differences are important drivers of gene flow, we predicted that connectivity would be more positively related to moisture in arid regions. We tested these predictions using eight microsatellite loci and gravity models in two R. pretiosa regions and four R. luteiventris regions (n = 1,168 frogs). In R. pretiosa, but not R. luteiventris, connectivity was positively related to mean annual precipitation, supporting our first prediction. In contrast, connectivity was not more positively related to moisture in more arid regions. Various temperature metrics were important predictors for both species and in all regions, but the directionality of their effects varied. Therefore, the pattern of variation in drivers of connectivity was consistent with predictions based on species traits rather than on environmental variation.
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Affiliation(s)
| | - Melanie A Murphy
- Department of Ecosystem Science and Management, Program in Ecology, University of Wyoming, Laramie, WY, USA
| | - Christopher A Pearl
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Corvallis, OR, USA
| | - Michael J Adams
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Corvallis, OR, USA
| | - Mónica I Páez-Vacas
- Centro de Investigación de la Biodiversidad y Cambio Climático, Universidad Tecnológica Indoamérica, Quito, Ecuador
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
| | - Susan M Haig
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Corvallis, OR, USA
| | - David S Pilliod
- U.S. Geological Survey, Forest and Rangeland Ecosystem Science Center, Boise, ID, USA
| | - Andrew Storfer
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - W Chris Funk
- Department of Biology, Graduate Degree Program in Ecology, Colorado State University, Fort Collins, CO, USA
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47
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Berkman LK, Nielsen CK, Roy CL, Heist EJ. A landscape genetic analysis of swamp rabbits (Sylvilagus aquaticus) suggests forest canopy cover enhances gene flow in an agricultural matrix. CAN J ZOOL 2018. [DOI: 10.1139/cjz-2017-0116] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Habitat loss and fragmentation pose a continued and immediate threat to wildlife and create a persistent need for ecological information at the landscape scale to guide conservation efforts. Landscape features influence population connectivity for many species and genetic analyses can be employed to determine which of these features are most important. Because population connectivity through dispersal is important to the persistence of swamp rabbits (Sylvilagus aquaticus (Bachman, 1837)) at the northern edge of their range, we used a landscape genetic approach to relate gene flow to landscape features that may impact dispersal success. We tested resistance values for attributes of land cover, watercourse corridors, canopy cover, and roads and used causal modeling and redundancy analysis to relate these representations of landscapes to genetic distance for swamp rabbits in southern Illinois, USA. Models that included canopy cover had the strongest correlations with genetic distance and were supported by our methods whereas other models were not. We concluded that high tree canopy cover enhances gene flow and landscape connectivity for swamp rabbits in southern Illinois. Our study provides important empirical evidence that landscape variables may impact the habitat connectivity of swamp rabbits. Preserving dispersal routes for swamp rabbits should focus on improving canopy cover, in both bottomland and upland, to connect suitable habitat.
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Affiliation(s)
- Leah K. Berkman
- Cooperative Wildlife Research Laboratory, Department of Zoology, Southern Illinois University, Carbondale, IL 62901-6504, USA
| | - Clayton K. Nielsen
- Cooperative Wildlife Research Laboratory, Department of Forestry, Southern Illinois University, Carbondale, IL 62901-6504, USA
| | - Charlotte L. Roy
- Forest Wildlife Populations and Research Group, Minnesota Department of Natural Resources, Grand Rapids, MN 55744, USA
| | - Edward J. Heist
- Department of Zoology, Southern Illinois University, Carbondale, IL 62901-6501, USA
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48
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Balbi M, Ernoult A, Poli P, Madec L, Guiller A, Martin MC, Nabucet J, Beaujouan V, Petit EJ. Functional connectivity in replicated urban landscapes in the land snail (Cornu aspersum). Mol Ecol 2018; 27:1357-1370. [PMID: 29412498 DOI: 10.1111/mec.14521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/16/2018] [Accepted: 01/29/2018] [Indexed: 12/11/2022]
Abstract
Urban areas are highly fragmented and thereby exert strong constraints on individual dispersal. Despite this, some species manage to persist in urban areas, such as the garden snail, Cornu aspersum, which is common in cityscapes despite its low mobility. Using landscape genetic approaches, we combined study area replication and multiscale analysis to determine how landscape composition, configuration and connectivity influence snail dispersal across urban areas. At the overall landscape scale, areas with a high percentage of roads decreased genetic differentiation between populations. At the population scale, genetic differentiation was positively linked with building surface, the proportion of borders where wooded patches and roads appeared side by side and the proportion of borders combining wooded patches and other impervious areas. Analyses based on pairwise genetic distances validated the isolation-by-distance and isolation-by-resistance models for this land snail, with an equal fit to least-cost paths and circuit-theory-based models. Each of the 12 landscapes analysed separately yielded specific relations to environmental features, whereas analyses integrating all replicates highlighted general common effects. Our results suggest that urban transport infrastructures facilitate passive snail dispersal. At a local scale, corresponding to active dispersal, unfavourable habitats (wooded and impervious areas) isolate populations. This work upholds the use of replicated landscapes to increase the generalizability of landscape genetics results and shows how multiscale analyses provide insight into scale-dependent processes.
