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Hohwieler KR, Villiers DL, Cristescu RH, Frere CH. Genetic erosion detected in a specialist mammal living in a fast‐developing environment. CONSERVATION SCIENCE AND PRACTICE 2022. [DOI: 10.1111/csp2.12738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Katrin R. Hohwieler
- Global Change Ecology Research Group University of the Sunshine Coast, School of Science, Technology and Engineering Sippy Down Queensland Australia
| | | | - Romane H. Cristescu
- Global Change Ecology Research Group University of the Sunshine Coast, School of Science, Technology and Engineering Sippy Down Queensland Australia
| | - Celine H. Frere
- School of Biological Sciences University of Queensland St Lucia QLD Australia
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2
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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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3
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Assessing the influence of the amount of reachable habitat on genetic structure using landscape and genetic graphs. Heredity (Edinb) 2022; 128:120-131. [PMID: 34963701 PMCID: PMC8814055 DOI: 10.1038/s41437-021-00495-w] [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: 07/05/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 02/03/2023] Open
Abstract
Genetic structure, i.e. intra-population genetic diversity and inter-population genetic differentiation, is influenced by the amount and spatial configuration of habitat. Measuring the amount of reachable habitat (ARH) makes it possible to describe habitat patterns by considering intra-patch and inter-patch connectivity, dispersal capacities and matrix resistance. Complementary ARH metrics computed under various resistance scenarios are expected to reflect both drift and gene flow influence on genetic structure. Using an empirical genetic dataset concerning the large marsh grasshopper (Stethophyma grossum), we tested whether ARH metrics are good predictors of genetic structure. We further investigated (i) how the components of the ARH influence genetic structure and (ii) which resistance scenario best explains these relationships. We computed local genetic diversity and genetic differentiation indices in genetic graphs, and ARH metrics in the unified and flexible framework offered by landscape graphs, and we tested the relationships between these variables. ARH metrics were relevant predictors of the two components of genetic structure, providing an advantage over commonly used habitat metrics. Although allelic richness was significantly explained by three complementary ARH metrics in the best PLS regression model, private allelic richness and MIW indices were essentially related with the ARH measured outside the focal patch. Considering several matrix resistance scenarios was also key for explaining the different genetic responses. We thus call for further use of ARH metrics in landscape genetics to explain the influence of habitat patterns on the different components of genetic structure.
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4
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Kunz F, Klinga P, Sittenthaler M, Schebeck M, Stauffer C, Grünschachner‐Berger V, Hackländer K, Nopp‐Mayr U. Assessment of drivers of spatial genetic variation of a ground-dwelling bird species and its implications for conservation. Ecol Evol 2022; 12:e8460. [PMID: 35127012 PMCID: PMC8796917 DOI: 10.1002/ece3.8460] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/29/2022] Open
Abstract
In modern wildlife ecology, spatial population genetic methods are becoming increasingly applied. Especially for animal species in fragmented landscapes, preservation of gene flow becomes a high priority target in order to restore genetic diversity and prevent local extinction. Within Central Europe, the Alps represent the core distribution area of the black grouse, Lyrurus tetrix. At its easternmost Alpine range, events of subpopulation extinction have already been documented in the past decades. Molecular data combined with spatial analyses can help to assess landscape effects on genetic variation and therefore can be informative for conservation management. Here, we addressed whether the genetic pattern of the easternmost Alpine black grouse metapopulation system is driven by isolation by distance or isolation by resistance. Correlative ecological niche modeling was used to assess geographic distances and landscape resistances. We then applied regression-based approaches combined with population genetic analyses based on microsatellite data to disentangle effects of isolation by distance and isolation by resistance among individuals and subpopulations. Although population genetic analyses revealed overall low levels of genetic differentiation, the ecological niche modeling showed subpopulations to be clearly delimited by habitat structures. Spatial genetic variation could be attributed to effects of isolation by distance among individuals and isolation by resistance among subpopulations, yet unknown effects might factor in. The easternmost subpopulation was the most differentiated, and at the same time, immigration was not detected; hence, its long-term survival might be threatened. Our study provides valuable insights into the spatial genetic variation of this small-scale metapopulation system of Alpine black grouse.
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Affiliation(s)
- Florian Kunz
- Department of Integrative Biology and Biodiversity ResearchInstitute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life Sciences, ViennaViennaAustria
| | - Peter Klinga
- Faculty of ForestryTechnical University in ZvolenZvolenSlovakia
- DIANA ‐ Carpathian Wildlife ResearchBanská BystricaSlovakia
| | - Marcia Sittenthaler
- Department of Integrative Biology and Biodiversity ResearchInstitute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life Sciences, ViennaViennaAustria
- Central Research LaboratoriesNatural History Museum ViennaViennaAustria
| | - Martin Schebeck
- Department of Forest and Soil SciencesInstitute of Forest Entomology, Forest Pathology and Forest ProtectionUniversity of Natural Resources and Life Sciences, ViennaViennaAustria
| | - Christian Stauffer
- Department of Forest and Soil SciencesInstitute of Forest Entomology, Forest Pathology and Forest ProtectionUniversity of Natural Resources and Life Sciences, ViennaViennaAustria
| | | | - Klaus Hackländer
- Department of Integrative Biology and Biodiversity ResearchInstitute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life Sciences, ViennaViennaAustria
- German Wildlife FoundationHamburgGermany
| | - Ursula Nopp‐Mayr
- Department of Integrative Biology and Biodiversity ResearchInstitute of Wildlife Biology and Game ManagementUniversity of Natural Resources and Life Sciences, ViennaViennaAustria
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5
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Grading Evaluation of the Structural Connectivity of River System Networks Based on Ecological Functions, and a Case Study of the Baiyangdian Wetland, China. WATER 2021. [DOI: 10.3390/w13131775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
River system network (RSN) connectivity is important to maintain the environmental and ecological functions of wetlands. Quantitative evaluation of connectivity can provide crucial support for efforts to improve wetland connectivity and to restore and protect wetland ecosystems. Most existing evaluation methods uniformly generalise RSN to form an undifferentiated RSN of edges and nodes that is taken as a whole to evaluate the connectivity. However, actual RSNs comprise rivers, canals, ditches, lakes, and ponds, which differ substantially in their structures, morphologies, and attributes. The mix of RSN elements therefore defines grades that give RSNs distinctive characteristics. Moreover, RSNs with different grades perform different ranges of environmental and ecological functions. The existing evaluation methods, which have some limitations, do not account for these characteristics. To account for these differences, we examined the grade characteristics and their impact on environmental and ecological functions. We established a grading system of RSN elements and a grading method of RSN, and constructed the structural connectivity evaluation indicator system for RSNs at different grades. On this basis, we propose a method for grading evaluation of RSN connectivity. We used China’s Baiyangdian Wetland to demonstrate the use of the system and validate the results. The proposed method provided an objective and accurate evaluation of RSN connectivity and clarified the differences in connectivity among RSNs with different grades, thereby providing improved guidance for the development and maintenance of the environmental and ecological functions of RSNs.
