1
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Savary P, Foltête JC, Moal H, Vuidel G, Garnier S. Inferring landscape resistance to gene flow when genetic drift is spatially heterogeneous. Mol Ecol Resour 2023; 23:1574-1588. [PMID: 37332161 DOI: 10.1111/1755-0998.13821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 05/12/2023] [Accepted: 05/24/2023] [Indexed: 06/20/2023]
Abstract
In connectivity models, land cover types are assigned cost values characterizing their resistance to species movements. Landscape genetic methods infer these values from the relationship between genetic differentiation and cost distances. The spatial heterogeneity of population sizes, and consequently genetic drift, is rarely included in this inference although it influences genetic differentiation. Similarly, migration rates and population spatial distributions potentially influence this inference. Here, we assessed the reliability of cost value inference under several migration rates, population spatial patterns and degrees of population size heterogeneity. Additionally, we assessed whether considering intra-population variables, here using gravity models, improved the inference when drift is spatially heterogeneous. We simulated several gene flow intensities between populations with varying local sizes and spatial distributions. We then fit gravity models of genetic distances as a function of (i) the 'true' cost distances driving simulations or alternative cost distances, and (ii) intra-population variables (population sizes, patch areas). We determined the conditions making the identification of the 'true' costs possible and assessed the contribution of intra-population variables to this objective. Overall, the inference ranked cost scenarios reliably in terms of similarity with the 'true' scenario (cost distance Mantel correlations), but this 'true' scenario rarely provided the best model goodness of fit. Ranking inaccuracies and failures to identify the 'true' scenario were more pronounced when migration was very restricted (<4 dispersal events/generation), population sizes were most heterogeneous and some populations were spatially aggregated. In these situations, considering intra-population variables helps identify cost scenarios reliably, thereby improving cost value inference from genetic data.
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Affiliation(s)
- Paul Savary
- ARP-Astrance, Paris, France
- UMR 6049 Thé MA, Université de Franche-Comté, CNRS, Besançon Cedex, France
- UMR 6282 Biogéosciences, Université Bourgogne Franche-Comté, CNRS, Dijon, France
| | | | | | - Gilles Vuidel
- UMR 6049 Thé MA, Université de Franche-Comté, CNRS, Besançon Cedex, France
| | - Stéphane Garnier
- UMR 6282 Biogéosciences, Université Bourgogne Franche-Comté, CNRS, Dijon, France
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2
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Vanhove M, Launey S. Estimating resistance surfaces using gradient forest and allelic frequencies. Mol Ecol Resour 2023. [PMID: 36847356 DOI: 10.1111/1755-0998.13778] [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: 05/24/2022] [Revised: 02/06/2023] [Accepted: 02/22/2023] [Indexed: 03/01/2023]
Abstract
Understanding landscape connectivity has become a global priority for mitigating the impact of landscape fragmentation on biodiversity. Connectivity methods that use link-based methods traditionally rely on relating pairwise genetic distance between individuals or demes to their landscape distance (e.g., geographic distance, cost distance). In this study, we present an alternative to conventional statistical approaches to refine cost surfaces by adapting the gradient forest approach to produce a resistance surface. Used in community ecology, gradient forest is an extension of random forest, and has been implemented in genomic studies to model species genetic offset under future climatic scenarios. By design, this adapted method, resGF, has the ability to handle multiple environmental predicators and is not subjected to traditional assumptions of linear models such as independence, normality and linearity. Using genetic simulations, resistance Gradient Forest (resGF) performance was compared to other published methods (maximum likelihood population effects model, random forest-based least-cost transect analysis and species distribution model). In univariate scenarios, resGF was able to distinguish the true surface contributing to genetic diversity among competing surfaces better than the compared methods. In multivariate scenarios, the gradient forest approach performed similarly to the other random forest-based approach using least-cost transect analysis but outperformed MLPE-based methods. Additionally, two worked examples are provided using two previously published data sets. This machine learning algorithm has the potential to improve our understanding of landscape connectivity and inform long-term biodiversity conservation strategies.
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Affiliation(s)
- Mathieu Vanhove
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
| | - Sophie Launey
- DECOD (Ecosystem Dynamics and Sustainability), INRAE, Institut Agro, IFREMER, Rennes, France
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3
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Salmona J, Dresen A, Ranaivoson AE, Manzi S, Le Pors B, Hong-Wa C, Razanatsoa J, Andriaholinirina NV, Rasoloharijaona S, Vavitsara ME, Besnard G. How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a microendemic Malagasy tree. Mol Ecol 2023; 32:299-315. [PMID: 36320175 PMCID: PMC10100191 DOI: 10.1111/mec.16759] [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: 11/20/2021] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022]
Abstract
Understanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human-driven deforestation is intense throughout Madagascar, exceptions in areas such as the Loky-Manambato region (north) raise questions regarding the causes and age of forest fragmentation. The Loky-Manambato region also harbours a rich and endemic flora, whose evolutionary origin remains poorly understood. We assessed the genetic diversity of an endangered microendemic Malagasy olive species (Noronhia spinifolia Hong-Wa) to better understand the vegetation dynamics in the Loky-Manambato region and its influence on past evolutionary processes. We characterized 72 individuals sampled across eight forests through nuclear and mitochondrial restriction-associated DNA sequencing data and chloroplast microsatellites. Combined population and landscape genetics analyses indicate that N. spinifolia diversity is largely explained by the current forest cover, highlighting a long-standing habitat mosaic in the region. This sustains a major and long-term role of riparian corridors in maintaining connectivity across these antique mosaic habitats, calling for the study of organismal interactions that promote gene flow.
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Affiliation(s)
- Jordi Salmona
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | - Axel Dresen
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | - Anicet E Ranaivoson
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France.,Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Sophie Manzi
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | | | - Cynthia Hong-Wa
- Claude E. Phillips Herbarium, Delaware State University, Dover, Delaware, USA
| | - Jacqueline Razanatsoa
- Herbier, Département Flore, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
| | | | | | | | - Guillaume Besnard
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
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4
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Maier PA, Vandergast AG, Ostoja SM, Aguilar A, Bohonak AJ. Landscape genetics of a sub-alpine toad: climate change predicted to induce upward range shifts via asymmetrical migration corridors. Heredity (Edinb) 2022; 129:257-272. [PMID: 36076071 PMCID: PMC9613655 DOI: 10.1038/s41437-022-00561-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 08/24/2022] [Accepted: 08/25/2022] [Indexed: 11/08/2022] Open
Abstract
Climate change is expected to have a major hydrological impact on the core breeding habitat and migration corridors of many amphibians in the twenty-first century. The Yosemite toad (Anaxyrus canorus) is a species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. Despite living entirely on federal lands, it has recently faced severe extirpations, yet our understanding of climatic influences on population connectivity is limited. In this study, we used a previously published double-digest RADseq dataset along with numerous remotely sensed habitat features in a landscape genetics framework to answer two primary questions in Yosemite National Park: (1) Which fine-scale climate, topographic, soil, and vegetation features most facilitate meadow connectivity? (2) How is climate change predicted to influence both the magnitude and net asymmetry of genetic migration? We developed an approach for simultaneously modeling multiple toad migration paths, akin to circuit theory, except raw environmental features can be separately considered. Our workflow identified the most likely migration corridors between meadows and used the unique cubist machine learning approach to fit and forecast environmental models of connectivity. We identified the permuted modeling importance of numerous snowpack-related features, such as runoff and groundwater recharge. Our results highlight the importance of considering phylogeographic structure, and asymmetrical migration in landscape genetics. We predict an upward elevational shift for this already high-elevation species, as measured by the net vector of anticipated genetic movement, and a north-eastward shift in species distribution via the network of genetic migration corridors across the park.
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Affiliation(s)
- Paul A Maier
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA.
- FamilyTreeDNA, Gene by Gene, 1445 N Loop W, Houston, TX, 77008, USA.
| | - Amy G Vandergast
- U.S. Geological Survey, Western Ecological Research Center, San Diego Field Station, San Diego, CA, 92101, USA
| | - Steven M Ostoja
- USDA California Climate Hub, Agricultural Research Service, John Muir Institute of the Environment, University of California, Davis, 1 Shields Ave., Davis, CA, 95616, USA
| | - Andres Aguilar
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Dr., Los Angeles, CA, 90032, USA
| | - Andrew J Bohonak
- Department of Biology, San Diego State University, 5500 Campanile Dr., San Diego, CA, 92182, USA
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5
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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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6
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Dondina O, Meriggi A, Bani L, Orioli V. Decoupling residents and dispersers from detection data improve habitat selection modelling: the case study of the wolf in a natural corridor. ETHOL ECOL EVOL 2022. [DOI: 10.1080/03949370.2021.1988724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Olivia Dondina
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, Milano 20126, Italy
| | - Alberto Meriggi
- Department of Earth and Environmental Sciences, University of Pavia, Via Ferrata 1, Pavia 27100, Italy
| | - Luciano Bani
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, Milano 20126, Italy
| | - Valerio Orioli
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 1, Milano 20126, Italy
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7
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Velo-Antón G, Lourenço A, Galán P, Nicieza A, Tarroso P. Landscape resistance constrains hybridization across contact zones in a reproductively and morphologically polymorphic salamander. Sci Rep 2021; 11:9259. [PMID: 33927228 PMCID: PMC8085075 DOI: 10.1038/s41598-021-88349-7] [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: 02/05/2021] [Accepted: 04/07/2021] [Indexed: 02/02/2023] Open
Abstract
Explicitly accounting for phenotypic differentiation together with environmental heterogeneity is crucial to understand the evolutionary dynamics in hybrid zones. Species showing intra-specific variation in phenotypic traits that meet across environmentally heterogeneous regions constitute excellent natural settings to study the role of phenotypic differentiation and environmental factors in shaping the spatial extent and patterns of admixture in hybrid zones. We studied three environmentally distinct contact zones where morphologically and reproductively divergent subspecies of Salamandra salamandra co-occur: the pueriparous S. s. bernardezi that is mostly parapatric to its three larviparous subspecies neighbours. We used a landscape genetics framework to: (i) characterise the spatial location and extent of each contact zone; (ii) assess patterns of introgression and hybridization between subspecies pairs; and (iii) examine the role of environmental heterogeneity in the evolutionary dynamics of hybrid zones. We found high levels of introgression between parity modes, and between distinct phenotypes, thus demonstrating the evolution to pueriparity alone or morphological differentiation do not lead to reproductive isolation between these highly divergent S. salamandra morphotypes. However, we detected substantial variation in patterns of hybridization across contact zones, being lower in the contact zone located on a topographically complex area. We highlight the importance of accounting for spatial environmental heterogeneity when studying evolutionary dynamics of hybrid zones.
