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Genomics-informed models reveal extensive stretches of coastline under threat by an ecologically dominant invasive species. Proc Natl Acad Sci U S A 2021; 118:2022169118. [PMID: 34083434 DOI: 10.1073/pnas.2022169118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Explaining why some species are widespread, while others are not, is fundamental to biogeography, ecology, and evolutionary biology. A unique way to study evolutionary and ecological mechanisms that either limit species' spread or facilitate range expansions is to conduct research on species that have restricted distributions. Nonindigenous species, particularly those that are highly invasive but have not yet spread beyond the introduced site, represent ideal systems to study range size changes. Here, we used species distribution modeling and genomic data to study the restricted range of a highly invasive Australian marine species, the ascidian Pyura praeputialis This species is an aggressive space occupier in its introduced range (Chile), where it has fundamentally altered the coastal community. We found high genomic diversity in Chile, indicating high adaptive potential. In addition, genomic data clearly showed that a single region from Australia was the only donor of genotypes to the introduced range. We identified over 3,500 km of suitable habitat adjacent to its current introduced range that has so far not been occupied, and importantly species distribution models were only accurate when genomic data were considered. Our results suggest that a slight change in currents, or a change in shipping routes, may lead to an expansion of the species' introduced range that will encompass a vast portion of the South American coast. Our study shows how the use of population genomics and species distribution modeling in combination can unravel mechanisms shaping range sizes and forecast future range shifts of invasive species.
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2
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Razgour O, Kasso M, Santos H, Juste J. Up in the air: Threats to Afromontane biodiversity from climate change and habitat loss revealed by genetic monitoring of the Ethiopian Highlands bat. Evol Appl 2021; 14:794-806. [PMID: 33767753 PMCID: PMC7980307 DOI: 10.1111/eva.13161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/02/2022] Open
Abstract
While climate change is recognized as a major future threat to biodiversity, most species are currently threatened by extensive human-induced habitat loss, fragmentation and degradation. Tropical high-altitude alpine and montane forest ecosystems and their biodiversity are particularly sensitive to temperature increases under climate change, but they are also subject to accelerated pressures from land conversion and degradation due to a growing human population. We studied the combined effects of anthropogenic land-use change, past and future climate changes and mountain range isolation on the endemic Ethiopian Highlands long-eared bat, Plecotus balensis, an understudied bat that is restricted to the remnant natural high-altitude Afroalpine and Afromontane habitats. We integrated ecological niche modelling, landscape genetics and model-based inference to assess the genetic, geographic and demographic impacts of past and recent environmental changes. We show that mountain range isolation and historic climates shaped population structure and patterns of genetic variation, but recent anthropogenic land-use change and habitat degradation are associated with a severe population decline and loss of genetic diversity. Models predict that the suitable niche of this bat has been progressively shrinking since the last glaciation period. This study highlights threats to Afroalpine and Afromontane biodiversity, squeezed to higher altitudes under climate change while losing genetic diversity and suffering population declines due to anthropogenic land-use change. We conclude that the conservation of tropical montane biodiversity requires a holistic approach, using genetic, ecological and geographic information to understand the effects of environmental changes across temporal scales and simultaneously addressing the impacts of multiple threats.
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Affiliation(s)
- Orly Razgour
- BiosciencesUniversity of ExeterExeterUK
- School of Biological and Environmental SciencesUniversity of StirlingStirlingUK
| | | | - Helena Santos
- Research Network in Biodiversity and Evolutionary BiologyResearch Centre in Biodiversity and Genetic Resources (InBIO‐CIBIO)VairãoPortugal
- Faculty of SciencesUniversity of PortoPortoPortugal
| | - Javier Juste
- Estación Biológica de Doñana (CSIC)SevillaSpain
- CIBER de Epidemiología y Salud Pública. CIBERESPMadridSpain
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3
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Richardson JL, Michaelides S, Combs M, Djan M, Bisch L, Barrett K, Silveira G, Butler J, Aye TT, Munshi‐South J, DiMatteo M, Brown C, McGreevy TJ. Dispersal ability predicts spatial genetic structure in native mammals persisting across an urbanization gradient. Evol Appl 2021; 14:163-177. [PMID: 33519963 PMCID: PMC7819555 DOI: 10.1111/eva.13133] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/17/2020] [Indexed: 01/31/2023] Open
Abstract
As the rate of urbanization continues to increase globally, a growing body of research is emerging that investigates how urbanization shapes the movement-and consequent gene flow-of species in cities. Of particular interest are native species that persist in cities, either as small relict populations or as larger populations of synanthropic species that thrive alongside humans in new urban environments. In this study, we used genomic sequence data (SNPs) and spatially explicit individual-based analyses to directly compare the genetic structure and patterns of gene flow in two small mammals with different dispersal abilities that occupy the same urbanized landscape to evaluate how mobility impacts genetic connectivity. We collected 215 white-footed mice (Peromyscus leucopus) and 380 big brown bats (Eptesicus fuscus) across an urban-to-rural gradient within the Providence, Rhode Island (U.S.A.) metropolitan area (population =1,600,000 people). We found that mice and bats exhibit clear differences in their spatial genetic structure that are consistent with their dispersal abilities, with urbanization having a stronger effect on Peromyscus mice. There were sharp breaks in the genetic structure of mice within the Providence urban core, as well as reduced rates of migration and an increase in inbreeding with more urbanization. In contrast, bats showed very weak genetic structuring across the entire study area, suggesting a near-panmictic gene pool likely due to the ability to disperse by flight. Genetic diversity remained stable for both species across the study region. Mice also exhibited a stronger reduction in gene flow between island and mainland populations than bats. This study represents one of the first to directly compare multiple species within the same urban-to-rural landscape gradient, an important gap to fill for urban ecology and evolution. Moreover, here we document the impacts of dispersal capacity on connectivity for native species that have persisted as the urban landscape matrix expands.