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6
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Burgess SM, Garrick RC. The effect of sampling density and study area size on landscape genetics inferences for the Mississippi slimy salamander ( Plethodon mississippi). Ecol Evol 2021; 11:6289-6304. [PMID: 34141218 PMCID: PMC8207395 DOI: 10.1002/ece3.7481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 02/27/2021] [Accepted: 03/08/2021] [Indexed: 11/30/2022] Open
Abstract
In landscape genetics, it is largely unknown how choices regarding sampling density and study area size impact inferences upon which habitat features impede vs. facilitate gene flow. While it is recommended that sampling locations be spaced no further apart than the average individual's dispersal distance, for low-mobility species, this could lead to a challenging number of sampling locations, or an unrepresentative study area. We assessed the effects of sampling density and study area size on landscape genetic inferences for a dispersal-limited amphibian, Plethodon mississippi, via analysis of nested datasets. Microsatellite-based genetic distances among individuals were divided into three datasets representing sparse sampling across a large study area, dense sampling across a small study area, or sparse sampling across the same small study area. These datasets were a proxy for gene flow (i.e., the response variable) in maximum-likelihood population effects models that assessed the nature and strength of their relationship with each of five land-use classes (i.e., potential predictor variables). Comparisons of outcomes were based on the rank order of effect, sign of effect (i.e., gene flow resistance vs. facilitation), spatial scale of effect, and functional relationship with gene flow. The best-fit model for each dataset had the same sign of effect for hardwood forests, manmade structures, and pine forests, indicating the impacts of these land-use classes on dispersal and gene flow in P. mississippi are robust to sampling scheme. Contrasting sampling densities led to a different inferred functional relationship between agricultural areas and gene flow. Study area size appeared to influence the scale of effect of manmade structures and the sign of effect of pine forests. Our findings provided evidence for an influence of sampling density, study area size, and sampling effort upon inferences. Accordingly, we recommend iterative subsampling of empirical datasets and continued investigation into the sensitivities of landscape genetic analyses using simulations.
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7
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Isolation-by-distance and male-biased dispersal at a fine spatial scale: a study of the common European adder (Vipera berus) in a rural landscape. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01365-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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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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Savary P, Foltête J, Moal H, Vuidel G, Garnier S. graph4lg: A package for constructing and analysing graphs for landscape genetics in R. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13530] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Paul Savary
- ARP‐Astrance Paris France
- ThéMA UMR 6049 CNRSUniversité Bourgogne‐Franche‐Comté Besançon Cedex France
- Biogéosciences UMR 6282 CNRSUniversité Bourgogne‐Franche‐Comté Dijon France
| | | | | | - Gilles Vuidel
- ThéMA UMR 6049 CNRSUniversité Bourgogne‐Franche‐Comté Besançon Cedex France
| | - Stéphane Garnier
- Biogéosciences UMR 6282 CNRSUniversité Bourgogne‐Franche‐Comté Dijon France
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10
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Marie-Jeanne V, Bonnot F, Thébaud G, Peccoud J, Labonne G, Sauvion N. Multi-scale spatial genetic structure of the vector-borne pathogen 'Candidatus Phytoplasma prunorum' in orchards and in wild habitats. Sci Rep 2020; 10:5002. [PMID: 32193489 PMCID: PMC7081303 DOI: 10.1038/s41598-020-61908-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/31/2020] [Indexed: 11/08/2022] Open
Abstract
Inferring the dispersal processes of vector-borne plant pathogens is a great challenge because the plausible epidemiological scenarios often involve complex spread patterns at multiple scales. The spatial genetic structure of 'Candidatus Phytoplasma prunorum', responsible for European stone fruit yellows disease, was investigated by the application of a combination of statistical approaches to genotype data of the pathogen sampled from cultivated and wild compartments in three French Prunus-growing regions. This work revealed that the prevalence of the different genotypes is highly uneven both between regions and compartments. In addition, we identified a significant clustering of similar genotypes within a radius of 50 km or less, but not between nearby wild and cultivated Prunus. We also provide evidence that infected plants are transferred between production areas, and that both species of the Cacopsylla pruni complex can spread the pathogen. Altogether, this work supports a main epidemiological scenario where 'Ca. P. prunorum' is endemic in - and generally acquired from - wild Prunus by its immature psyllid vectors. The latter then migrate to shelter plants that epidemiologically connect sites less than 50 km apart by later providing infectious mature psyllids to their "migration basins". Such multi-scale studies could be useful for other pathosystems.
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Affiliation(s)
| | - François Bonnot
- BGPI, Univ Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France
| | - Gaël Thébaud
- BGPI, Univ Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France
| | - Jean Peccoud
- BGPI, Univ Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France
- Université de Poitiers, Laboratoire Ecologie et Biologie des Interactions, (EBI-Joint Research Unit 7267, CNRS), 86000, Poitiers, France
| | - Gérard Labonne
- BGPI, Univ Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France
| | - Nicolas Sauvion
- BGPI, Univ Montpellier, INRAE, CIRAD, Institut Agro, Montpellier, France.