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Affiliation(s)
- Guillermo Velo-Antón
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.6312.60000 0001 2097 6738Universidade de Vigo, Grupo de Ecoloxía Animal, Departamento de Ecoloxía e Bioloxía Animal, Torre Cacti (Lab 97), 36310 Vigo, Spain
| | - André Lourenço
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal ,grid.5808.50000 0001 1503 7226Departamento de Biologia da Faculdade de Ciências, Universidade do Porto. Rua Campo Alegre, 4169-007 Porto, Portugal
| | - Pedro Galán
- grid.8073.c0000 0001 2176 8535Grupo de Investigación en Bioloxía Evolutiva (GIBE), Departamento de Bioloxía, Facultade de Ciencias, Universidade da Coruña, Campus da Zapateira, s/n, 15071 A Coruña, Spain
| | - Alfredo Nicieza
- grid.10863.3c0000 0001 2164 6351Departamento de Biologıa de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain ,grid.10863.3c0000 0001 2164 6351Unidad Mixta de Investigacion en Biodiversidad (UMIB), CSIC-Universidad de Oviedo-Principado de Asturias, Mieres, Spain
| | - Pedro Tarroso
- grid.5808.50000 0001 1503 7226CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto, Instituto de Ciências Agrárias de Vairão. R. Padre Armando Quintas, 4485-661 Vairão, Portugal
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8
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Savary P, Foltête JC, Moal H, Vuidel G, Garnier S. Analysing landscape effects on dispersal networks and gene flow with genetic graphs. Mol Ecol Resour 2021; 21:1167-1185. [PMID: 33460526 DOI: 10.1111/1755-0998.13333] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 12/16/2022]
Abstract
Graph-theoretic approaches have relevant applications in landscape genetic analyses. When species form populations in discrete habitat patches, genetic graphs can be used (a) to identify direct dispersal paths followed by propagules or (b) to quantify landscape effects on multi-generational gene flow. However, the influence of their construction parameters remains to be explored. Using a simulation approach, we constructed genetic graphs using several pruning methods (geographical distance thresholds, topological constraints, statistical inference) and genetic distances to weight graph links (FST , DPS , Euclidean genetic distances). We then compared the capacity of these different graphs to (a) identify the precise topology of the dispersal network and (b) to infer landscape resistance to gene flow from the relationship between cost-distances and genetic distances. Although not always clear-cut, our results showed that methods based on geographical distance thresholds seem to better identify dispersal networks in most cases. More interestingly, our study demonstrates that a sub-selection of pairwise distances through graph pruning (thereby reducing the number of data points) can counter-intuitively lead to improved inferences of landscape effects on dispersal. Finally, we showed that genetic distances such as the DPS or Euclidean genetic distances should be preferred over the FST for landscape effect inference as they respond faster to landscape changes.
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Affiliation(s)
- Paul Savary
- ARP-Astrance, 9 Avenue Percier, Paris, 75008, France.,ThéMA, UMR 6049 CNRS, Université Bourgogne-Franche-Comté, 32 Rue Mégevand, Besançon Cedex, 25030, France.,Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, 6 Boulevard Gabriel, Dijon, 21000, France
| | - Jean-Christophe Foltête
- ThéMA, UMR 6049 CNRS, Université Bourgogne-Franche-Comté, 32 Rue Mégevand, Besançon Cedex, 25030, France
| | - Hervé Moal
- ARP-Astrance, 9 Avenue Percier, Paris, 75008, France
| | - Gilles Vuidel
- ThéMA, UMR 6049 CNRS, Université Bourgogne-Franche-Comté, 32 Rue Mégevand, Besançon Cedex, 25030, France
| | - Stéphane Garnier
- Biogéosciences, UMR 6282 CNRS, Université Bourgogne-Franche-Comté, 6 Boulevard Gabriel, Dijon, 21000, France
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9
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Winiarski KJ, Peterman WE, McGarigal K. Evaluation of the R package ‘
resistancega
’: A promising approach towards the accurate optimization of landscape resistance surfaces. Mol Ecol Resour 2020; 20:1583-1596. [DOI: 10.1111/1755-0998.13217] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 06/01/2020] [Accepted: 06/15/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Kristopher Jonathan Winiarski
- Department of Environmental Conservation University of Massachusetts Amherst MA USA
- Northeast Climate Adaptation Science Center University of Massachusetts Amherst MA USA
| | - William E. Peterman
- School of Environment and Natural Resources Ohio State University Columbus OH USA
| | - Kevin McGarigal
- Department of Environmental Conservation University of Massachusetts Amherst MA USA
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10
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Hague MTJ, Stokes AN, Feldman CR, Brodie ED, Brodie ED. The geographic mosaic of arms race coevolution is closely matched to prey population structure. Evol Lett 2020; 4:317-332. [PMID: 32774881 PMCID: PMC7403720 DOI: 10.1002/evl3.184] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/11/2020] [Accepted: 05/22/2020] [Indexed: 01/09/2023] Open
Abstract
Reciprocal adaptation is the hallmark of arms race coevolution. Local coadaptation between natural enemies should generate a geographic mosaic pattern where both species have roughly matched abilities across their shared range. However, mosaic variation in ecologically relevant traits can also arise from processes unrelated to reciprocal selection, such as population structure or local environmental conditions. We tested whether these alternative processes can account for trait variation in the geographic mosaic of arms race coevolution between resistant garter snakes (Thamnophis sirtalis) and toxic newts (Taricha granulosa). We found that predator resistance and prey toxin levels are functionally matched in co-occurring populations, suggesting that mosaic variation in the armaments of both species results from the local pressures of reciprocal selection. By the same token, phenotypic and genetic variation in snake resistance deviates from neutral expectations of population genetic differentiation, showing a clear signature of adaptation to local toxin levels in newts. Contrastingly, newt toxin levels are best predicted by genetic differentiation among newt populations, and to a lesser extent, by the local environment and snake resistance. Exaggerated armaments suggest that coevolution occurs in certain hotspots, but prey population structure seems to be of particular influence on local phenotypic variation in both species throughout the geographic mosaic. Our results imply that processes other than reciprocal selection, like historical biogeography and environmental pressures, represent an important source of variation in the geographic mosaic of coevolution. Such a pattern supports the role of "trait remixing" in the geographic mosaic theory, the process by which non-adaptive forces dictate spatial variation in the interactions among species.
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Affiliation(s)
- Michael T J Hague
- Division of Biological Sciences University of Montana Missoula Montana 59812.,Department of Biology University of Virginia Charlottesville Virginia 22904
| | - Amber N Stokes
- Department of Biology California State University Bakersfield California 93311
| | - Chris R Feldman
- Department of Biology University of Nevada Reno Nevada 89557
| | - Edmund D Brodie
- Department of Biology Utah State University Logan Utah 84322
| | - Edmund D Brodie
- Department of Biology University of Virginia Charlottesville Virginia 22904
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11
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Alexander NB, Statham MJ, Sacks BN, Bean WT. Generalist dispersal and gene flow of an endangered keystone specialist (Dipodomys ingens). J Mammal 2019. [DOI: 10.1093/jmammal/gyz118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Movement ecology and dispersal capabilities inherently drive genetic structure across landscapes. Through understanding dispersal and gene flow of giant kangaroo rats (Dipodomys ingens), conservation efforts can be focused, and we can further understand how genetic structure persists in this highly endemic small mammal. Here, we genetically identify parent–offspring and sibship relationships among 239 giant kangaroo rats using 15 microsatellites in the northern part of the species range and describe the individual genetic-spatial variation using a Moran eigenvector map (MEM). We further employ two landscape genetic analyses (isolation by resistance [IBR] and least cost paths [LCPs]) and two individual-based genetic metrics (Dps and a codominant marker distance from GenAlEx) to determine landscape factors (precipitation, slope, vegetation community, and roads) that influence gene flow. We found 19 pairs of related individuals, of which 18 were less than 250 m apart, but one sibling pair was 5.52 km apart, suggesting greater dispersal capabilities than previously noted. We found hierarchal spatial genetic structure using a MEM, with 3–4 genetically similar regions and two genetically similar subregions. Finally, we found low correlative strength between landscape features and gene flow. IBR consistently outperformed LCPs, and there was evidence that regions with 250–350 mm of precipitation and slope ≤ 5° promoted connectivity. We recommend that managers focus on habitat protection rather than corridor maintenance, with the caveat that anthropogenic factors were minimally considered in this study.