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Affiliation(s)
| | - Sozos Michaelides
- Department of Natural Resources ScienceUniversity of Rhode IslandKingstonRIUSA
| | - Matthew Combs
- Ecology, Evolution and Environmental Biology DepartmentColumbia UniversityNew YorkNYUSA
| | - Mihajla Djan
- Department of Natural Resources ScienceUniversity of Rhode IslandKingstonRIUSA
- Department of Biology and EcologyFaculty of SciencesUniversity of Novi SadNovi SadSerbia
| | - Lianne Bisch
- Department of BiologyProvidence CollegeProvidenceRIUSA
| | - Kerry Barrett
- Department of BiologyProvidence CollegeProvidenceRIUSA
| | | | - Justin Butler
- Department of BiologyUniversity of RichmondRichmondVAUSA
| | - Than Thar Aye
- Department of BiologyUniversity of RichmondRichmondVAUSA
| | | | - Michael DiMatteo
- State Health LaboratoryRhode Island Department of HealthProvidenceRIUSA
| | - Charles Brown
- Division of Fish & WildlifeRhode Island Department of Environmental ManagementWest KingstonRIUSA
| | - Thomas J. McGreevy
- Department of Natural Resources ScienceUniversity of Rhode IslandKingstonRIUSA
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4
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Toffoli R, Cucco M. Habitat Suitability, Connection Analysis and Effectiveness of Protected Areas for Conservation of the Barbastelle Bat Barbastella barbastellus in NW Italy. ACTA CHIROPTEROLOGICA 2020. [DOI: 10.3161/15081109acc2020.22.2.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Roberto Toffoli
- Associazione Chirosphera, Via Tetti Barbiere 11, 10026 Santena, Italy
| | - Marco Cucco
- Department of Science and Technological Innovation, University of Eastern Piedmont, Viale T. Michel 11, 15100 Alessandria, Italy
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5
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Collevatti RG, Vitorino LC, Vieira TB, Oprea M, Telles MP. Landscape changes decrease genetic diversity in the Pallas’ long-tongued bat. Perspect Ecol Conserv 2020. [DOI: 10.1016/j.pecon.2020.06.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
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6
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Bakovic V, Schuler H, Schebeck M, Feder JL, Stauffer C, Ragland GJ. Host plant-related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi. Mol Ecol 2019; 28:4648-4666. [PMID: 31495015 PMCID: PMC6899720 DOI: 10.1111/mec.15239] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/13/2022]
Abstract
Elucidating the mechanisms and conditions facilitating the formation of biodiversity are central topics in evolutionary biology. A growing number of studies imply that divergent ecological selection may often play a critical role in speciation by counteracting the homogenising effects of gene flow. Several examples involve phytophagous insects, where divergent selection pressures associated with host plant shifts may generate reproductive isolation, promoting speciation. Here, we use ddRADseq to assess the population structure and to test for host‐related genomic differentiation in the European cherry fruit fly, Rhagoletis cerasi (L., 1758) (Diptera: Tephritidae). This tephritid is distributed throughout Europe and western Asia, and has adapted to two different genera of host plants, Prunus spp. (cherries) and Lonicera spp. (honeysuckle). Our data imply that geographic distance and geomorphic barriers serve as the primary factors shaping genetic population structure across the species range. Locally, however, flies genetically cluster according to host plant, with consistent allele frequency differences displayed by a subset of loci between Prunus and Lonicera flies across four sites surveyed in Germany and Norway. These 17 loci display significantly higher FST values between host plants than others. They also showed high levels of linkage disequilibrium within and between Prunus and Lonicera flies, supporting host‐related selection and reduced gene flow. Our findings support the existence of sympatric host races in R. cerasi embedded within broader patterns of geographic variation in the fly, similar to the related apple maggot, Rhagoletis pomonella, in North America.