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11
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Dupuis JR, Cullingham CI, Nielsen SE, Sperling FAH. Environmental effects on gene flow in a species complex of vagile, hilltopping butterflies. Biol J Linn Soc Lond 2019. [DOI: 10.1093/biolinnean/blz043] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Julian R Dupuis
- Department of Plant and Environmental Protection Services, University of Hawai’i at Mānoa, Honolulu, HI, USA
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Scott E Nielsen
- Department of Renewable Resources, University of Alberta, Edmonton, Alberta Canada
| | - Felix A H Sperling
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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12
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Milanesi P, Caniglia R, Fabbri E, Puopolo F, Galaverni M, Holderegger R. Combining Bayesian genetic clustering and ecological niche modeling: Insights into wolf intraspecific genetic structure. Ecol Evol 2018; 8:11224-11234. [PMID: 30519439 PMCID: PMC6262746 DOI: 10.1002/ece3.4594] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 07/10/2018] [Accepted: 09/12/2018] [Indexed: 12/30/2022] Open
Abstract
The distribution of intraspecific genetic variation and how it relates to environmental factors is of increasing interest to researchers in macroecology and biogeography. Recent studies investigated the relationships between the environment and patterns of intraspecific genetic variation across species ranges but only few rigorously tested the relation between genetic groups and their ecological niches. We quantified the relationship of genetic differentiation (F ST) and the overlap of ecological niches (as measured by n-dimensional hypervolumes) among genetic groups resulting from spatial Bayesian genetic clustering in the wolf (Canis lupus) in the Italian peninsula. Within the Italian wolf population, four genetic clusters were detected, and these clusters showed different ecological niches. Moreover, different wolf clusters were significantly related to differences in land cover and human disturbance features. Such differences in the ecological niches of genetic clusters should be interpreted in light of neutral processes that hinder movement, dispersal, and gene flow among the genetic clusters, in order to not prematurely assume any selective or adaptive processes. In the present study, we found that both the plasticity of wolves-a habitat generalist-to cope with different environmental conditions and the occurrence of barriers that limit gene flow lead to the formation of genetic intraspecific genetic clusters and their distinct ecological niches.
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Affiliation(s)
- Pietro Milanesi
- Swiss Ornithological InstituteSempachSwitzerland
- Area per la Genetica della ConservazioneIstituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA)BolognaItaly
| | - Romolo Caniglia
- Area per la Genetica della ConservazioneIstituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA)BolognaItaly
| | - Elena Fabbri
- Area per la Genetica della ConservazioneIstituto Superiore per la Protezione e la Ricerca Ambientale (ISPRA)BolognaItaly
| | | | | | - Rolf Holderegger
- WSL Swiss Federal Research InstituteBirmensdorfSwitzerland
- Department of Environmental Systems SciencesETH ZürichZürichSwitzerland
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13
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Cayuela H, Rougemont Q, Prunier JG, Moore JS, Clobert J, Besnard A, Bernatchez L. Demographic and genetic approaches to study dispersal in wild animal populations: A methodological review. Mol Ecol 2018; 27:3976-4010. [DOI: 10.1111/mec.14848] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/17/2018] [Accepted: 08/19/2018] [Indexed: 12/31/2022]
Affiliation(s)
- Hugo Cayuela
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
| | - Quentin Rougemont
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
| | - Jérôme G. Prunier
- Station d'Ecologie Théorique et Expérimentale; Unité Mixte de Recherche (UMR) 5321; Centre National de la Recherche Scientifique (CNRS); Université Paul Sabatier (UPS); Moulis France
| | - Jean-Sébastien Moore
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
| | - Jean Clobert
- Station d'Ecologie Théorique et Expérimentale; Unité Mixte de Recherche (UMR) 5321; Centre National de la Recherche Scientifique (CNRS); Université Paul Sabatier (UPS); Moulis France
| | - Aurélien Besnard
- CNRS; PSL Research University; EPHE; UM, SupAgro, IRD; INRA; UMR 5175 CEFE; Montpellier France
| | - Louis Bernatchez
- Institut de Biologie Intégrative et des Systèmes (IBIS); Université Laval; Québec City Québec Canada
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14
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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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15
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Schregel J, Remm J, Eiken HG, Swenson JE, Saarma U, Hagen SB. Multi‐level patterns in population genetics: Variogram series detects a hidden isolation‐by‐distance‐dominated structure of Scandinavian brown bears
Ursus arctos. Methods Ecol Evol 2018. [DOI: 10.1111/2041-210x.12980] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Julia Schregel
- Norwegian Institute of Bioeconomy ResearchNIBIO ‐ Svanhovd Svanvik Norway
- Faculty of Environmental Science and Natural Resource ManagementNorwegian University of Life Sciences Ǻs Norway
| | - Jaanus Remm
- Department of ZoologyInstitute of Ecology and Earth SciencesUniversity of Tartu Tartu Estonia
| | - Hans Geir Eiken
- Norwegian Institute of Bioeconomy ResearchNIBIO ‐ Svanhovd Svanvik Norway
| | - Jon E. Swenson
- Faculty of Environmental Science and Natural Resource ManagementNorwegian University of Life Sciences Ǻs Norway
- Norwegian Institute for Nature Research Trondheim Norway
| | - Urmas Saarma
- Department of ZoologyInstitute of Ecology and Earth SciencesUniversity of Tartu Tartu Estonia
| | - Snorre B. Hagen
- Norwegian Institute of Bioeconomy ResearchNIBIO ‐ Svanhovd Svanvik Norway
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16
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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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17
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Haran JM, Rossi JP, Pajares J, Bonifacio L, Naves P, Roques A, Roux G. Multi-scale and multi-site resampling of a study area in spatial genetics: implications for flying insect species. PeerJ 2017; 5:e4135. [PMID: 29259842 PMCID: PMC5733902 DOI: 10.7717/peerj.4135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 11/14/2017] [Indexed: 11/25/2022] Open
Abstract
The use of multiple sampling areas in landscape genetic analysis has been recognized as a useful way of generalizing the patterns of environmental effects on organism gene flow. It reduces the variability in inference which can be substantially affected by the scale of the study area and its geographic location. However, empirical landscape genetic studies rarely consider multiple sampling areas due to the sampling effort required. In this study, we explored the effects of environmental features on the gene flow of a flying long-horned beetle (Monochamus galloprovincialis) using a landscape genetics approach. To account for the unknown scale of gene flow and the multiple local confounding effects of evolutionary history and landscape changes on inference, we developed a way of resampling study areas on multiple scales and in multiple locations (sliding windows) in a single large-scale sampling design. Landscape analyses were conducted in 3*104 study areas ranging in scale from 220 to 1,000 km and spread over 132 locations on the Iberian Peninsula. The resampling approach made it possible to identify the features affecting the gene flow of this species but also showed high variability in inference among the scales and the locations tested, independent of the variation in environmental features. This method provides an opportunity to explore the effects of environmental features on organism gene flow on the whole and reach conclusions about general landscape effects on their dispersal, while limiting the sampling effort to a reasonable level.