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Affiliation(s)
- Nathan B Alexander
- Department of Natural Resources and Environmental Sciences, University of Illinois, Urbana, IL, USA
- Department of Wildlife, Humboldt State University, Arcata, CA, USA
| | - Mark J Statham
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Benjamin N Sacks
- Mammalian Ecology and Conservation Unit, Veterinary Genetics Laboratory, University of California, Davis, CA, USA
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - William T Bean
- Department of Wildlife, Humboldt State University, Arcata, CA, USA
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12
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Lundgren E, Ralph PL. Are populations like a circuit? Comparing isolation by resistance to a new coalescent-based method. Mol Ecol Resour 2019; 19:1388-1406. [PMID: 31099173 DOI: 10.1111/1755-0998.13035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 04/22/2019] [Accepted: 05/01/2019] [Indexed: 11/27/2022]
Abstract
A number of methods commonly used in landscape genetics use an analogy to electrical resistance on a network to describe and fit barriers to movement across the landscape using genetic distance data. These are motivated by a mathematical equivalence between electrical resistance between two nodes of a network and the 'commute time', which is the mean time for a random walk on that network to leave one node, visit the other, and return. However, genetic data are more accurately modelled by a different quantity, the coalescence time. Here, we describe the differences between resistance distance and coalescence time, and explore the consequences for inference. We implemented a Bayesian method to infer effective movement rates and population sizes under both these models, and found that inference using commute times could produce misleading results in the presence of biased gene flow. We then used forwards-time simulation with continuous geography to demonstrate that coalescence-based inference remains more accurate than resistance-based methods on realistic data, but difficulties highlight the need for methods that explicitly model continuous, heterogeneous geography.
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Affiliation(s)
- Erik Lundgren
- Computational Biology, University of Southern California, Los Angeles, CA, USA
| | - Peter L Ralph
- Institute for Ecology and Evolution, University of Oregon, Eugene, OR, USA
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13
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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: 10] [Impact Index Per Article: 2.0] [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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14
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Grummer JA, Beheregaray LB, Bernatchez L, Hand BK, Luikart G, Narum SR, Taylor EB. Aquatic Landscape Genomics and Environmental Effects on Genetic Variation. Trends Ecol Evol 2019; 34:641-654. [DOI: 10.1016/j.tree.2019.02.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 02/15/2019] [Accepted: 02/22/2019] [Indexed: 01/17/2023]
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15
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Dickson BG, Albano CM, Anantharaman R, Beier P, Fargione J, Graves TA, Gray ME, Hall KR, Lawler JJ, Leonard PB, Littlefield CE, McClure ML, Novembre J, Schloss CA, Schumaker NH, Shah VB, Theobald DM. Circuit-theory applications to connectivity science and conservation. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2019; 33:239-249. [PMID: 30311266 PMCID: PMC6727660 DOI: 10.1111/cobi.13230] [Citation(s) in RCA: 86] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Revised: 09/29/2018] [Accepted: 09/30/2018] [Indexed: 05/25/2023]
Abstract
Conservation practitioners have long recognized ecological connectivity as a global priority for preserving biodiversity and ecosystem function. In the early years of conservation science, ecologists extended principles of island biogeography to assess connectivity based on source patch proximity and other metrics derived from binary maps of habitat. From 2006 to 2008, the late Brad McRae introduced circuit theory as an alternative approach to model gene flow and the dispersal or movement routes of organisms. He posited concepts and metrics from electrical circuit theory as a robust way to quantify movement across multiple possible paths in a landscape, not just a single least-cost path or corridor. Circuit theory offers many theoretical, conceptual, and practical linkages to conservation science. We reviewed 459 recent studies citing circuit theory or the open-source software Circuitscape. We focused on applications of circuit theory to the science and practice of connectivity conservation, including topics in landscape and population genetics, movement and dispersal paths of organisms, anthropogenic barriers to connectivity, fire behavior, water flow, and ecosystem services. Circuit theory is likely to have an effect on conservation science and practitioners through improved insights into landscape dynamics, animal movement, and habitat-use studies and through the development of new software tools for data analysis and visualization. The influence of circuit theory on conservation comes from the theoretical basis and elegance of the approach and the powerful collaborations and active user community that have emerged. Circuit theory provides a springboard for ecological understanding and will remain an important conservation tool for researchers and practitioners around the globe.
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Affiliation(s)
- Brett G. Dickson
- Conservation Science Partners Inc., 11050 Pioneer Trail, Suite 202, Truckee, CA, 96161, U.S.A
- Landscape Conservation Initiative, Northern Arizona University, Box 5694, Flagstaff, AZ, 86011, U.S.A
| | - Christine M. Albano
- Conservation Science Partners Inc., 11050 Pioneer Trail, Suite 202, Truckee, CA, 96161, U.S.A
| | | | - Paul Beier
- School of Forestry, Northern Arizona University, Box 15018, Flagstaff, AZ, 86011, U.S.A
| | - Joe Fargione
- The Nature Conservancy – North America Region, 1101 West River Parkway, Suite 200, Minneapolis, MN, 55415, U.S.A
| | - Tabitha A. Graves
- U.S. Geological Survey, Northern Rocky Mountain Science Center, 38 Mather Drive, West Glacier, MT, 59936, U.S.A
| | - Miranda E. Gray
- Conservation Science Partners Inc., 11050 Pioneer Trail, Suite 202, Truckee, CA, 96161, U.S.A
| | - Kimberly R. Hall
- The Nature Conservancy – North America Region, 1101 West River Parkway, Suite 200, Minneapolis, MN, 55415, U.S.A
| | - Josh J. Lawler
- School of Environmental and Forest Sciences, University of Washington, Box 352100, Seattle, WA, 98195, U.S.A
| | - Paul B. Leonard
- U.S. Fish & Wildlife Service, Science Applications, 101 12th Avenue, Number 110, Fairbanks, AK, 99701, U.S.A
| | - Caitlin E. Littlefield
- School of Environmental and Forest Sciences, University of Washington, Box 352100, Seattle, WA, 98195, U.S.A
| | - Meredith L. McClure
- Conservation Science Partners Inc., 11050 Pioneer Trail, Suite 202, Truckee, CA, 96161, U.S.A
| | - John Novembre
- Department of Human Genetics, Department of Ecology and Evolution, University of Chicago, 920 East 58th Street, Chicago, IL, 60637, U.S.A
| | - Carrie A. Schloss
- The Nature Conservancy, 201 Mission Street, San Francisco, CA, 94105, U.S.A
| | - Nathan H. Schumaker
- U.S. Environmental Protection Agency, 200 Southwest 35th Street, Corvallis, OR, 97330, U.S.A
| | - Viral B. Shah
- Julia Computing, 45 Prospect Street, Cambridge, MA, 02139, U.S.A
| | - David M. Theobald
- Conservation Science Partners Inc., 11050 Pioneer Trail, Suite 202, Truckee, CA, 96161, U.S.A
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16
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Wan HY, Cushman SA, Ganey JL. Habitat Fragmentation Reduces Genetic Diversity and Connectivity of the Mexican Spotted Owl: A Simulation Study Using Empirical Resistance Models. Genes (Basel) 2018; 9:genes9080403. [PMID: 30103436 PMCID: PMC6115790 DOI: 10.3390/genes9080403] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 08/07/2018] [Indexed: 11/16/2022] Open
Abstract
We evaluated how differences between two empirical resistance models for the same geographic area affected predictions of gene flow processes and genetic diversity for the Mexican spotted owl (Strix occidentalis lucida). The two resistance models represented the landscape under low- and high-fragmentation parameters. Under low fragmentation, the landscape had larger but highly concentrated habitat patches, whereas under high fragmentation, the landscape had smaller habitat patches that scattered across a broader area. Overall habitat amount differed little between resistance models. We tested eight scenarios reflecting a factorial design of three factors: resistance model (low vs. high fragmentation), isolation hypothesis (isolation-by-distance, IBD, vs. isolation-by-resistance, IBR), and dispersal limit of species (200 km vs. 300 km). Higher dispersal limit generally had a positive but small influence on genetic diversity. Genetic distance increased with both geographic distance and landscape resistance, but landscape resistance displayed a stronger influence. Connectivity was positively related to genetic diversity under IBR but was less important under IBD. Fragmentation had a strong negative influence on the spatial patterns of genetic diversity and effective population size (Ns). Despite habitats being more concentrated and less widely distributed, the low-fragmentation landscape had greater genetic diversity than the high-fragmentation landscape, suggesting that highly concentrated but larger habitat patches may provide a genetic refuge for the Mexican spotted owl.
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Affiliation(s)
- Ho Yi Wan
- School of Earth Sciences and Environmental Sustainability, Northern Arizona University, Flagstaff, AZ 86011, USA.
| | - Samuel A Cushman
- USDA Forest Service Rocky Mountain Research Station, 2500 S. Pine Knoll, Flagstaff, AZ 86001, USA.
| | - Joseph L Ganey
- USDA Forest Service Rocky Mountain Research Station, 2500 S. Pine Knoll, Flagstaff, AZ 86001, USA.