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Affiliation(s)
- Manon Balbi
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Aude Ernoult
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Pedro Poli
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Luc Madec
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Annie Guiller
- Edysan FRE 3498, CNRS, Université de Picardie Jules Vernes, Amiens, France
| | - Marie-Claire Martin
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Jean Nabucet
- UMR LETG, CNRS, Université de Rennes 2, Rennes Cedex, France
| | | | - Eric J Petit
- ESE, Ecology and Ecosystem Health, INRA, Rennes, France
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49
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Haran JM, Rossi JP, Pajares J, Bonifacio L, Naves P, Roques A, Roux G. Multi-scale and multi-site resampling of a study area in spatial genetics: implications for flying insect species. PeerJ 2017; 5:e4135. [PMID: 29259842 PMCID: PMC5733902 DOI: 10.7717/peerj.4135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 11/14/2017] [Indexed: 11/25/2022] Open
Abstract
The use of multiple sampling areas in landscape genetic analysis has been recognized as a useful way of generalizing the patterns of environmental effects on organism gene flow. It reduces the variability in inference which can be substantially affected by the scale of the study area and its geographic location. However, empirical landscape genetic studies rarely consider multiple sampling areas due to the sampling effort required. In this study, we explored the effects of environmental features on the gene flow of a flying long-horned beetle (Monochamus galloprovincialis) using a landscape genetics approach. To account for the unknown scale of gene flow and the multiple local confounding effects of evolutionary history and landscape changes on inference, we developed a way of resampling study areas on multiple scales and in multiple locations (sliding windows) in a single large-scale sampling design. Landscape analyses were conducted in 3*104 study areas ranging in scale from 220 to 1,000 km and spread over 132 locations on the Iberian Peninsula. The resampling approach made it possible to identify the features affecting the gene flow of this species but also showed high variability in inference among the scales and the locations tested, independent of the variation in environmental features. This method provides an opportunity to explore the effects of environmental features on organism gene flow on the whole and reach conclusions about general landscape effects on their dispersal, while limiting the sampling effort to a reasonable level.
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Affiliation(s)
- Julien M. Haran
- UR633 Zoologie Forestière, INRA, Orléans, France
- CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Univ. Montpellier, Montpellier, France CIRAD, CBGP, Montpellier, France
| | - Jean-Pierre Rossi
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, INRA, Montpellier, France
| | - Juan Pajares
- Sustainable Forest Management Res Inst, Universidad de Valladolid, Palencia, Spain
| | - Luis Bonifacio
- Instituto Nacional de Investigacao Agraria e Veterinaria, INIAV, Oeiras, Portugal
| | - Pedro Naves
- Instituto Nacional de Investigacao Agraria e Veterinaria, INIAV, Oeiras, Portugal
| | - Alain Roques
- UR633 Zoologie Forestière, INRA, Orléans, France
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50
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Zero VH, Barocas A, Jochimsen DM, Pelletier A, Giroux-Bougard X, Trumbo DR, Castillo JA, Evans Mack D, Linnell MA, Pigg RM, Hoisington-Lopez J, Spear SF, Murphy MA, Waits LP. Complementary Network-Based Approaches for Exploring Genetic Structure and Functional Connectivity in Two Vulnerable, Endemic Ground Squirrels. Front Genet 2017; 8:81. [PMID: 28659969 PMCID: PMC5469978 DOI: 10.3389/fgene.2017.00081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 05/29/2017] [Indexed: 11/18/2022] Open
Abstract
The persistence of small populations is influenced by genetic structure and functional connectivity. We used two network-based approaches to understand the persistence of the northern Idaho ground squirrel (Urocitellus brunneus) and the southern Idaho ground squirrel (U. endemicus), two congeners of conservation concern. These graph theoretic approaches are conventionally applied to social or transportation networks, but here are used to study population persistence and connectivity. Population graph analyses revealed that local extinction rapidly reduced connectivity for the southern species, while connectivity for the northern species could be maintained following local extinction. Results from gravity models complemented those of population graph analyses, and indicated that potential vegetation productivity and topography drove connectivity in the northern species. For the southern species, development (roads) and small-scale topography reduced connectivity, while greater potential vegetation productivity increased connectivity. Taken together, the results of the two network-based methods (population graph analyses and gravity models) suggest the need for increased conservation action for the southern species, and that management efforts have been effective at maintaining habitat quality throughout the current range of the northern species. To prevent further declines, we encourage the continuation of management efforts for the northern species, whereas conservation of the southern species requires active management and additional measures to curtail habitat fragmentation. Our combination of population graph analyses and gravity models can inform conservation strategies of other species exhibiting patchy distributions.
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Affiliation(s)
- Victoria H. Zero
- Haub School of Environment and Natural Resources, University of WyomingLaramie, WY, United States
| | - Adi Barocas
- Department of Zoology and Physiology, University of WyomingLaramie, WY, United States
- Program in Ecology, University of WyomingLaramie, WY, United States
| | - Denim M. Jochimsen
- Department of Biological Sciences, University of IdahoMoscow, ID, United States
| | - Agnès Pelletier
- Department of Environmental Studies and Sciences, University of WinnipegWinnipeg, MB, Canada
| | | | - Daryl R. Trumbo
- School of Biological Sciences, Washington State UniversityPullman, WA, United States
| | - Jessica A. Castillo
- Department of Fisheries and Wildlife, Oregon State UniversityCorvallis, OR, United States
| | - Diane Evans Mack
- Idaho Department of Fish and Game, McCall SubregionMcCall, ID, United States
| | - Mark A. Linnell
- Department of Fisheries and Wildlife, Oregon State UniversityCorvallis, OR, United States
| | - Rachel M. Pigg
- Division of Biology, Kansas State UniversityManhattan, KS, United States
| | - Jessica Hoisington-Lopez
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of MedicineSt. Louis, MO, United States
| | | | - Melanie A. Murphy
- Program in Ecology, University of WyomingLaramie, WY, United States
- Department of Ecosystem Science and Management, University of WyomingLaramie, WY, United States
| | - Lisette P. Waits
- Department of Fish and Wildlife Sciences, University of IdahoMoscow, ID, United States
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