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Affiliation(s)
- Julien M. Haran
- UR633 Zoologie Forestière, INRA, Orléans, France
- CBGP, CIRAD, Montpellier SupAgro, INRA, IRD, Univ. Montpellier, Montpellier, France CIRAD, CBGP, Montpellier, France
| | - Jean-Pierre Rossi
- CBGP, INRA, CIRAD, IRD, Montpellier SupAgro, Univ. Montpellier, INRA, Montpellier, France
| | - Juan Pajares
- Sustainable Forest Management Res Inst, Universidad de Valladolid, Palencia, Spain
| | - Luis Bonifacio
- Instituto Nacional de Investigacao Agraria e Veterinaria, INIAV, Oeiras, Portugal
| | - Pedro Naves
- Instituto Nacional de Investigacao Agraria e Veterinaria, INIAV, Oeiras, Portugal
| | - Alain Roques
- UR633 Zoologie Forestière, INRA, Orléans, France
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18
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van Strien MJ. Consequences of population topology for studying gene flow using link-based landscape genetic methods. Ecol Evol 2017; 7:5070-5081. [PMID: 28770047 PMCID: PMC5528204 DOI: 10.1002/ece3.3075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/29/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022] Open
Abstract
Many landscape genetic studies aim to determine the effect of landscape on gene flow between populations. These studies frequently employ link‐based methods that relate pairwise measures of historical gene flow to measures of the landscape and the geographical distance between populations. However, apart from landscape and distance, there is a third important factor that can influence historical gene flow, that is, population topology (i.e., the arrangement of populations throughout a landscape). As the population topology is determined in part by the landscape configuration, I argue that it should play a more prominent role in landscape genetics. Making use of existing literature and theoretical examples, I discuss how population topology can influence results in landscape genetic studies and how it can be taken into account to improve the accuracy of these results. In support of my arguments, I have performed a literature review of landscape genetic studies published during the first half of 2015 as well as several computer simulations of gene flow between populations. First, I argue why one should carefully consider which population pairs should be included in link‐based analyses. Second, I discuss several ways in which the population topology can be incorporated in response and explanatory variables. Third, I outline why it is important to sample populations in such a way that a good representation of the population topology is obtained. Fourth, I discuss how statistical testing for link‐based approaches could be influenced by the population topology. I conclude the article with six recommendations geared toward better incorporating population topology in link‐based landscape genetic studies.
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Affiliation(s)
- Maarten J van Strien
- Planning of Landscape and Urban Systems (PLUS) Institute for Spatial and Landscape Planning ETH Zurich Zürich Switzerland
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19
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Richardson JL, Burak MK, Hernandez C, Shirvell JM, Mariani C, Carvalho‐Pereira TSA, Pertile AC, Panti‐May JA, Pedra GG, Serrano S, Taylor J, Carvalho M, Rodrigues G, Costa F, Childs JE, Ko AI, Caccone A. Using fine-scale spatial genetics of Norway rats to improve control efforts and reduce leptospirosis risk in urban slum environments. Evol Appl 2017; 10:323-337. [PMID: 28352293 PMCID: PMC5367079 DOI: 10.1111/eva.12449] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/24/2016] [Indexed: 12/27/2022] Open
Abstract
The Norway rat (Rattus norvegicus) is a key pest species globally and responsible for seasonal outbreaks of the zoonotic bacterial disease leptospirosis in the tropics. The city of Salvador, Brazil, has seen recent and dramatic increases in human population residing in slums, where conditions foster high rat density and increasing leptospirosis infection rates. Intervention campaigns have been used to drastically reduce rat numbers. In planning these interventions, it is important to define the eradication units - the spatial scale at which rats constitute continuous populations and from where rats are likely recolonizing, post-intervention. To provide this information, we applied spatial genetic analyses to 706 rats collected across Salvador and genotyped at 16 microsatellite loci. We performed spatially explicit analyses and estimated migration levels to identify distinct genetic units and landscape features associated with genetic divergence at different spatial scales, ranging from valleys within a slum community to city-wide analyses. Clear genetic breaks exist between rats not only across Salvador but also between valleys of slums separated by <100 m-well within the dispersal capacity of rats. The genetic data indicate that valleys may be considered separate units and identified high-traffic roads as strong impediments to rat movement. Migration data suggest that most (71-90%) movement is contained within valleys, with no clear source population contributing to migrant rats. We use these data to recommend eradication units and discuss the importance of carrying out individual-based analyses at different spatial scales in urban landscapes.