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17
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Milligan BG, Archer FI, Ferchaud A, Hand BK, Kierepka EM, Waples RS. Disentangling genetic structure for genetic monitoring of complex populations. Evol Appl 2018; 11:1149-1161. [PMID: 30026803 PMCID: PMC6050185 DOI: 10.1111/eva.12622] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 02/14/2018] [Indexed: 12/25/2022] Open
Abstract
Genetic monitoring estimates temporal changes in population parameters from molecular marker information. Most populations are complex in structure and change through time by expanding or contracting their geographic range, becoming fragmented or coalescing, or increasing or decreasing density. Traditional approaches to genetic monitoring rely on quantifying temporal shifts of specific population metrics-heterozygosity, numbers of alleles, effective population size-or measures of geographic differentiation such as FST. However, the accuracy and precision of the results can be heavily influenced by the type of genetic marker used and how closely they adhere to analytical assumptions. Care must be taken to ensure that inferences reflect actual population processes rather than changing molecular techniques or incorrect assumptions of an underlying model of population structure. In many species of conservation concern, true population structure is unknown, or structure might shift over time. In these cases, metrics based on inappropriate assumptions of population structure may not provide quality information regarding the monitored population. Thus, we need an inference model that decouples the complex elements that define population structure from estimation of population parameters of interest and reveals, rather than assumes, fine details of population structure. Encompassing a broad range of possible population structures would enable comparable inferences across biological systems, even in the face of range expansion or contraction, fragmentation, or changes in density. Currently, the best candidate is the spatial Λ-Fleming-Viot (SLFV) model, a spatially explicit individually based coalescent model that allows independent inference of two of the most important elements of population structure: local population density and local dispersal. We support increased use of the SLFV model for genetic monitoring by highlighting its benefits over traditional approaches. We also discuss necessary future directions for model development to support large genomic datasets informing real-world management and conservation issues.
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Affiliation(s)
| | | | - Anne‐Laure Ferchaud
- Institut de Biologie Intégrative et des Systèmes (IBIS)Université LavalQuébecQCCanada
| | - Brian K. Hand
- Flathead Lake Biological StationUniversity of MontanaPolsonMTUSA
| | | | - Robin S. Waples
- NOAA FisheriesNorthwest Fisheries Science CenterSeattleWAUSA
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18
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van Rees CB, Reed JM, Wilson RE, Underwood JG, Sonsthagen SA. Landscape genetics identifies streams and drainage infrastructure as dispersal corridors for an endangered wetland bird. Ecol Evol 2018; 8:8328-8343. [PMID: 30250706 PMCID: PMC6145004 DOI: 10.1002/ece3.4296] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 05/03/2018] [Accepted: 05/14/2018] [Indexed: 12/28/2022] Open
Abstract
Anthropogenic alterations to landscape structure and composition can have significant impacts on biodiversity, potentially leading to species extinctions. Population‐level impacts of landscape change are mediated by animal behaviors, in particular dispersal behavior. Little is known about the dispersal habits of rails (Rallidae) due to their cryptic behavior and tendency to occupy densely vegetated habitats. The effects of landscape structure on the movement behavior of waterbirds in general are poorly studied due to their reputation for having high dispersal abilities. We used a landscape genetic approach to test hypotheses of landscape effects on dispersal behavior of the Hawaiian gallinule (Gallinula galeata sandvicensis), an endangered subspecies endemic to the Hawaiian Islands. We created a suite of alternative resistance surfaces representing biologically plausible a priori hypotheses of how gallinules might navigate the landscape matrix and ranked these surfaces by their ability to explain observed patterns in genetic distance among 12 populations on the island of O`ahu. We modeled effective distance among wetland locations on all surfaces using both cumulative least‐cost‐path and resistance‐distance approaches and evaluated relative model performance using Mantel tests, a causal modeling approach, and the mixed‐model maximum‐likelihood population‐effects framework. Across all genetic markers, simulation methods, and model comparison metrics, surfaces that treated linear water features like streams, ditches, and canals as corridors for gallinule movement outperformed all other models. This is the first landscape genetic study on the movement behavior of any waterbird species to our knowledge. Our results indicate that lotic water features, including drainage infrastructure previously thought to be of minimal habitat value, contribute to habitat connectivity in this listed subspecies.
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Affiliation(s)
| | - J Michael Reed
- Department of Biology Tufts University Medford Massachusetts
| | - Robert E Wilson
- U. S. Geological Survey Alaska Science Center Anchorage Alaska
| | - Jared G Underwood
- Pacific Reefs National Wildlife Refuge Complex U.S. Fish and Wildlife Service Honolulu Hawaii.,Present address: Don Edwards San Francisco Bay National Wildlife Refuge Fremont California
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19
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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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20
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Howell PE, Muths E, Hossack BR, Sigafus BH, Chandler RB. Increasing connectivity between metapopulation ecology and landscape ecology. Ecology 2018; 99:1119-1128. [PMID: 29453767 DOI: 10.1002/ecy.2189] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 11/07/2017] [Accepted: 12/18/2017] [Indexed: 11/06/2022]
Abstract
Metapopulation ecology and landscape ecology aim to understand how spatial structure influences ecological processes, yet these disciplines address the problem using fundamentally different modeling approaches. Metapopulation models describe how the spatial distribution of patches affects colonization and extinction, but often do not account for the heterogeneity in the landscape between patches. Models in landscape ecology use detailed descriptions of landscape structure, but often without considering colonization and extinction dynamics. We present a novel spatially explicit modeling framework for narrowing the divide between these disciplines to advance understanding of the effects of landscape structure on metapopulation dynamics. Unlike previous efforts, this framework allows for statistical inference on landscape resistance to colonization using empirical data. We demonstrate the approach using 11 yr of data on a threatened amphibian in a desert ecosystem. Occupancy data for Lithobates chiricahuensis (Chiricahua leopard frog) were collected on the Buenos Aires National Wildlife Refuge (BANWR), Arizona, USA from 2007 to 2017 following a reintroduction in 2003. Results indicated that colonization dynamics were influenced by both patch characteristics and landscape structure. Landscape resistance increased with increasing elevation and distance to the nearest streambed. Colonization rate was also influenced by patch quality, with semi-permanent and permanent ponds contributing substantially more to the colonization of neighboring ponds relative to intermittent ponds. Ponds that only hold water intermittently also had the highest extinction rate. Our modeling framework can be widely applied to understand metapopulation dynamics in complex landscapes, particularly in systems in which the environment between habitat patches influences the colonization process.
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Affiliation(s)
- Paige E Howell
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, 30602, USA
| | - Erin Muths
- U.S. Geological Survey, Fort Collins Science Center, Fort Collins, Colorado, 80526, USA
| | - Blake R Hossack
- U.S. Geological Survey, Northern Rocky Mountain Science Center, Aldo Leopold Wilderness Research Institute, Missoula, Montana, 59801, USA
| | - Brent H Sigafus
- U.S. Geological Survey, Southwest Biological Science Center, Tucson, Arizona, 85719, USA
| | - Richard B Chandler
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia, 30602, USA
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21
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Hemming-Schroeder E, Lo E, Salazar C, Puente S, Yan G. Landscape Genetics: A Toolbox for Studying Vector-Borne Diseases. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00021] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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22
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Peterman WE. ResistanceGA: An R package for the optimization of resistance surfaces using genetic algorithms. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.12984] [Citation(s) in RCA: 144] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- William E. Peterman
- School of Environment and Natural ResourcesThe Ohio State University Columbus OH USA
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23
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Fourtune L, Prunier JG, Paz-Vinas I, Loot G, Veyssière C, Blanchet S. Inferring Causalities in Landscape Genetics: An Extension of Wright's Causal Modeling to Distance Matrices. Am Nat 2018; 191:491-508. [PMID: 29570400 DOI: 10.1086/696233] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Identifying landscape features that affect functional connectivity among populations is a major challenge in fundamental and applied sciences. Landscape genetics combines landscape and genetic data to address this issue, with the main objective of disentangling direct and indirect relationships among an intricate set of variables. Causal modeling has strong potential to address the complex nature of landscape genetic data sets. However, this statistical approach was not initially developed to address the pairwise distance matrices commonly used in landscape genetics. Here, we aimed to extend the applicability of two causal modeling methods-that is, maximum-likelihood path analysis and the directional separation test-by developing statistical approaches aimed at handling distance matrices and improving functional connectivity inference. Using simulations, we showed that these approaches greatly improved the robustness of the absolute (using a frequentist approach) and relative (using an information-theoretic approach) fits of the tested models. We used an empirical data set combining genetic information on a freshwater fish species (Gobio occitaniae) and detailed landscape descriptors to demonstrate the usefulness of causal modeling to identify functional connectivity in wild populations. Specifically, we demonstrated how direct and indirect relationships involving altitude, temperature, and oxygen concentration influenced within- and between-population genetic diversity of G. occitaniae.
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24
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Sakaguchi S, Horie K, Ishikawa N, Nagano AJ, Yasugi M, Kudoh H, Ito M. Simultaneous evaluation of the effects of geographic, environmental and temporal isolation in ecotypic populations of Solidago virgaurea. THE NEW PHYTOLOGIST 2017; 216:1268-1280. [PMID: 28833204 DOI: 10.1111/nph.14744] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 07/07/2017] [Indexed: 05/14/2023]
Abstract
Early stages of ecological speciation can create populations with an ecology and reproduction timing distinct from those of related populations. Landscape genetic models incorporating environmental heterogeneity and population-specific reproductive traits enable the processes of population genetic differentiation to be inferred. We investigated genome-wide genetic variation in ecotypic populations of Solidago virgaurea sensu lato, a herbaceous plant inhabiting a wide range of habitats (woodlands, serpentine barrens and alpine grasslands) and displaying remarkable variation in flowering time. Simultaneous evaluation of environmental factors revealed an overwhelming effect of soil type differences on neutral genetic differentiation, compared with elevational differences. This result probably reflects the abrupt environmental changes generated by geological boundaries, whereas mountain slopes exhibit clinal changes, facilitating gene exchange between neighbouring populations. Temporal isolation was positively associated with genetic differentiation, with some early-flowering serpentine populations having allele frequencies distinct from adjacent nonserpentine populations. Overall, this study highlights the importance of ecological processes and of evolution of flowering time to promote genetic differentiation of S. virgaurea populations in a complex landscape.