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Affiliation(s)
- Vid Bakovic
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.,Department of Biology, IFM, University of Linköping, Linköping, Sweden
| | - Hannes Schuler
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Martin Schebeck
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Jeffrey L Feder
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Christian Stauffer
- Department of Forest and Soil Sciences, BOKU, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Gregory J Ragland
- Department of Integrative Biology, University of Colorado-Denver, Denver, CO, USA
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7
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Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections. Proc Natl Acad Sci U S A 2019; 116:10418-10423. [PMID: 31061126 PMCID: PMC6535011 DOI: 10.1073/pnas.1820663116] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Forecasts of species vulnerability and extinction risk under future climate change commonly ignore local adaptations despite their importance for determining the potential of populations to respond to future changes. We present an approach to assess the impacts of global climate change on biodiversity that takes into account adaptive genetic variation and evolutionary potential. We show that considering local climatic adaptations reduces range loss projections but increases the potential for competition between species. Our findings suggest that failure to account for within-species variability can result in overestimation of future biodiversity losses. Therefore, it is important to identify the climate-adaptive potential of populations and to increase landscape connectivity between populations to enable the spread of adaptive genetic variation. Local adaptations can determine the potential of populations to respond to environmental changes, yet adaptive genetic variation is commonly ignored in models forecasting species vulnerability and biogeographical shifts under future climate change. Here we integrate genomic and ecological modeling approaches to identify genetic adaptations associated with climate in two cryptic forest bats. We then incorporate this information directly into forecasts of range changes under future climate change and assessment of population persistence through the spread of climate-adaptive genetic variation (evolutionary rescue potential). Considering climate-adaptive potential reduced range loss projections, suggesting that failure to account for intraspecific variability can result in overestimation of future losses. On the other hand, range overlap between species was projected to increase, indicating that interspecific competition is likely to play an important role in limiting species’ future ranges. We show that although evolutionary rescue is possible, it depends on a population’s adaptive capacity and connectivity. Hence, we stress the importance of incorporating genomic data and landscape connectivity in climate change vulnerability assessments and conservation management.
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8
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Pahad G, Montgelard C, Jansen van Vuuren B. Phylogeography and niche modelling: reciprocal enlightenment. MAMMALIA 2019. [DOI: 10.1515/mammalia-2018-0191] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Phylogeography examines the spatial genetic structure of species. Environmental niche modelling (or ecological niche modelling; ENM) examines the environmental limits of a species’ ecological niche. These two fields have great potential to be used together. ENM can shed light on how phylogeographical patterns develop and help identify possible drivers of spatial structure that need to be further investigated. Specifically, ENM can be used to test for niche differentiation among clades, identify factors limiting individual clades and identify barriers and contact zones. It can also be used to test hypotheses regarding the effects of historical and future climate change on spatial genetic patterns by projecting niches using palaeoclimate or future climate data. Conversely, phylogeographical information can populate ENM with within-species genetic diversity. Where adaptive variation exists among clades within a species, modelling their niches separately can improve predictions of historical distribution patterns and future responses to climate change. Awareness of patterns of genetic diversity in niche modelling can also alert conservationists to the potential loss of genetically diverse areas in a species’ range. Here, we provide a simplistic overview of both fields, and focus on their potential for integration, encouraging researchers on both sides to take advantage of the opportunities available.