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Affiliation(s)
| | - Mary K. Burak
- Department of BiologyProvidence CollegeProvidenceRIUSA
| | | | - James M. Shirvell
- Department of Ecology & Evolutionary BiologyYale UniversityNew HavenCTUSA
| | - Carol Mariani
- Department of Ecology & Evolutionary BiologyYale UniversityNew HavenCTUSA
| | | | - Arsinoê C. Pertile
- Centro de Pesquisas Gonçalo MonizFundação Oswaldo CruzMinistério da SaúdeSalvadorBrazil
| | - Jesus A. Panti‐May
- Centro de Pesquisas Gonçalo MonizFundação Oswaldo CruzMinistério da SaúdeSalvadorBrazil
| | - Gabriel G. Pedra
- Centro de Pesquisas Gonçalo MonizFundação Oswaldo CruzMinistério da SaúdeSalvadorBrazil
| | - Soledad Serrano
- Centro de Pesquisas Gonçalo MonizFundação Oswaldo CruzMinistério da SaúdeSalvadorBrazil
| | - Josh Taylor
- Centro de Pesquisas Gonçalo MonizFundação Oswaldo CruzMinistério da SaúdeSalvadorBrazil
| | - Mayara Carvalho
- Centro de Pesquisas Gonçalo MonizFundação Oswaldo CruzMinistério da SaúdeSalvadorBrazil
| | - Gorete Rodrigues
- Centro de Controle de ZoonosesSecretaria Municipal de SaúdeMinistério da SaúdeSalvadorBrazil
| | - Federico Costa
- Instituto de Saúde ColetivaUniversidade Federal da Bahia, UFBASalvadorBrazil
| | - James E. Childs
- Department of Epidemiology of Microbial DiseaseYale School of Public HealthNew HavenCTUSA
| | - Albert I. Ko
- Centro de Pesquisas Gonçalo MonizFundação Oswaldo CruzMinistério da SaúdeSalvadorBrazil
- Department of Epidemiology of Microbial DiseaseYale School of Public HealthNew HavenCTUSA
| | - Adalgisa Caccone
- Department of Ecology & Evolutionary BiologyYale UniversityNew HavenCTUSA
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20
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Noguerales V, Cordero PJ, Ortego J. Testing the role of ancient and contemporary landscapes on structuring genetic variation in a specialist grasshopper. Ecol Evol 2017; 7:3110-3122. [PMID: 28480010 PMCID: PMC5415511 DOI: 10.1002/ece3.2810] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 12/31/2016] [Accepted: 01/24/2017] [Indexed: 12/19/2022] Open
Abstract
Understanding the processes underlying spatial patterns of genetic diversity and structure of natural populations is a central topic in evolutionary biogeography. In this study, we combine data on ancient and contemporary landscape composition to get a comprehensive view of the factors shaping genetic variation across the populations of the scrub‐legume grasshopper (Chorthippus binotatus binotatus) from the biogeographically complex region of southeast Iberia. First, we examined geographical patterns of genetic structure and employed an approximate Bayesian computation (ABC) approach to compare different plausible scenarios of population divergence. Second, we used a landscape genetic framework to test for the effects of (1) Late Miocene paleogeography, (2) Pleistocene climate fluctuations, and (3) contemporary topographic complexity on the spatial patterns of population genetic differentiation. Genetic structure and ABC analyses supported the presence of three genetic clusters and a sequential west‐to‐east splitting model that predated the last glacial maximum (LGM, c. 21 Kya). Landscape genetic analyses revealed that population genetic differentiation was primarily shaped by contemporary topographic complexity, but was not explained by any paleogeographic scenario or resistance distances based on climate suitability in the present or during the LGM. Overall, this study emphasizes the need of integrating information on ancient and contemporary landscape composition to get a comprehensive view of their relative importance to explain spatial patterns of genetic variation in organisms inhabiting regions with complex biogeographical histories.
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Affiliation(s)
- Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM) Ciudad Real Spain
| | - Pedro J Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM) Ciudad Real Spain
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD-CSIC) Seville Spain
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21
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How is habitat connectivity affected by settlement and road network configurations? Results from simulating coupled habitat and human networks. Ecol Modell 2016. [DOI: 10.1016/j.ecolmodel.2016.09.025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Milanesi P, Holderegger R, Caniglia R, Fabbri E, Galaverni M, Randi E. Expert-based versus habitat-suitability models to develop resistance surfaces in landscape genetics. Oecologia 2016; 183:67-79. [DOI: 10.1007/s00442-016-3751-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 10/04/2016] [Indexed: 11/29/2022]
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23
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Abdel Moniem HEM, Schemerhorn BJ, DeWoody JA, Holland JD. Landscape genetics of a pollinator longhorn beetle [Typocerus v. velutinus (Olivier)] on a continuous habitat surface. Mol Ecol 2016; 25:5015-5028. [PMID: 27552358 DOI: 10.1111/mec.13819] [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: 11/07/2014] [Revised: 07/28/2016] [Accepted: 08/12/2016] [Indexed: 11/30/2022]
Abstract
Landscape connectivity, the degree to which the landscape structure facilitates or impedes organismal movement and gene flow, is increasingly important to conservationists and land managers. Metrics for describing the undulating shape of continuous habitat surfaces can expand the usefulness of continuous gradient surfaces that describe habitat and predict the flow of organisms and genes. We adopted a landscape gradient model of habitat and used surface metrics of connectivity to model the genetic continuity between populations of the banded longhorn beetle [Typocerus v. velutinus (Olivier)] collected at 17 sites across a fragmentation gradient in Indiana, USA. We tested the hypothesis that greater habitat connectivity facilitates gene flow between beetle populations against a null model of isolation by distance (IBD). We used next-generation sequencing to develop 10 polymorphic microsatellite loci and genotype the individual beetles to assess the population genetic structure. Isolation by distance did not explain the population genetic structure. The surface metrics model of habitat connectivity explained the variance in genetic dissimilarities 30 times better than the IBD model. We conclude that surface metrology of habitat maps is a powerful extension of landscape genetics in heterogeneous landscapes.
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Affiliation(s)
- H E M Abdel Moniem
- Department of Entomology, Purdue University, 901 W. State St., West Lafayette, IN, 47907, USA.,Department of Zoology, Faculty of Science, Suez Canal University, Ismailia, 41522, Egypt
| | - B J Schemerhorn
- Department of Entomology, Purdue University, 901 W. State St., West Lafayette, IN, 47907, USA
| | - J A DeWoody
- Department of Forestry and Natural Resources, Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - J D Holland
- Department of Entomology, Purdue University, 901 W. State St., West Lafayette, IN, 47907, USA.