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Affiliation(s)
- Shota Sakaguchi
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida-nihonmatsu-cho, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Kenji Horie
- Asahikawa City Northern Wild Plants Garden, Asahikawa, 071-1200, Japan
| | - Naoko Ishikawa
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Shiga, 520-2194, Japan
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
- JST CREST, Honcho 4-1-8, Kawaguchi, Saitama, 332-0012, Japan
| | - Masaki Yasugi
- National Institute for Basic Biology, Higashiyama 5-1, Myodaiji, Okazaki, 444-8787, Aichi, Japan
| | - Hiroshi Kudoh
- Center for Ecological Research, Kyoto University, Otsu, Shiga, 520-2113, Japan
| | - Motomi Ito
- Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
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25
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Phylogeographic testing of alternative histories of single-origin versus parallel evolution of early flowering serpentine populations of Picris hieracioides L. (Asteraceae) in Japan. Ecol Res 2017. [DOI: 10.1007/s11284-017-1536-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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26
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Shirk AJ, Landguth EL, Cushman SA. A comparison of regression methods for model selection in individual‐based landscape genetic analysis. Mol Ecol Resour 2017; 18:55-67. [DOI: 10.1111/1755-0998.12709] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 06/06/2017] [Accepted: 07/25/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew J. Shirk
- Climate Impacts Group College of the Environment University of Washington Seattle WA USA
| | - Erin L. Landguth
- Computational Ecology Laboratory Division of Biological Sciences University of Montana Missoula MT USA
| | - Samuel A. Cushman
- USDA Forest Service Rocky Mountain Research Station Flagstaff AZ USA
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27
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Reddy PA, Cushman SA, Srivastava A, Sarkar MS, Shivaji S. Tiger abundance and gene flow in Central India are driven by disparate combinations of topography and land cover. DIVERS DISTRIB 2017. [DOI: 10.1111/ddi.12580] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
| | - Samuel A. Cushman
- US Forest Service; Rocky Mountain Research Station; Flagstaff AZ USA
| | | | - Mriganka Shekhar Sarkar
- CSIR-Centre for Cellular and Molecular Biology; Hyderabad India
- Wildlife Institute of India; Dehradun India
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28
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Shirk AJ, Landguth EL, Cushman SA. A comparison of individual‐based genetic distance metrics for landscape genetics. Mol Ecol Resour 2017; 17:1308-1317. [DOI: 10.1111/1755-0998.12684] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 03/21/2017] [Accepted: 04/14/2017] [Indexed: 11/28/2022]
Affiliation(s)
- A. J. Shirk
- Climate Impacts Group College of the Environment University of Washington Seattle WA USA
| | - E. L. Landguth
- Computational Ecology Laboratory Division of Biological Sciences University of Montana Missoula MT USA
| | - S. A. Cushman
- USDA Forest Service, Rocky Mountain Research Station Flagstaff AZ USA
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29
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Tucker JM, Allendorf FW, Truex RL, Schwartz MK. Sex‐biased dispersal and spatial heterogeneity affect landscape resistance to gene flow in fisher. Ecosphere 2017. [DOI: 10.1002/ecs2.1839] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Affiliation(s)
- Jody M. Tucker
- Sequoia National Forest U.S. Forest Service, Pacific Southwest Region 1839 S. Newcomb Street Porterville California 93257 USA
| | - Fred W. Allendorf
- Division of Biological Sciences University of Montana 32 Campus Drive Missoula Montana 59812 USA
| | - Richard L. Truex
- U.S. Forest Service, Rocky Mountain Region 1617 Cole Boulevard Lakewood Colorado 80401 USA
| | - Michael K. Schwartz
- U.S. Forest Service, Rocky Mountain Research Station 800 East Beckwith Avenue Missoula Montana 59801 USA
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Creech TG, Epps CW, Landguth EL, Wehausen JD, Crowhurst RS, Holton B, Monello RJ. Simulating the spread of selection-driven genotypes using landscape resistance models for desert bighorn sheep. PLoS One 2017; 12:e0176960. [PMID: 28464013 PMCID: PMC5413035 DOI: 10.1371/journal.pone.0176960] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 04/19/2017] [Indexed: 11/30/2022] Open
Abstract
Landscape genetic studies based on neutral genetic markers have contributed to our understanding of the influence of landscape composition and configuration on gene flow and genetic variation. However, the potential for species to adapt to changing landscapes will depend on how natural selection influences adaptive genetic variation. We demonstrate how landscape resistance models can be combined with genetic simulations incorporating natural selection to explore how the spread of adaptive variation is affected by landscape characteristics, using desert bighorn sheep (Ovis canadensis nelsoni) in three differing regions of the southwestern United States as an example. We conducted genetic sampling and least-cost path modeling to optimize landscape resistance models independently for each region, and then simulated the spread of an adaptive allele favored by selection across each region. Optimized landscape resistance models differed between regions with respect to landscape variables included and their relationships to resistance, but the slope of terrain and the presence of water barriers and major roads had the greatest impacts on gene flow. Genetic simulations showed that differences among landscapes strongly influenced spread of adaptive genetic variation, with faster spread (1) in landscapes with more continuously distributed habitat and (2) when a pre-existing allele (i.e., standing genetic variation) rather than a novel allele (i.e., mutation) served as the source of adaptive genetic variation. The combination of landscape resistance models and genetic simulations has broad conservation applications and can facilitate comparisons of adaptive potential within and between landscapes.
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Affiliation(s)
- Tyler G. Creech
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
| | - Clinton W. Epps
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
| | - Erin L. Landguth
- Computational Ecology Laboratory, Division of Biological Sciences, University of Montana, Missoula, Montana, United States of America
| | - John D. Wehausen
- White Mountain Research Center, University of California, Bishop, California, United States of America
| | - Rachel S. Crowhurst
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, Oregon, United States of America
| | - Brandon Holton
- Grand Canyon National Park, National Park Service, Grand Canyon, Arizona, United States of America
| | - Ryan J. Monello
- Biological Resources Division, National Park Service, Fort Collins, Colorado, United States of America
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31
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Dilkina B, Houtman R, Gomes CP, Montgomery CA, McKelvey KS, Kendall K, Graves TA, Bernstein R, Schwartz MK. Trade-offs and efficiencies in optimal budget-constrained multispecies corridor networks. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2017; 31:192-202. [PMID: 27677418 DOI: 10.1111/cobi.12814] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 03/30/2016] [Accepted: 06/18/2016] [Indexed: 06/06/2023]
Abstract
Conservation biologists recognize that a system of isolated protected areas will be necessary but insufficient to meet biodiversity objectives. Current approaches to connecting core conservation areas through corridors consider optimal corridor placement based on a single optimization goal: commonly, maximizing the movement for a target species across a network of protected areas. We show that designing corridors for single species based on purely ecological criteria leads to extremely expensive linkages that are suboptimal for multispecies connectivity objectives. Similarly, acquiring the least-expensive linkages leads to ecologically poor solutions. We developed algorithms for optimizing corridors for multispecies use given a specific budget. We applied our approach in western Montana to demonstrate how the solutions may be used to evaluate trade-offs in connectivity for 2 species with different habitat requirements, different core areas, and different conservation values under different budgets. We evaluated corridors that were optimal for each species individually and for both species jointly. Incorporating a budget constraint and jointly optimizing for both species resulted in corridors that were close to the individual species movement-potential optima but with substantial cost savings. Our approach produced corridors that were within 14% and 11% of the best possible corridor connectivity for grizzly bears (Ursus arctos) and wolverines (Gulo gulo), respectively, and saved 75% of the cost. Similarly, joint optimization under a combined budget resulted in improved connectivity for both species relative to splitting the budget in 2 to optimize for each species individually. Our results demonstrate economies of scale and complementarities conservation planners can achieve by optimizing corridor designs for financial costs and for multiple species connectivity jointly. We believe that our approach will facilitate corridor conservation by reducing acquisition costs and by allowing derived corridors to more closely reflect conservation priorities.