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Affiliation(s)
- Govan Pahad
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology , University of Johannesburg , PO Box 524 , Auckland Park, Johannesburg 2000 , South Africa
| | - Claudine Montgelard
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology , University of Johannesburg , PO Box 524 , Auckland Park, Johannesburg 2000 , South Africa
- PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier , EPHE, Biogéographie et Ecologie des Vertébrés , 1919 route de Mende , 34293 Montpellier , France
| | - Bettine Jansen van Vuuren
- Centre for Ecological Genomics and Wildlife Conservation, Department of Zoology , University of Johannesburg , PO Box 524 , Auckland Park, Johannesburg 2000 , South Africa
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9
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Andriollo T, Ashrafi S, Arlettaz R, Ruedi M. Porous barriers? Assessment of gene flow within and among sympatric long-eared bat species. Ecol Evol 2018; 8:12841-12854. [PMID: 30619587 PMCID: PMC6309003 DOI: 10.1002/ece3.4714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 10/18/2018] [Accepted: 10/30/2018] [Indexed: 11/11/2022] Open
Abstract
Species are the basic units for measuring biodiversity and for comprehending biological interactions. Yet, their delineation is often contentious, especially in groups that are both diverse and phenotypically conservative. Three cryptic species of long-eared bats, Plecotus auritus, P. austriacus, and P. macrobullaris, co-occur over extensive areas of Western Europe. The latter is a fairly recent discovery, questioning the overall diversity of the entire Plecotus complex. Yet, high morphological and acoustic similarities compromise the reliable identification of long-eared bats in the field. We postulate that such extensive phenotypic overlap, along with the recurrent observation of morphologically intermediate individuals, may hide rampant interspecific hybridization. Based on a geographic sampling centered on areas of sympatry in the Alps and Corsica, we assessed the level of reproductive isolation of these three Plecotus species with mitochondrial and nuclear markers, looking at both inter- and intraspecific genetic population structuring. No sign of hybridization was detected between these three species that appear well separated biologically. Genetic structuring of populations, however, reflected different species-specific responses to environmental connectivity, that is, to the presence of orographic or sea barriers. While the Alpine range and the Ligurian Sea coincided with sharp genetic discontinuities in P. macrobullaris and P. austriacus, the more ubiquitous P. auritus showed no significant population structuration. There were clear phylogeographic discrepancies between microsatellite and mitochondrial markers at the intraspecific level, however, which challenges the reliance on simple barcoding approaches for the delineation of sound conservation units.
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Affiliation(s)
- Tommy Andriollo
- Department of Mammalogy and OrnithologyNatural History Museum of GenevaGenevaSwitzerland
- Section of Biology, Faculty of SciencesUniversity of GenevaGenevaSwitzerland
| | - Sohrab Ashrafi
- Department of Environmental Sciences, Faculty of Natural ResourcesUniversity of TehranKarajIran
| | - Raphaël Arlettaz
- Division of Conservation Biology, Institute of Ecology and EvolutionUniversity of BernBernSwitzerland
| | - Manuel Ruedi
- Department of Mammalogy and OrnithologyNatural History Museum of GenevaGenevaSwitzerland
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10
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Balbi M, Ernoult A, Poli P, Madec L, Guiller A, Martin MC, Nabucet J, Beaujouan V, Petit EJ. Functional connectivity in replicated urban landscapes in the land snail (Cornu aspersum). Mol Ecol 2018; 27:1357-1370. [PMID: 29412498 DOI: 10.1111/mec.14521] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/16/2018] [Accepted: 01/29/2018] [Indexed: 12/11/2022]
Abstract
Urban areas are highly fragmented and thereby exert strong constraints on individual dispersal. Despite this, some species manage to persist in urban areas, such as the garden snail, Cornu aspersum, which is common in cityscapes despite its low mobility. Using landscape genetic approaches, we combined study area replication and multiscale analysis to determine how landscape composition, configuration and connectivity influence snail dispersal across urban areas. At the overall landscape scale, areas with a high percentage of roads decreased genetic differentiation between populations. At the population scale, genetic differentiation was positively linked with building surface, the proportion of borders where wooded patches and roads appeared side by side and the proportion of borders combining wooded patches and other impervious areas. Analyses based on pairwise genetic distances validated the isolation-by-distance and isolation-by-resistance models for this land snail, with an equal fit to least-cost paths and circuit-theory-based models. Each of the 12 landscapes analysed separately yielded specific relations to environmental features, whereas analyses integrating all replicates highlighted general common effects. Our results suggest that urban transport infrastructures facilitate passive snail dispersal. At a local scale, corresponding to active dispersal, unfavourable habitats (wooded and impervious areas) isolate populations. This work upholds the use of replicated landscapes to increase the generalizability of landscape genetics results and shows how multiscale analyses provide insight into scale-dependent processes.