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24
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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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25
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Noguerales V, Cordero PJ, Ortego J. Hierarchical genetic structure shaped by topography in a narrow-endemic montane grasshopper. BMC Evol Biol 2016; 16:96. [PMID: 27149952 PMCID: PMC4858822 DOI: 10.1186/s12862-016-0663-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 04/21/2016] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Understanding the underlying processes shaping spatial patterns of genetic structure in free-ranging organisms is a central topic in evolutionary biology. Here, we aim to disentangle the relative importance of neutral (i.e. genetic drift) and local adaptation (i.e. ecological divergence) processes in the evolution of spatial genetic structure of the Morales grasshopper (Chorthippus saulcyi moralesi), a narrow-endemic taxon restricted to the Central Pyrenees. More specifically, we analysed range-wide patterns of genetic structure and tested whether they were shaped by geography (isolation-by-distance, IBD), topographic complexity and present and past habitat suitability models (isolation-by-resistance, IBR), and environmental dissimilarity (isolation-by-environment, IBE). RESULTS Different clustering analyses revealed a deep genetic structure that was best explained by IBR based on topographic complexity. Our analyses did not reveal a significant role of IBE, a fact that may be due to low environmental variation among populations and/or consequence of other ecological factors not considered in this study are involved in local adaptation processes. IBR scenarios informed by current and past climate distribution models did not show either a significant impact on genetic differentiation after controlling for the effects of topographic complexity, which may indicate that they are not capturing well microhabitat structure in the present or the genetic signal left by dispersal routes defined by habitat corridors in the past. CONCLUSIONS Overall, these results indicate that spatial patterns of genetic variation in our study system are primarily explained by neutral divergence and migration-drift equilibrium due to limited dispersal across abrupt reliefs, whereas environmental variation or spatial heterogeneity in habitat suitability associated with the complex topography of the region had no significant effect on genetic discontinuities after controlling for geography. Our study highlights the importance of considering a comprehensive suite of potential isolating mechanisms and analytical approaches in order to get robust inferences on the processes promoting genetic divergence of natural populations.
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Affiliation(s)
- Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM), Ronda de Toledo 12, E-13071, Ciudad Real, Spain.
| | - Pedro J Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM), Ronda de Toledo 12, E-13071, Ciudad Real, Spain
| | - Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC), Avda. Américo Vespucio s/n, E-41092, Seville, Spain
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26
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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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27
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Milanesi P, Holderegger R, Caniglia R, Fabbri E, Randi E. Different habitat suitability models yield different least-cost path distances for landscape genetic analysis. Basic Appl Ecol 2016. [DOI: 10.1016/j.baae.2015.08.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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28
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Ortego J, García-Navas V, Noguerales V, Cordero PJ. Discordant patterns of genetic and phenotypic differentiation in five grasshopper species codistributed across a microreserve network. Mol Ecol 2015; 24:5796-812. [DOI: 10.1111/mec.13426] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 10/11/2015] [Accepted: 10/14/2015] [Indexed: 01/23/2023]
Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology; Estación Biológica de Doñana; EBD-CSIC; Avda. Américo Vespucio s/n E-41092 Seville Spain
| | - Vicente García-Navas
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM); Ronda de Toledo s/n E-13005 Ciudad Real Spain
| | - Pedro J. Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM); Ronda de Toledo s/n E-13005 Ciudad Real Spain
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29
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Johansson ML, Alberto F, Reed DC, Raimondi PT, Coelho NC, Young MA, Drake PT, Edwards CA, Cavanaugh K, Assis J, Ladah LB, Bell TW, Coyer JA, Siegel DA, Serrão EA. Seascape drivers of Macrocystis pyrifera population genetic structure in the northeast Pacific. Mol Ecol 2015; 24:4866-85. [PMID: 26339775 DOI: 10.1111/mec.13371] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 08/26/2015] [Accepted: 09/01/2015] [Indexed: 01/10/2023]
Abstract
At small spatial and temporal scales, genetic differentiation is largely controlled by constraints on gene flow, while genetic diversity across a species' distribution is shaped on longer temporal and spatial scales. We assess the hypothesis that oceanographic transport and other seascape features explain different scales of genetic structure of giant kelp, Macrocystis pyrifera. We followed a hierarchical approach to perform a microsatellite-based analysis of genetic differentiation in Macrocystis across its distribution in the northeast Pacific. We used seascape genetic approaches to identify large-scale biogeographic population clusters and investigate whether they could be explained by oceanographic transport and other environmental drivers. We then modelled population genetic differentiation within clusters as a function of oceanographic transport and other environmental factors. Five geographic clusters were identified: Alaska/Canada, central California, continental Santa Barbara, California Channel Islands and mainland southern California/Baja California peninsula. The strongest break occurred between central and southern California, with mainland Santa Barbara sites forming a transition zone between the two. Breaks between clusters corresponded approximately to previously identified biogeographic breaks, but were not solely explained by oceanographic transport. An isolation-by-environment (IBE) pattern was observed where the northern and southern Channel Islands clustered together, but not with closer mainland sites, despite the greater distance between them. The strongest environmental association with this IBE pattern was observed with light extinction coefficient, which extends suitable habitat to deeper areas. Within clusters, we found support for previous results showing that oceanographic connectivity plays an important role in the population genetic structure of Macrocystis in the Northern hemisphere.
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Affiliation(s)
- Mattias L Johansson
- Department of Biological Sciences, University of Wisconsin - Milwaukee, PO Box 413, Milwaukee, WI, 53201, USA
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Filipe Alberto
- Department of Biological Sciences, University of Wisconsin - Milwaukee, PO Box 413, Milwaukee, WI, 53201, USA
| | - Daniel C Reed
- Marine Science Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Peter T Raimondi
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Nelson C Coelho
- Department of Biological Sciences, University of Wisconsin - Milwaukee, PO Box 413, Milwaukee, WI, 53201, USA
| | - Mary A Young
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA, 95064, USA
| | - Patrick T Drake
- Ocean Sciences Department, University of California, Santa Cruz, CA, 95064, USA
| | | | - Kyle Cavanaugh
- Department of Geography, University of California, Los Angeles, CA, 90095, USA
| | - Jorge Assis
- Center of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Lydia B Ladah
- Department of Biological Oceanography, CISESE, Ensenada, C.P. 22860, Baja California, México
| | - Tom W Bell
- Earth Research Institute, University of California, Santa Barbara, CA, 93106, USA
| | - James A Coyer
- Shoals Marine Laboratory, Cornell University, Portsmouth, NH, 03801, USA
| | - David A Siegel
- Earth Research Institute, University of California, Santa Barbara, CA, 93106, USA
| | - Ester A Serrão
- Center of Marine Sciences, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
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30
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Ortego J, Aguirre MP, Noguerales V, Cordero PJ. Consequences of extensive habitat fragmentation in landscape-level patterns of genetic diversity and structure in the Mediterranean esparto grasshopper. Evol Appl 2015; 8:621-32. [PMID: 26136826 PMCID: PMC4479516 DOI: 10.1111/eva.12273] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 04/27/2015] [Indexed: 11/28/2022] Open
Abstract
Anthropogenic habitat fragmentation has altered the distribution and population sizes in many organisms worldwide. For this reason, understanding the demographic and genetic consequences of this process is necessary to predict the fate of populations and establish management practices aimed to ensure their viability. In this study, we analyse whether the spatial configuration of remnant semi-natural habitat patches within a chronically fragmented landscape has shaped the patterns of genetic diversity and structure in the habitat-specialist esparto grasshopper (Ramburiella hispanica). In particular, we predict that agricultural lands constitute barriers to gene flow and hypothesize that fragmentation has restricted interpopulation dispersal and reduced local levels of genetic diversity. Our results confirmed the expectation that isolation and habitat fragmentation have reduced the genetic diversity of local populations. Landscape genetic analyses based on circuit theory showed that agricultural land offers ∽1000 times more resistance to gene flow than semi-natural habitats, indicating that patterns of dispersal are constrained by the spatial configuration of remnant patches of suitable habitat. Overall, this study shows that semi-natural habitat patches act as corridors for interpopulation gene flow and should be preserved due to the disproportionately large ecological function that they provide considering their insignificant area within these human-modified landscapes.