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Affiliation(s)
- Bistra Dilkina
- Georgia Institute of Technology, School of Computational Science and Engineering, College of Computing, 266 Ferst Drive, Atlanta, GA, 30332, U.S.A
| | - Rachel Houtman
- Oregon State University, Department of Forest Engineering, Resources, and Management, 280 Peavy Hall, Corvallis, OR, 97331, U.S.A
| | - Carla P Gomes
- Cornell University, Institute for Computational Sustainability, Department of Computer Science, 353 Gates Hall, Ithaca, NY, 14853, U.S.A
| | - Claire A Montgomery
- Oregon State University, Department of Forest Engineering, Resources, and Management, 280 Peavy Hall, Corvallis, OR, 97331, U.S.A
| | - Kevin S McKelvey
- U.S. Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT, U.S.A
| | - Katherine Kendall
- U.S. Geological Survey, Glacier Field Station, Northern Rocky Mountain Science Center, 38 Mather Drive, West Glacier, MT, 59936, U.S.A
| | - Tabitha A Graves
- U.S. Geological Survey, Glacier Field Station, Northern Rocky Mountain Science Center, 38 Mather Drive, West Glacier, MT, 59936, U.S.A
| | - Richard Bernstein
- Cornell University, Institute for Computational Sustainability, Department of Computer Science, 353 Gates Hall, Ithaca, NY, 14853, U.S.A
| | - Michael K Schwartz
- U.S. Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, Missoula, MT, U.S.A
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32
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Reid BN, Mladenoff DJ, Peery MZ. Genetic effects of landscape, habitat preference and demography on three co‐occurring turtle species. Mol Ecol 2017; 26:781-798. [DOI: 10.1111/mec.13962] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 10/28/2016] [Accepted: 11/14/2016] [Indexed: 01/05/2023]
Affiliation(s)
- Brendan N. Reid
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison 1630 Linden Drive Madison WI 53706 USA
- Department of Herpetology American Museum of Natural History Central Park West at 79th Street New York NY 10024 USA
| | - David J. Mladenoff
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison 1630 Linden Drive Madison WI 53706 USA
| | - M. Zachariah Peery
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison 1630 Linden Drive Madison WI 53706 USA
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33
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Morin DJ, Fuller AK, Royle JA, Sutherland C. Model-based estimators of density and connectivity to inform conservation of spatially structured populations. Ecosphere 2017. [DOI: 10.1002/ecs2.1623] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Dana J. Morin
- New York Cooperative Fish and Wildlife Research Unit; Department of Natural Resources; Cornell University; 211 Fernow Hall Ithaca New York 14853 USA
| | - Angela K. Fuller
- U.S. Geological Survey; New York Cooperative Fish and Wildlife Research Unit; Department of Natural Resources; Cornell University; 211 Fernow Hall Ithaca New York 14853 USA
| | - J. Andrew Royle
- U.S. Geological Survey; Patuxent Wildlife Research Center; 12000 Beech Forest Road Laurel Maryland 20708 USA
| | - Chris Sutherland
- Department of Environmental Conservation; University of Massachusetts-Amherst; 118 Holdsworth Hall Amherst Massachusetts 01003 USA
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34
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Castillo JA, Epps CW, Jeffress MR, Ray C, Rodhouse TJ, Schwalm D. Replicated landscape genetic and network analyses reveal wide variation in functional connectivity for American pikas. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2016; 26:1660-1676. [PMID: 27755691 DOI: 10.1890/15-1452.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 12/16/2015] [Accepted: 02/10/2016] [Indexed: 06/06/2023]
Abstract
Landscape connectivity is essential for maintaining viable populations, particularly for species restricted to fragmented habitats or naturally arrayed in metapopulations and facing rapid climate change. The importance of assessing both structural connectivity (physical distribution of favorable habitat patches) and functional connectivity (how species move among habitat patches) for managing such species is well understood. However, the degree to which functional connectivity for a species varies among landscapes, and the resulting implications for conservation, have rarely been assessed. We used a landscape genetics approach to evaluate resistance to gene flow and, thus, to determine how landscape and climate-related variables influence gene flow for American pikas (Ochotona princeps) in eight federally managed sites in the western United States. We used empirically derived, individual-based landscape resistance models in conjunction with predictive occupancy models to generate patch-based network models describing functional landscape connectivity. Metareplication across landscapes enabled identification of limiting factors for dispersal that would not otherwise have been apparent. Despite the cool microclimates characteristic of pika habitat, south-facing aspects consistently represented higher resistance to movement, supporting the previous hypothesis that exposure to relatively high temperatures may limit dispersal in American pikas. We found that other barriers to dispersal included areas with a high degree of topographic relief, such as cliffs and ravines, as well as streams and distances greater than 1-4 km depending on the site. Using the empirically derived network models of habitat patch connectivity, we identified habitat patches that were likely disproportionately important for maintaining functional connectivity, areas in which habitat appeared fragmented, and locations that could be targeted for management actions to improve functional connectivity. We concluded that climate change, besides influencing patch occupancy as predicted by other studies, may alter landscape resistance for pikas, thereby influencing functional connectivity through multiple pathways simultaneously. Spatial autocorrelation among genotypes varied across study sites and was largest where habitat was most dispersed, suggesting that dispersal distances increased with habitat fragmentation, up to a point. This study demonstrates how landscape features linked to climate can affect functional connectivity for species with naturally fragmented distributions, and reinforces the importance of replicating studies across landscapes.
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Affiliation(s)
- Jessica A Castillo
- Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, Corvallis, Oregon, 97331, USA.
| | - Clinton W Epps
- Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, Corvallis, Oregon, 97331, USA
| | | | - Chris Ray
- Institute of Arctic and Alpine Research, University of Colorado-Boulder, Boulder, Colorado, 80309, USA
| | - Thomas J Rodhouse
- Upper Columbia Basin Network, National Park Service, 63095 Deschutes Market Road, Bend, Oregon, 97701, USA
| | - Donelle Schwalm
- Department of Fisheries and Wildlife, Oregon State University, 104 Nash Hall, Corvallis, Oregon, 97331, USA
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35
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Barros T, Cushman SA, Carvalho J, Fonseca C. Mediterranean scrubland and elevation drive gene flow of a Mediterranean carnivore, the Egyptian mongoose Herpestes ichneumon(Herpestidae). Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12867] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tânia Barros
- Departamento de Biologia & Centro de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; Campus Universitário de Santiago 3810-193; Aveiro Portugal
| | - Samuel A. Cushman
- US Forest Service; Rocky Mountain Research Station; 2500, S Pine Knoll Dr. Flagstaff AZ 86001 USA
| | - João Carvalho
- Departamento de Biologia & Centro de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; Campus Universitário de Santiago 3810-193; Aveiro Portugal
- Servei d'Ecopatologia de Fauna Salvatge (SEFaS); Departament de Medicina i Cirurgia Animals; Universitat Autònoma de Barcelona; E-08193 Bellaterra Barcelona Spain
| | - Carlos Fonseca
- Departamento de Biologia & Centro de Estudos do Ambiente e do Mar (CESAM); Universidade de Aveiro; Campus Universitário de Santiago 3810-193; Aveiro Portugal
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36
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Richardson JL, Brady SP, Wang IJ, Spear SF. Navigating the pitfalls and promise of landscape genetics. Mol Ecol 2016; 25:849-63. [PMID: 26756865 DOI: 10.1111/mec.13527] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2015] [Revised: 12/12/2015] [Accepted: 01/07/2016] [Indexed: 12/17/2022]
Abstract
The field of landscape genetics has been evolving rapidly since its emergence in the early 2000s. New applications, techniques and criticisms of techniques appear like clockwork with each new journal issue. The developments are an encouraging, and at times bewildering, sign of progress in an exciting new field of study. However, we suggest that the rapid expansion of landscape genetics has belied important flaws in the development of the field, and we add an air of caution to this breakneck pace of expansion. Specifically, landscape genetic studies often lose sight of the fundamental principles and complex consequences of gene flow, instead favouring simplistic interpretations and broad inferences not necessarily warranted by the data. Here, we describe common pitfalls that characterize such studies, and provide practical guidance to improve landscape genetic investigation, with careful consideration of inferential limits, scale, replication, and the ecological and evolutionary context of spatial genetic patterns. Ultimately, the utility of landscape genetics will depend on translating the relationship between gene flow and landscape features into an understanding of long-term population outcomes. We hope the perspective presented here will steer landscape genetics down a more scientifically sound and productive path, garnering a field that is as informative in the future as it is popular now.
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Affiliation(s)
- Jonathan L Richardson
- Department of Biology, Providence College, 1 Cunningham Square, Providence, RI, 02918, USA
| | - Steven P Brady
- Department of Biological Sciences, Dartmouth College, Hanover, NH, 03755, USA
| | - Ian J Wang
- Department of Environmental Science, Policy & Management, University of California, Berkeley, CA, 94720, USA
| | - Stephen F Spear
- The Orianne Society, 100 Phoenix Rd., Athens, GA, 30605, USA
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37
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Abrahms B, Sawyer SC, Jordan NR, McNutt JW, Wilson AM, Brashares JS. Does wildlife resource selection accurately inform corridor conservation? J Appl Ecol 2016. [DOI: 10.1111/1365-2664.12714] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Briana Abrahms
- Department of Environmental Science, Policy, and Management University of California‐Berkeley 130 Mulford Hall #3114 Berkeley CA 94720 USA
| | - Sarah C. Sawyer
- USDA Forest Service Pacific Southwest Region 1323 Club Drive Vallejo CA 94592 USA
| | - Neil R. Jordan
- Centre for Ecosystem Science School of Biological, Earth and Environmental Sciences University of New South Wales (UNSW) Sydney NSW 2052 Australia
- Taronga Conservation Society Australia Taronga Western Plains Zoo Wildlife Reproduction Centre Obley Road Dubbo NSW 2830 Australia
- Botswana Predator Conservation Trust Private Bag 13 Maun Botswana
| | - J. Weldon McNutt
- Botswana Predator Conservation Trust Private Bag 13 Maun Botswana
| | - Alan M. Wilson
- Structure & Motion Lab Royal Veterinary College University of London Hatfield AL97TA UK
| | - Justin S. Brashares
- Department of Environmental Science, Policy, and Management University of California‐Berkeley 130 Mulford Hall #3114 Berkeley CA 94720 USA
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38
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Roffler GH, Schwartz MK, Pilgrim KL, Talbot SL, Sage GK, Adams LG, Luikart G. Identification of landscape features influencing gene flow: How useful are habitat selection models? Evol Appl 2016; 9:805-17. [PMID: 27330556 PMCID: PMC4908466 DOI: 10.1111/eva.12389] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 04/26/2016] [Indexed: 01/05/2023] Open
Abstract
Understanding how dispersal patterns are influenced by landscape heterogeneity is critical for modeling species connectivity. Resource selection function (RSF) models are increasingly used in landscape genetics approaches. However, because the ecological factors that drive habitat selection may be different from those influencing dispersal and gene flow, it is important to consider explicit assumptions and spatial scales of measurement. We calculated pairwise genetic distance among 301 Dall's sheep (Ovis dalli dalli) in southcentral Alaska using an intensive noninvasive sampling effort and 15 microsatellite loci. We used multiple regression of distance matrices to assess the correlation of pairwise genetic distance and landscape resistance derived from an RSF, and combinations of landscape features hypothesized to influence dispersal. Dall's sheep gene flow was positively correlated with steep slopes, moderate peak normalized difference vegetation indices (NDVI), and open land cover. Whereas RSF covariates were significant in predicting genetic distance, the RSF model itself was not significantly correlated with Dall's sheep gene flow, suggesting that certain habitat features important during summer (rugged terrain, mid-range elevation) were not influential to effective dispersal. This work underscores that consideration of both habitat selection and landscape genetics models may be useful in developing management strategies to both meet the immediate survival of a species and allow for long-term genetic connectivity.