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Affiliation(s)
- Manon Balbi
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Aude Ernoult
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Pedro Poli
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Luc Madec
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Annie Guiller
- Edysan FRE 3498, CNRS, Université de Picardie Jules Vernes, Amiens, France
| | - Marie-Claire Martin
- UMR 6553 Ecosystems, Biodiversity, Evolution (Ecobio), CNRS, Université Rennes 1, Rennes, France
| | - Jean Nabucet
- UMR LETG, CNRS, Université de Rennes 2, Rennes Cedex, France
| | | | - Eric J Petit
- ESE, Ecology and Ecosystem Health, INRA, Rennes, France
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11
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Razgour O, Taggart JB, Manel S, Juste J, Ibáñez C, Rebelo H, Alberdi A, Jones G, Park K. An integrated framework to identify wildlife populations under threat from climate change. Mol Ecol Resour 2018; 18:18-31. [PMID: 28649779 PMCID: PMC6849758 DOI: 10.1111/1755-0998.12694] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Revised: 06/14/2017] [Accepted: 06/16/2017] [Indexed: 11/29/2022]
Abstract
Climate change is a major threat to global biodiversity that will produce a range of new selection pressures. Understanding species responses to climate change requires an interdisciplinary perspective, combining ecological, molecular and environmental approaches. We propose an applied integrated framework to identify populations under threat from climate change based on their extent of exposure, inherent sensitivity due to adaptive and neutral genetic variation and range shift potential. We consider intraspecific vulnerability and population-level responses, an important but often neglected conservation research priority. We demonstrate how this framework can be applied to vertebrates with limited dispersal abilities using empirical data for the bat Plecotus austriacus. We use ecological niche modelling and environmental dissimilarity analysis to locate areas at high risk of exposure to future changes. Combining outlier tests with genotype-environment association analysis, we identify potential climate-adaptive SNPs in our genomic data set and differences in the frequency of adaptive and neutral variation between populations. We assess landscape connectivity and show that changing environmental suitability may limit the future movement of individuals, thus affecting both the ability of populations to shift their distribution to climatically suitable areas and the probability of evolutionary rescue through the spread of adaptive genetic variation among populations. Therefore, a better understanding of movement ecology and landscape connectivity is needed for predicting population persistence under climate change. Our study highlights the importance of incorporating genomic data to determine sensitivity, adaptive potential and range shift potential, instead of relying solely on exposure to guide species vulnerability assessments and conservation planning.
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Affiliation(s)
- Orly Razgour
- Biological SciencesUniversity of SouthamptonSouthamptonUK
- School of Biological SciencesUniversity of BristolBristolUK
- Biological & Environmental SciencesUniversity of StirlingStirlingUK
| | | | - Stephanie Manel
- EPHEPSL Research UniversityCNRSUMSupAgroINDINRAUMR 5175 CEFEMontpellierFrance
| | | | | | - Hugo Rebelo
- School of Biological SciencesUniversity of BristolBristolUK
- Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto (CIBIO/UP)VairãoPortugal
| | - Antton Alberdi
- Natural History Museum of DenmarkUniversity of CopenhagenCopenhagen KDenmark
| | - Gareth Jones
- School of Biological SciencesUniversity of BristolBristolUK
| | - Kirsty Park
- Biological & Environmental SciencesUniversity of StirlingStirlingUK
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12
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Centeno-Cuadros A, Hulva P, Romportl D, Santoro S, Stříbná T, Shohami D, Evin A, Tsoar A, Benda P, Horáček I, Nathan R. Habitat use, but not gene flow, is influenced by human activities in two ecotypes of Egyptian fruit bat (Rousettus aegyptiacus). Mol Ecol 2017; 26:6224-6237. [DOI: 10.1111/mec.14365] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 09/05/2017] [Indexed: 12/20/2022]
Affiliation(s)
- A. Centeno-Cuadros
- Movement Ecology Laboratory; Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences; Hebrew University of Jerusalem; Jerusalem Israel
- Department of Molecular Biology and Biochemical Engineering; University Pablo de Olavide; Sevilla Spain
| | - P. Hulva
- Department of Zoology; Charles University; Prague Czech Republic
- Department of Biology and Ecology; University of Ostrava; Ostrava Czech Republic
| | - D. Romportl
- Department of Physical Geography and Geoecology; Charles University in Prague; Prague Czech Republic
| | - S. Santoro
- Department of Molecular Biology and Biochemical Engineering; University Pablo de Olavide; Sevilla Spain
- Department of Ethology and Biodiversity Conservation; Estación Biológica de Doñana (CSIC); Seville Spain
| | - T. Stříbná
- Department of Zoology; Charles University; Prague Czech Republic
| | - D. Shohami
- Movement Ecology Laboratory; Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences; Hebrew University of Jerusalem; Jerusalem Israel
| | - A. Evin
- Institut des Sciences de l'Evolution; Université de Montpellier; Montpellier France
| | - A. Tsoar
- Movement Ecology Laboratory; Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences; Hebrew University of Jerusalem; Jerusalem Israel
| | - P. Benda
- Department of Zoology; Charles University; Prague Czech Republic
- Department of Zoology; National Museum (Natural History); Prague Czech Republic
| | - I. Horáček
- Department of Zoology; Charles University; Prague Czech Republic
| | - R. Nathan
- Movement Ecology Laboratory; Department of Ecology, Evolution and Behavior; Alexander Silberman Institute of Life Sciences; Hebrew University of Jerusalem; Jerusalem Israel
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13