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Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology, Estación Biológica de Doñana (EBD-CSIC) Seville, Spain
| | - María P Aguirre
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM) Ciudad Real, Spain
| | - Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM) Ciudad Real, Spain
| | - Pedro J Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM) Ciudad Real, Spain
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Coster SS, Babbitt KJ, Cooper A, Kovach AI. Limited influence of local and landscape factors on finescale gene flow in two pond-breeding amphibians. Mol Ecol 2015; 24:742-58. [DOI: 10.1111/mec.13062] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 12/12/2014] [Accepted: 01/02/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Stephanie S. Coster
- Department of Natural Resources and the Environment; University of New Hampshire; 114 James Hall Durham NH 03824 USA
| | - Kimberly J. Babbitt
- Department of Natural Resources and the Environment; University of New Hampshire; 114 James Hall Durham NH 03824 USA
| | - Andrew Cooper
- School of Resource and Environmental Management; Simon Fraser University; 8888 University Drive Burnaby BC V5A 1S6 Canada
| | - Adrienne I. Kovach
- Department of Natural Resources and the Environment; University of New Hampshire; 114 James Hall Durham NH 03824 USA
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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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van Strien MJ, Holderegger R, Van Heck HJ. Isolation-by-distance in landscapes: considerations for landscape genetics. Heredity (Edinb) 2015; 114:27-37. [PMID: 25052412 PMCID: PMC4815601 DOI: 10.1038/hdy.2014.62] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 05/13/2014] [Accepted: 05/27/2014] [Indexed: 11/08/2022] Open
Abstract
In landscape genetics, isolation-by-distance (IBD) is regarded as a baseline pattern that is obtained without additional effects of landscape elements on gene flow. However, the configuration of suitable habitat patches determines deme topology, which in turn should affect rates of gene flow. IBD patterns can be characterized either by monotonically increasing pairwise genetic differentiation (for example, FST) with increasing interdeme geographic distance (case-I pattern) or by monotonically increasing pairwise genetic differentiation up to a certain geographical distance beyond which no correlation is detectable anymore (case-IV pattern). We investigated if landscape configuration influenced the rate at which a case-IV pattern changed to a case-I pattern. We also determined at what interdeme distance the highest correlation was measured between genetic differentiation and geographic distance and whether this distance corresponded to the maximum migration distance. We set up a population genetic simulation study and assessed the development of IBD patterns for several habitat configurations and maximum migration distances. We show that the rate and likelihood of the transition of case-IV to case-I FST-distance relationships was strongly influenced by habitat configuration and maximum migration distance. We also found that the maximum correlation between genetic differentiation and geographic distance was not related to the maximum migration distance and was measured across all deme pairs in a case-I pattern and, for a case-IV pattern, at the distance where the FST-distance curve flattens out. We argue that in landscape genetics, separate analyses should be performed to either assess IBD or the landscape effects on gene flow.
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Affiliation(s)
- M J van Strien
- Planning of Landscape and Urban Systems, ETH Zurich, Stefano-Franscini-Platz 5, Zurich, Switzerland
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, Birmensdorf, Switzerland
| | - R Holderegger
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, Birmensdorf, Switzerland
- Department of Environmental System Sciences, ETH Zurich, Universitätsstrasse 16, Zurich, Switzerland
| | - H J Van Heck
- Earth and Ocean Sciences, Cardiff University, Main Building, Park Place, Cardiff, UK
- Institute of Earth Sciences, Utrecht University, Budapestlaan 4, Utrecht, The Netherlands
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Keller D, Holderegger R, van Strien MJ, Bolliger J. How to make landscape genetics beneficial for conservation management? CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0684-y] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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36
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Affiliation(s)
- Vincent Miele
- Laboratoire Biométrie et Biologie Evolutive; CNRS; UMR5558; Université de Lyon; Université Lyon 1 Villeurbanne F-69622 France
| | - Franck Picard
- Laboratoire Biométrie et Biologie Evolutive; CNRS; UMR5558; Université de Lyon; Université Lyon 1 Villeurbanne F-69622 France
| | - Stéphane Dray
- Laboratoire Biométrie et Biologie Evolutive; CNRS; UMR5558; Université de Lyon; Université Lyon 1 Villeurbanne F-69622 France
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Razgour O, Rebelo H, Puechmaille SJ, Juste J, Ibáñez C, Kiefer A, Burke T, Dawson DA, Jones G. Scale‐dependent effects of landscape variables on gene flow and population structure in bats. DIVERS DISTRIB 2014. [DOI: 10.1111/ddi.12200] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Orly Razgour
- School of Biological Sciences University of Bristol Woodland Rd. Bristol BS8 1UG UK
- NERC Biomolecular Analysis Facility Animal and Plant Sciences University of Sheffield Western Bank Sheffield S10 2TN UK
| | - Hugo Rebelo
- School of Biological Sciences University of Bristol Woodland Rd. Bristol BS8 1UG UK
- CIBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Campus Agrário de Vairão R. Padre Armando Quintas Vairão 4485‐661 Portugal
| | - Sébastien J. Puechmaille
- Zoological Institute & Museum Greifswald University Greifswald D‐17489 Germany
- University College Dublin School of Biological and Environmental Sciences Belfield, Dublin 4 Ireland
| | - Javier Juste
- Estación Biológica de Doñana (CSIC) Apdo 1056 Sevilla 41080 Spain
| | - Carlos Ibáñez
- Estación Biológica de Doñana (CSIC) Apdo 1056 Sevilla 41080 Spain
| | - Andreas Kiefer
- Department of Biogeography Trier University Trier D‐54286 Germany
| | - Terry Burke
- NERC Biomolecular Analysis Facility Animal and Plant Sciences University of Sheffield Western Bank Sheffield S10 2TN UK
| | - Deborah A. Dawson
- NERC Biomolecular Analysis Facility Animal and Plant Sciences University of Sheffield Western Bank Sheffield S10 2TN UK