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Affiliation(s)
- Gretchen H. Roffler
- US Geological SurveyAlaska Science CenterAnchorageAKUSA
- Wildlife Biology ProgramDepartment of Ecosystem Sciences and ConservationCollege of Forestry and ConservationUniversity of MontanaMissoulaMTUSA
- Present address: Alaska Department of Fish and GameDivision of Wildlife ConservationDouglasAKUSA
| | - Michael K. Schwartz
- Wildlife Biology ProgramDepartment of Ecosystem Sciences and ConservationCollege of Forestry and ConservationUniversity of MontanaMissoulaMTUSA
- US Forest Service Rocky Mountain Research StationMissoulaMTUSA
| | | | | | | | | | - Gordon Luikart
- Flathead Lake Biological StationUniversity of MontanaPolsonMTUSA
- Fish and Wildlife Genomics GroupDivision of Biological SciencesUniversity of MontanaMissoulaMTUSA
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39
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Least-Cost Modelling and Landscape Ecology: Concepts, Applications, and Opportunities. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s40823-016-0006-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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40
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Zeller KA, Creech TG, Millette KL, Crowhurst RS, Long RA, Wagner HH, Balkenhol N, Landguth EL. Using simulations to evaluate Mantel-based methods for assessing landscape resistance to gene flow. Ecol Evol 2016; 6:4115-28. [PMID: 27516868 PMCID: PMC4879002 DOI: 10.1002/ece3.2154] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Revised: 03/29/2016] [Accepted: 04/01/2016] [Indexed: 01/04/2023] Open
Abstract
Mantel‐based tests have been the primary analytical methods for understanding how landscape features influence observed spatial genetic structure. Simulation studies examining Mantel‐based approaches have highlighted major challenges associated with the use of such tests and fueled debate on when the Mantel test is appropriate for landscape genetics studies. We aim to provide some clarity in this debate using spatially explicit, individual‐based, genetic simulations to examine the effects of the following on the performance of Mantel‐based methods: (1) landscape configuration, (2) spatial genetic nonequilibrium, (3) nonlinear relationships between genetic and cost distances, and (4) correlation among cost distances derived from competing resistance models. Under most conditions, Mantel‐based methods performed poorly. Causal modeling identified the true model only 22% of the time. Using relative support and simple Mantel r values boosted performance to approximately 50%. Across all methods, performance increased when landscapes were more fragmented, spatial genetic equilibrium was reached, and the relationship between cost distance and genetic distance was linearized. Performance depended on cost distance correlations among resistance models rather than cell‐wise resistance correlations. Given these results, we suggest that the use of Mantel tests with linearized relationships is appropriate for discriminating among resistance models that have cost distance correlations <0.85 with each other for causal modeling, or <0.95 for relative support or simple Mantel r. Because most alternative parameterizations of resistance for the same landscape variable will result in highly correlated cost distances, the use of Mantel test‐based methods to fine‐tune resistance values will often not be effective.
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Affiliation(s)
- Katherine A Zeller
- Department of Environmental Conservation University of Massachusetts Amherst Massachusetts 01003
| | - Tyler G Creech
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon 97331
| | - Katie L Millette
- Department of Biology McGill University Montreal Quebec H3A 1B1 Canada
| | - Rachel S Crowhurst
- Department of Fisheries and Wildlife Oregon State University Corvallis Oregon 97331
| | - Robert A Long
- Field Conservation Program Woodland Park Zoo Seattle Washington 98103
| | - Helene H Wagner
- Department of Ecology and Evolutionary Biology University of Toronto Mississauga Ontario L5L 1C6 Canada
| | - Niko Balkenhol
- Department of Wildlife Sciences University of Göttingen Büsgenweg 3 37077 Göttingen Germany
| | - Erin L Landguth
- Division of Biological Sciences University of Montana Missoula Montana 59846
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41
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Munshi‐South J, Zolnik CP, Harris SE. Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations. Evol Appl 2016; 9:546-64. [PMID: 27099621 PMCID: PMC4831458 DOI: 10.1111/eva.12357] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 12/27/2015] [Indexed: 12/16/2022] Open
Abstract
Urbanization results in pervasive habitat fragmentation and reduces standing genetic variation through bottlenecks and drift. Loss of genomewide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genomewide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genomewide variation was estimated as a proxy for evolutionary potential using more than 10 000 single nucleotide polymorphism (SNP) markers generated by ddRAD-Seq. We found that genomewide variation is inversely related to urbanization as measured by percent impervious surface cover, and to a lesser extent, human population density. We also report that urbanization results in enhanced genomewide differentiation between populations in cities. There was no pattern of isolation by distance among these populations, but an isolation by resistance model based on impervious surface significantly explained patterns of genetic differentiation. Isolation by environment modeling also indicated that urban populations deviate much more strongly from global allele frequencies than suburban or rural populations. This study is the first to examine loss of genomewide SNP variation along an urban-to-rural gradient and quantify urbanization as a driver of population genomic patterns.
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Affiliation(s)
- Jason Munshi‐South
- Department of Biological Sciences and the Louis Calder Center—Biological Field StationFordham UniversityArmonkNYUSA
| | - Christine P. Zolnik
- Department of Biological Sciences and the Louis Calder Center—Biological Field StationFordham UniversityArmonkNYUSA
| | - Stephen E. Harris
- Ph.D. Program in EcologyEvolutionary Biology and Behaviorthe Graduate Center of the City University of New YorkNew YorkNYUSA
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42
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Amaral KE, Palace M, O'Brien KM, Fenderson LE, Kovach AI. Anthropogenic Habitats Facilitate Dispersal of an Early Successional Obligate: Implications for Restoration of an Endangered Ecosystem. PLoS One 2016; 11:e0148842. [PMID: 26954014 PMCID: PMC4783018 DOI: 10.1371/journal.pone.0148842] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/25/2016] [Indexed: 01/15/2023] Open
Abstract
Landscape modification and habitat fragmentation disrupt the connectivity of natural landscapes, with major consequences for biodiversity. Species that require patchily distributed habitats, such as those that specialize on early successional ecosystems, must disperse through a landscape matrix with unsuitable habitat types. We evaluated landscape effects on dispersal of an early successional obligate, the New England cottontail (Sylvilagus transitionalis). Using a landscape genetics approach, we identified barriers and facilitators of gene flow and connectivity corridors for a population of cottontails in the northeastern United States. We modeled dispersal in relation to landscape structure and composition and tested hypotheses about the influence of habitat fragmentation on gene flow. Anthropogenic and natural shrubland habitats facilitated gene flow, while the remainder of the matrix, particularly development and forest, impeded gene flow. The relative influence of matrix habitats differed between study areas in relation to a fragmentation gradient. Barrier features had higher explanatory power in the more fragmented site, while facilitating features were important in the less fragmented site. Landscape models that included a simultaneous barrier and facilitating effect of roads had higher explanatory power than models that considered either effect separately, supporting the hypothesis that roads act as both barriers and facilitators at all spatial scales. The inclusion of LiDAR-identified shrubland habitat improved the fit of our facilitator models. Corridor analyses using circuit and least cost path approaches revealed the importance of anthropogenic, linear features for restoring connectivity between the study areas. In fragmented landscapes, human-modified habitats may enhance functional connectivity by providing suitable dispersal conduits for early successional specialists.