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Davy CM, Donaldson ME, Rico Y, Lausen CL, Dogantzis K, Ritchie K, Willis CK, Burles DW, Jung TS, McBurney S, Park A, McAlpine DF, Vanderwolf KJ, Kyle CJ. Prelude to a panzootic: Gene flow and immunogenetic variation in northern little brown myotis vulnerable to bat white-nose syndrome. Facets (Ott) 2017. [DOI: 10.1139/facets-2017-0022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The fungus that causes bat white-nose syndrome (WNS) recently leaped from eastern North America to the Pacific Coast. The pathogen’s spread is associated with the genetic population structure of a host ( Myotis lucifugus). To understand the fine-scale neutral and immunogenetic variation among northern populations of M. lucifugus, we sampled 1142 individuals across the species’ northern range. We used genotypes at 11 microsatellite loci to reveal the genetic structure of, and directional gene flow among, populations to predict the likely future spread of the pathogen in the northwest and to estimate effective population size ( Ne). We also pyrosequenced the DRB1-like exon 2 of the class II major histocompatibility complex (MHC) in 160 individuals to explore immunogenetic selection by WNS. We identified three major neutral genetic clusters: Eastern, Montane Cordillera (and adjacent sampling areas), and Haida Gwaii, with admixture at intermediate areas and significant substructure west of the prairies. Estimates of Ne were unexpectedly low (289–16 000). Haida Gwaii may provide temporary refuge from WNS, but the western mountain ranges are not barriers to its dispersal in M. lucifugus and are unlikely to slow its spread. Our major histocompatibility complex (MHC) data suggest potential selection by WNS on the MHC, but gene duplication limited the immunogenetic analyses.
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Affiliation(s)
- Christina M. Davy
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
- Department of Biology, University of Winnipeg, 515 Portage Avenue, Winnipeg, MB R3B 2E9, Canada
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON K9J 7B8, Canada
| | - Michael E. Donaldson
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON K9J 7B8, Canada
- Forensic Science Department, Trent University, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - Yessica Rico
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
- Catedrático CONACYT, Instituto de Ecología A.C., Centro Regional del Bajío, Avenida Lázaro Cárdenas 253, Pátzcuaro, Michoacán 61600, México
| | - Cori L. Lausen
- Wildlife Conservation Society Canada, P.O. Box 606, Kaslo, BC V0G 1M0, Canada
| | - Kathleen Dogantzis
- Forensic Science Department, Trent University, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - Kyle Ritchie
- Forensic Science Department, Trent University, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
| | - Craig K.R. Willis
- Department of Biology, University of Winnipeg, 515 Portage Avenue, Winnipeg, MB R3B 2E9, Canada
| | - Douglas W. Burles
- Gwaii Haanas National Park Reserve/Haida Heritage Site, P.O. Box 37, Queen Charlotte City, BC V0T 1S0, Canada
| | - Thomas S. Jung
- Yukon Department of Environment, P.O. Box 2703, Whitehorse, YT Y1A 2C6, Canada
| | - Scott McBurney
- Canadian Wildlife Health Cooperative, Atlantic Region, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, PEI C1A 4P3, Canada
| | - Allysia Park
- Canadian Wildlife Health Cooperative, Atlantic Region, Atlantic Veterinary College, University of Prince Edward Island, 550 University Avenue, Charlottetown, PEI C1A 4P3, Canada
| | - Donald F. McAlpine
- New Brunswick Museum, 277 Douglas Avenue, Saint John, NB E2K 1E5, Canada
| | - Karen J. Vanderwolf
- New Brunswick Museum, 277 Douglas Avenue, Saint John, NB E2K 1E5, Canada
- Canadian Wildlife Federation, 350 Promenade Michael Cowpland Drive, Kanata, ON K2M 2G4, Canada
| | - Christopher J. Kyle
- Wildlife Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, ON K9J 7B8, Canada
- Forensic Science Department, Trent University, 2140 East Bank Drive, Peterborough, ON K9J 7B8, Canada
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14
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Cleary KA, Waits LP, Finegan B. Comparative landscape genetics of two frugivorous bats in a biological corridor undergoing agricultural intensification. Mol Ecol 2017; 26:4603-4617. [PMID: 28672105 DOI: 10.1111/mec.14230] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 06/05/2017] [Indexed: 01/18/2023]
Abstract
Agricultural intensification in tropical landscapes poses a new threat to the ability of biological corridors to maintain functional connectivity for native species. We use a landscape genetics approach to evaluate impacts of expanding pineapple plantations on two widespread and abundant frugivorous bats in a biological corridor in Costa Rica. We hypothesize that the larger, more mobile Artibeus jamaicensis will be less impacted by pineapple than the smaller Carollia castanea. In 2012 and 2013, we sampled 735 bats in 26 remnant forest patches surrounded by different proportions of forest, pasture, crops and pineapple. We used 10 microsatellite loci for A. jamaicensis and 16 microsatellite loci for C. castanea to estimate genetic diversity and gene flow. Canonical correspondence analyses indicate that land cover type surrounding patches has no impact on genetic diversity of A. jamaicensis. However, for C. castanea, both percentage forest and pineapple surrounding patches explained a significant proportion of the variation in genetic diversity. Least-cost transect analyses (LCTA) and pairwise G″st suggest that for A. jamaicensis, pineapple is more permeable to gene flow than expected, while as expected, forest is the most permeable land cover for gene flow of C. castanea. For both species, LCTA indicate that development may play a role in inhibiting gene flow. The current study answers the call for landscape genetic research focused on tropical and agricultural landscapes, highlights the value of comparative landscape genetics in biological corridor design and management and is one of the few studies of biological corridors in any ecosystem to implement a genetic approach to test corridor efficacy.