| | - Gareth Jones
- School of Biological Sciences University of Bristol Woodland Rd. Bristol BS8 1UG UK
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van Strien MJ, Keller D, Holderegger R, Ghazoul J, Kienast F, Bolliger J. Landscape genetics as a tool for conservation planning: predicting the effects of landscape change on gene flow. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2014; 24:327-339. [PMID: 24689144 DOI: 10.1890/13-0442.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
For conservation managers, it is important to know whether landscape changes lead to increasing or decreasing gene flow. Although the discipline of landscape genetics assesses the influence of landscape elements on gene flow, no studies have yet used landscape-genetic models to predict gene flow resulting from landscape change. A species that has already been severely affected by landscape change is the large marsh grasshopper (Stethophyma grossum), which inhabits moist areas in fragmented agricultural landscapes in Switzerland. From transects drawn between all population pairs within maximum dispersal distance (< 3 km), we calculated several measures of landscape composition as well as some measures of habitat configuration. Additionally, a complete sampling of all populations in our study area allowed incorporating measures of population topology. These measures together with the landscape metrics formed the predictor variables in linear models with gene flow as response variable (F(ST) and mean pairwise assignment probability). With a modified leave-one-out cross-validation approach, we selected the model with the highest predictive accuracy. With this model, we predicted gene flow under several landscape-change scenarios, which simulated construction, rezoning or restoration projects, and the establishment of a new population. For some landscape-change scenarios, significant increase or decrease in gene flow was predicted, while for others little change was forecast. Furthermore, we found that the measures of population topology strongly increase model fit in landscape genetic analysis. This study demonstrates the use of predictive landscape-genetic models in conservation and landscape planning.
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Population distribution and synchronized dynamics in a metapopulation model in two geographic scales. Math Biosci 2014; 250:1-9. [PMID: 24530805 DOI: 10.1016/j.mbs.2014.02.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 09/17/2013] [Accepted: 02/04/2014] [Indexed: 10/25/2022]
Abstract
In this paper, a metapopulation model composed of patches distributed in two spatial scales is proposed in order to study the stability of synchronous dynamics. Clusters of patches connected by short-range dispersal are assumed to be formed. Long distance dispersal is responsible to link patches that are in different clusters. During each time step, we assume that there are three processes involved in the population dynamics: (a) the local dynamics, which consists of reproduction and survival; (b) short-range dispersal of individuals between the patches of each cluster; and (c) the movement between the clusters. First we present an analytic criterion for regional synchronization, where the clusters evolve with the same dynamics. We then discuss the possibility of a full synchronism, where all patches in the network follow the same time evolution. The existence of such a state is not always ensured, even considering that all patches have the same local dynamics. It depends on how the individuals are distributed among the local patches that compose a cluster after long-range dispersal takes place in the regional scale. An analytic criterion for the stability of synchronized trajectories in this case is obtained.
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Etherington TR, Perry GLW, Cowan PE, Clout MN. Quantifying the direct transfer costs of common brushtail possum dispersal using least-cost modelling: a combined cost-surface and accumulated-cost dispersal kernel approach. PLoS One 2014; 9:e88293. [PMID: 24505467 PMCID: PMC3914968 DOI: 10.1371/journal.pone.0088293] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Accepted: 01/06/2014] [Indexed: 11/21/2022] Open
Abstract
Dispersal costs need to be quantified from empirical data and incorporated into dispersal models to improve our understanding of the dispersal process. We are interested in quantifying how landscape features affect the immediately incurred direct costs associated with the transfer of an organism from one location to another. We propose that least-cost modelling is one method that can be used to quantify direct transfer costs. By representing the landscape as a cost-surface, which describes the costs associated with traversing different landscape features, least-cost modelling is often applied to measure connectivity between locations in accumulated-cost units that are a combination of both the distance travelled and the costs traversed. However, we take an additional step by defining an accumulated-cost dispersal kernel, which describes the probability of dispersal in accumulated-cost units. This novel combination of cost-surface and accumulated-cost dispersal kernel enables the transfer stage of dispersal to incorporate the effects of landscape features by modifying the direction of dispersal based on the cost-surface and the distance of dispersal based on the accumulated-cost dispersal kernel. We apply this approach to the common brushtail possum (Trichosurus vulpecula) within the North Island of New Zealand, demonstrating how commonly collected empirical dispersal data can be used to calibrate a cost-surface and associated accumulated-cost dispersal kernel. Our results indicate that considerable improvements could be made to the modelling of the transfer stage of possum dispersal by using a cost-surface and associated accumulated-cost dispersal kernel instead of a more traditional straight-line distance based dispersal kernel. We envisage a variety of ways in which the information from this novel combination of a cost-surface and accumulated-cost dispersal kernel could be gainfully incorporated into existing dispersal models. This would enable more realistic modelling of the direct transfer costs associated with the dispersal process, without requiring existing dispersal models to be abandoned.
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Affiliation(s)
| | - George L. W. Perry
- School of Environment, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | | | - Mick N. Clout
- School of Environment, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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