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Affiliation(s)
- Katrina E Amaral
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Michael Palace
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, United States of America.,Institute for the Study of Earth, Oceans, and Space, University of New Hampshire, Durham, New Hampshire, United States of America
| | - Kathleen M O'Brien
- United States Fish and Wildlife Service, Rachel Carson National Wildlife Refuge, Wells, Maine, United States of America
| | - Lindsey E Fenderson
- United States Fish and Wildlife Service, Northeast Fishery Center, Conservation Genetics Lab, Lamar, Pennsylvania, United States of America
| | - Adrienne I Kovach
- Department of Natural Resources and the Environment, University of New Hampshire, Durham, New Hampshire, United States of America
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43
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Dudaniec RY, Worthington Wilmer J, Hanson JO, Warren M, Bell S, Rhodes JR. Dealing with uncertainty in landscape genetic resistance models: a case of three co-occurring marsupials. Mol Ecol 2016; 25:470-86. [DOI: 10.1111/mec.13482] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 11/08/2015] [Accepted: 11/10/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Rachael Y. Dudaniec
- Department of Biological Sciences; Macquarie University; Sydney NSW 2109 Australia
| | | | - Jeffrey O. Hanson
- School of Biological Sciences; The University of Queensland; Brisbane Qld 4072 Australia
| | - Matthew Warren
- School of Geography, Planning and Environmental Management; The University of Queensland; Brisbane Qld 4072 Australia
| | - Sarah Bell
- School of Biomedical Sciences; The University of Queensland; Brisbane Qld 4072 Australia
| | - Jonathan R. Rhodes
- School of Geography, Planning and Environmental Management; The University of Queensland; Brisbane Qld 4072 Australia
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44
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Kierepka EM, Latch EK. Fine-scale landscape genetics of the American badger (Taxidea taxus): disentangling landscape effects and sampling artifacts in a poorly understood species. Heredity (Edinb) 2016; 116:33-43. [PMID: 26243136 PMCID: PMC4675871 DOI: 10.1038/hdy.2015.67] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 06/05/2015] [Accepted: 06/12/2015] [Indexed: 11/09/2022] Open
Abstract
Landscape genetics is a powerful tool for conservation because it identifies landscape features that are important for maintaining genetic connectivity between populations within heterogeneous landscapes. However, using landscape genetics in poorly understood species presents a number of challenges, namely, limited life history information for the focal population and spatially biased sampling. Both obstacles can reduce power in statistics, particularly in individual-based studies. In this study, we genotyped 233 American badgers in Wisconsin at 12 microsatellite loci to identify alternative statistical approaches that can be applied to poorly understood species in an individual-based framework. Badgers are protected in Wisconsin owing to an overall lack in life history information, so our study utilized partial redundancy analysis (RDA) and spatially lagged regressions to quantify how three landscape factors (Wisconsin River, Ecoregions and land cover) impacted gene flow. We also performed simulations to quantify errors created by spatially biased sampling. Statistical analyses first found that geographic distance was an important influence on gene flow, mainly driven by fine-scale positive spatial autocorrelations. After controlling for geographic distance, both RDA and regressions found that Wisconsin River and Agriculture were correlated with genetic differentiation. However, only Agriculture had an acceptable type I error rate (3-5%) to be considered biologically relevant. Collectively, this study highlights the benefits of combining robust statistics and error assessment via simulations and provides a method for hypothesis testing in individual-based landscape genetics.
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Affiliation(s)
- E M Kierepka
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - E K Latch
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
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Using genetic data to estimate diffusion rates in heterogeneous landscapes. J Math Biol 2015; 73:397-422. [DOI: 10.1007/s00285-015-0954-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 11/19/2015] [Indexed: 10/22/2022]
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Parks LC, Wallin DO, Cushman SA, McRae BH. Landscape-level analysis of mountain goat population connectivity in Washington and southern British Columbia. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0732-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Prunier JG, Colyn M, Legendre X, Nimon KF, Flamand MC. Multicollinearity in spatial genetics: separating the wheat from the chaff using commonality analyses. Mol Ecol 2015; 24:263-83. [PMID: 25495950 DOI: 10.1111/mec.13029] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 02/02/2023]
Abstract
Direct gradient analyses in spatial genetics provide unique opportunities to describe the inherent complexity of genetic variation in wildlife species and are the object of many methodological developments. However, multicollinearity among explanatory variables is a systemic issue in multivariate regression analyses and is likely to cause serious difficulties in properly interpreting results of direct gradient analyses, with the risk of erroneous conclusions, misdirected research and inefficient or counterproductive conservation measures. Using simulated data sets along with linear and logistic regressions on distance matrices, we illustrate how commonality analysis (CA), a detailed variance-partitioning procedure that was recently introduced in the field of ecology, can be used to deal with nonindependence among spatial predictors. By decomposing model fit indices into unique and common (or shared) variance components, CA allows identifying the location and magnitude of multicollinearity, revealing spurious correlations and thus thoroughly improving the interpretation of multivariate regressions. Despite a few inherent limitations, especially in the case of resistance model optimization, this review highlights the great potential of CA to account for complex multicollinearity patterns in spatial genetics and identifies future applications and lines of research. We strongly urge spatial geneticists to systematically investigate commonalities when performing direct gradient analyses.
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Affiliation(s)
- J G Prunier
- Institut des Sciences de la Vie, Université catholique de Louvain, Croix du Sud 4, L7.07.14, 1348, Louvain-la-Neuve, Belgium
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Ruiz-González A, Gurrutxaga M, Cushman SA, Madeira MJ, Randi E, Gómez-Moliner BJ. Landscape genetics for the empirical assessment of resistance surfaces: the European pine marten (Martes martes) as a target-species of a regional ecological network. PLoS One 2014; 9:e110552. [PMID: 25329047 PMCID: PMC4199733 DOI: 10.1371/journal.pone.0110552] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 09/23/2014] [Indexed: 11/24/2022] Open
Abstract
Coherent ecological networks (EN) composed of core areas linked by ecological corridors are being developed worldwide with the goal of promoting landscape connectivity and biodiversity conservation. However, empirical assessment of the performance of EN designs is critical to evaluate the utility of these networks to mitigate effects of habitat loss and fragmentation. Landscape genetics provides a particularly valuable framework to address the question of functional connectivity by providing a direct means to investigate the effects of landscape structure on gene flow. The goals of this study are (1) to evaluate the landscape features that drive gene flow of an EN target species (European pine marten), and (2) evaluate the optimality of a regional EN design in providing connectivity for this species within the Basque Country (North Spain). Using partial Mantel tests in a reciprocal causal modeling framework we competed 59 alternative models, including isolation by distance and the regional EN. Our analysis indicated that the regional EN was among the most supported resistance models for the pine marten, but was not the best supported model. Gene flow of pine marten in northern Spain is facilitated by natural vegetation, and is resisted by anthropogenic landcover types and roads. Our results suggest that the regional EN design being implemented in the Basque Country will effectively facilitate gene flow of forest dwelling species at regional scale.
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Affiliation(s)
- Aritz Ruiz-González
- Department of Zoology and Animal Cell Biology, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- Conservation Genetics Laboratory, National Institute for Environmental Protection and Research, ISPRA, Ozzano dell'Emilia, Bologna, Italy
- * E-mail:
| | - Mikel Gurrutxaga
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- Department of Geography, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Samuel A. Cushman
- U.S. Forest Service, Rocky Mountain Research Station, Flagstaff, AZ, United States of America
| | - María José Madeira
- Department of Zoology and Animal Cell Biology, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Ettore Randi
- Conservation Genetics Laboratory, National Institute for Environmental Protection and Research, ISPRA, Ozzano dell'Emilia, Bologna, Italy
- Department 18/Section of Environmental Engineering, Aalborg University, Aalborg, Denmark
| | - Benjamin J. Gómez-Moliner
- Department of Zoology and Animal Cell Biology, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- Systematics, Biogeography and Population Dynamics Research Group, Lascaray Research Center, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
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Kierepka EM, Latch EK. Performance of partial statistics in individual-based landscape genetics. Mol Ecol Resour 2014; 15:512-25. [DOI: 10.1111/1755-0998.12332] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/07/2014] [Accepted: 09/10/2014] [Indexed: 11/29/2022]
Affiliation(s)
- E. M. Kierepka
- Behavioral and Molecular Ecology Research Group; Department of Biological Sciences; University of Wisconsin-Milwaukee; Milwaukee WI 53211 USA
| | - E. K. Latch
- Behavioral and Molecular Ecology Research Group; Department of Biological Sciences; University of Wisconsin-Milwaukee; Milwaukee WI 53211 USA
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Amos N, Harrisson KA, Radford JQ, White M, Newell G, Mac Nally R, Sunnucks P, Pavlova A. Species- and sex-specific connectivity effects of habitat fragmentation in a suite of woodland birds. Ecology 2014; 95:1556-68. [PMID: 25039220 DOI: 10.1890/13-1328.1] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Loss of functional connectivity following habitat loss and fragmentation could drive species declines. A comprehensive understanding of fragmentation effects on functional connectivity of an ecological assemblage requires investigation of multiple species with different mobilities, at different spatial scales, for each sex, and in different landscapes. Based on published data on mobility and ecological responses to fragmentation of 10 woodland-dependent birds, and using simulation studies, we predicted that (1) fragmentation would impede dispersal and gene flow of eight "decliners" (species that disappear from suitable patches when landscape-level tree cover falls below species-specific thresholds), but not of two "tolerant" species (whose occurrence in suitable habitat patches is independent of landscape tree cover); and that fragmentation effects would be stronger (2) in the least mobile species, (3) in the more philopatric sex, and (4) in the more fragmented region. We tested these predictions by evaluating spatially explicit isolation-by-landscape-resistance models of gene flow in fragmented landscapes across a 50 x 170 km study area in central Victoria, Australia, using individual and population genetic distances. To account for sex-biased dispersal and potential scale- and configuration-specific effects, we fitted models specific to sex and geographic zones. As predicted, four of the least mobile decliners showed evidence of reduced genetic connectivity. The responses were strongly sex specific, but in opposite directions in the two most sedentary species. Both tolerant species and (unexpectedly) four of the more mobile decliners showed no reduction in gene flow. This is unlikely to be due to time lags because more mobile species develop genetic signatures of fragmentation faster than do less mobile ones. Weaker genetic effects were observed in the geographic zone with more aggregated vegetation, consistent with gene flow being unimpeded by landscape structure. Our results indicate that for all but the most sedentary species in our system, the movement of the more dispersive sex (females in most cases) maintains overall genetic connectivity across fragmented landscapes in the study area, despite some small-scale effects on the more philopatric sex for some species. Nevertheless, to improve population viability for the less mobile bird species, structural landscape connectivity must be increased.
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