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Affiliation(s)
- Katherine A Cleary
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA.,Department of Biology, Clarkson University, Potsdam, NY, USA
| | - Lisette P Waits
- Department of Fish and Wildlife Sciences, University of Idaho, Moscow, ID, USA
| | - Bryan Finegan
- Forests, Biodiversity and Climate Change Program, CATIE, Turrialba, Cartago, Costa Rica
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15
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Dool SE, Puechmaille SJ, Kelleher C, McAney K, Teeling EC. The Effects of Human-Mediated Habitat Fragmentation on a Sedentary Woodland-Associated Species (Rhinolophus hipposideros) at Its Range Margin. ACTA CHIROPTEROLOGICA 2016. [DOI: 10.3161/15081109acc2016.18.2.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Serena E. Dool
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Sébastien J. Puechmaille
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
| | - Conor Kelleher
- Spring Lane, Carrigagulla, Ballinagree, Macroom, County Cork, Ireland
| | - Kate McAney
- The Vincent Wildlife Trust, Donaghpatrick, Headford, County Galway, Ireland
| | - Emma C. Teeling
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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16
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Petit EJ, Puechmaille SJ. Will reduced host connectivity curb the spread of a devastating epidemic? Mol Ecol 2016; 24:5491-4. [PMID: 26769309 DOI: 10.1111/mec.13406] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 09/18/2015] [Accepted: 09/21/2015] [Indexed: 01/01/2023]
Abstract
The white-nose syndrome (WNS), caused by the fungal pathogen Pseudogymnoascus destructans, is threatening the cave-dwelling bat fauna of North America by killing individuals by the thousands in hibernacula each winter since its appearance in New York State less than ten years ago. Epidemiological models predict that WNS will reach the western coast of the USA by 2035, potentially eliminating most populations of susceptible bat species in its path (Frick et al. 2015; O'Regan et al. 2015). These models were built and validated using distributional data from the early years of the epidemic, which spread throughout eastern North America following a route driven by cave density and winter severity (Maher et al. 2012). In this issue of Molecular Ecology, Wilder et al. (2015) refine these findings by showing that connectivity among host populations, as assessed by population genetic markers, is crucial in determining the spread of the pathogen. Because host connectivity is much reduced in the hitherto disease free western half of North America, Wilder et al. make the reassuring prediction that the disease will spread more slowly west of the Great Plains.
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Affiliation(s)
- Eric J Petit
- INRA, Agrocampus-Ouest, UMR Ecologie et Santé des Ecosystèmes, 65 rue de St-Brieuc, 35042 Rennes cedex, France
| | - Sebastien J Puechmaille
- Zoological Institute & Museum, Ernst-Moritz-Arndt University, Johann Sebastian Bach-Str. 11/12, 17489 Greifswald, Germany.,UCD School of Biology and Environmental Science, University College Dublin, Belfield, D4 Dublin, Ireland
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17
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Dool SE, O’Donnell CFJ, Monks JM, Puechmaille SJ, Kerth G. Phylogeographic-based conservation implications for the New Zealand long-tailed bat, (Chalinolobus tuberculatus): identification of a single ESU and a candidate population for genetic rescue. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0844-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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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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19
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Razgour O. Beyond species distribution modeling: A landscape genetics approach to investigating range shifts under future climate change. ECOL INFORM 2015. [DOI: 10.1016/j.ecoinf.2015.05.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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20
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Razgour O, Salicini I, Ibáñez C, Randi E, Juste J. Unravelling the evolutionary history and future prospects of endemic species restricted to former glacial refugia. Mol Ecol 2015; 24:5267-83. [PMID: 26346923 DOI: 10.1111/mec.13379] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 09/03/2015] [Accepted: 09/04/2015] [Indexed: 11/28/2022]
Abstract
The contemporary distribution and genetic composition of biodiversity bear a signature of species' evolutionary histories and the effects of past climatic oscillations. For many European species, the Mediterranean peninsulas of Iberia, Italy and the Balkans acted as glacial refugia and the source of range recolonization, and as a result, they contain disproportionately high levels of diversity. As these areas are particularly threatened by future climate change, it is important to understand how past climatic changes affected their biodiversity. We use an integrated approach, combining markers with different evolutionary rates and combining phylogenetic analysis with approximate Bayesian computation and species distribution modelling across temporal scales. We relate phylogeographic processes to patterns of genetic variation in Myotis escalerai, a bat species endemic to the Iberian Peninsula. We found a distinct population structure at the mitochondrial level with a strong geographic signature, indicating lineage divergence into separate glacial refugia within the Iberian refugium. However, microsatellite markers suggest higher levels of gene flow resulting in more limited structure at recent time frames. The evolutionary history of M. escalerai was shaped by the effects of climatic oscillations and changes in forest cover and composition, while its future is threatened by climatically induced range contractions and the role of ecological barriers due to competition interactions in restricting its distribution. This study warns that Mediterranean peninsulas, which provided refuge for European biodiversity during past glaciation events, may become a trap for limited dispersal and ecologically limited endemic species under future climate change, resulting in loss of entire lineages.
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Affiliation(s)
- Orly Razgour
- Division of Biological and Environmental Sciences, School of Natural Sciences, University of Stirling, Stirling, Scotland, FK9 4LA, UK
| | - Irene Salicini
- Estación Biológica de Doñana (CSIC), Avda Americo Vespucio s/n, 41092, Seville, Spain
| | - Carlos Ibáñez
- Estación Biológica de Doñana (CSIC), Avda Americo Vespucio s/n, 41092, Seville, Spain
| | - Ettore Randi
- Laboratorio di Genetica, Istituto Superiore per la Protezione e Ricerca Ambientale, Via Ca' Fornacetta 9, Ozzano dell' Emilia, Bologna, Italy.,Department 18/ Section of Environmental Engineering, Aalborg University, Sohngårdsholmsvej 57, 9000, Aalborg, Denmark
| | - Javier Juste
- Estación Biológica de Doñana (CSIC), Avda Americo Vespucio s/n, 41092, Seville, Spain
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21
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Row JR, Oyler-McCance SJ, Fike JA, O'Donnell MS, Doherty KE, Aldridge CL, Bowen ZH, Fedy BC. Landscape characteristics influencing the genetic structure of greater sage-grouse within the stronghold of their range: a holistic modeling approach. Ecol Evol 2015; 5:1955-69. [PMID: 26045948 PMCID: PMC4449751 DOI: 10.1002/ece3.1479] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 02/23/2015] [Accepted: 03/05/2015] [Indexed: 11/09/2022] Open
Abstract
Given the significance of animal dispersal to population dynamics and geographic variability, understanding how dispersal is impacted by landscape patterns has major ecological and conservation importance. Speaking to the importance of dispersal, the use of linear mixed models to compare genetic differentiation with pairwise resistance derived from landscape resistance surfaces has presented new opportunities to disentangle the menagerie of factors behind effective dispersal across a given landscape. Here, we combine these approaches with novel resistance surface parameterization to determine how the distribution of high- and low-quality seasonal habitat and individual landscape components shape patterns of gene flow for the greater sage-grouse (Centrocercus urophasianus) across Wyoming. We found that pairwise resistance derived from the distribution of low-quality nesting and winter, but not summer, seasonal habitat had the strongest correlation with genetic differentiation. Although the patterns were not as strong as with habitat distribution, multivariate models with sagebrush cover and landscape ruggedness or forest cover and ruggedness similarly had a much stronger fit with genetic differentiation than an undifferentiated landscape. In most cases, landscape resistance surfaces transformed with 17.33-km-diameter moving windows were preferred, suggesting small-scale differences in habitat were unimportant at this large spatial extent. Despite the emergence of these overall patterns, there were differences in the selection of top models depending on the model selection criteria, suggesting research into the most appropriate criteria for landscape genetics is required. Overall, our results highlight the importance of differences in seasonal habitat preferences to patterns of gene flow and suggest the combination of habitat suitability modeling and linear mixed models with our resistance parameterization is a powerful approach to discerning the effects of landscape on gene flow.
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Affiliation(s)
- Jeffrey R Row
- Environment and Resource Studies, University of Waterloo Waterloo, Ontario, Canada
| | | | | | | | | | | | | | - Bradley C Fedy
- Environment and Resource Studies, University of Waterloo Waterloo, Ontario, Canada
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