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Seymour M, Räsänen K, Holderegger R, Kristjánsson BK. Connectivity in a pond system influences migration and genetic structure in threespine stickleback. Ecol Evol 2013; 3:492-502. [PMID: 23531709 PMCID: PMC3605840 DOI: 10.1002/ece3.476] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2012] [Revised: 12/11/2012] [Accepted: 12/11/2012] [Indexed: 11/08/2022] Open
Abstract
Neutral genetic structure of natural populations is primarily influenced by migration (the movement of individuals and, subsequently, their genes) and drift (the statistical chance of losing genetic diversity over time). Migration between populations is influenced by several factors, including individual behavior, physical barriers, and environmental heterogeneity among populations. However, drift is expected to be stronger in populations with low immigration rate and small effective population size. With the technological advancement in geological information systems and spatial analysis tools, landscape genetics now allows the development of realistic migration models and increased insight to important processes influencing diversity of natural populations. In this study, we investigated the relationship between landscape connectivity and genetic distance of threespine stickleback (Gasterosteus aculeatus) inhabiting a pond complex in Belgjarskógur, Northeast Iceland. We used two landscape genetic approaches (i.e., least-cost-path and isolation-by-resistance) and asked whether gene flow, as measured by genetic distance, was more strongly associated with Euclidean distance (isolation-by-distance) or with landscape connectivity provided by areas prone to flooding (as indicated by Carex sp. cover)? We found substantial genetic structure across the study area, with pairwise genetic distances among populations (DPS) ranging from 0.118 to 0.488. Genetic distances among populations were more strongly correlated with least-cost-path and isolation-by-resistance than with Euclidean distance, whereas the relative contribution of isolation-by-resistance and Euclidian distance could not be disentangled. These results indicate that migration among stickleback populations occurs via periodically flooded areas. Overall, this study highlights the importance of transient landscape elements influencing migration and genetic structure of populations at small spatial scales.
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Affiliation(s)
- Mathew Seymour
- Department of Aquatic Ecology and Institute of Integrative Biology, EAWAGETH Zurich, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
- Department of Aquaculture and Fish Biology, Hólar University CollegeHáeyri 1, 550 Skagafjörður, Iceland
| | - Katja Räsänen
- Department of Aquatic Ecology and Institute of Integrative Biology, EAWAGETH Zurich, Überlandstrasse 133, CH-8600 Dübendorf, Switzerland
| | - Rolf Holderegger
- Biodiversity and Conservation Biology, WSL Swiss Federal Research InstituteCH-8903 Birmensdorf, Switzerland
| | - Bjarni K Kristjánsson
- Department of Aquaculture and Fish Biology, Hólar University CollegeHáeyri 1, 550 Skagafjörður, Iceland
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252
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Blair C, Jiménez Arcos VH, Mendez de la Cruz FR, Murphy RW. Landscape genetics of leaf-toed geckos in the tropical dry forest of northern Mexico. PLoS One 2013; 8:e57433. [PMID: 23451230 PMCID: PMC3581464 DOI: 10.1371/journal.pone.0057433] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 01/21/2013] [Indexed: 11/19/2022] Open
Abstract
Habitat fragmentation due to both natural and anthropogenic forces continues to threaten the evolution and maintenance of biological diversity. This is of particular concern in tropical regions that are experiencing elevated rates of habitat loss. Although less well-studied than tropical rain forests, tropical dry forests (TDF) contain an enormous diversity of species and continue to be threatened by anthropogenic activities including grazing and agriculture. However, little is known about the processes that shape genetic connectivity in species inhabiting TDF ecosystems. We adopt a landscape genetic approach to understanding functional connectivity for leaf-toed geckos (Phyllodactylus tuberculosus) at multiple sites near the northernmost limit of this ecosystem at Alamos, Sonora, Mexico. Traditional analyses of population genetics are combined with multivariate GIS-based landscape analyses to test hypotheses on the potential drivers of spatial genetic variation. Moderate levels of within-population diversity and substantial levels of population differentiation are revealed by FST and Dest. Analyses using structure suggest the occurrence of from 2 to 9 genetic clusters depending on the model used. Landscape genetic analysis suggests that forest cover, stream connectivity, undisturbed habitat, slope, and minimum temperature of the coldest period explain more genetic variation than do simple Euclidean distances. Additional landscape genetic studies throughout TDF habitat are required to understand species-specific responses to landscape and climate change and to identify common drivers. We urge researchers interested in using multivariate distance methods to test for, and report, significant correlations among predictor matrices that can impact results, particularly when adopting least-cost path approaches. Further investigation into the use of information theoretic approaches for model selection is also warranted.
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Affiliation(s)
- Christopher Blair
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada.
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253
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Atickem A, Rueness EK, Loe LE, Serbezov D, Bekele A, Stenseth NC. Population genetic structure and connectivity in the endangered Ethiopian mountain Nyala (Tragelaphus buxtoni): recommending dispersal corridors for future conservation. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0450-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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254
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Pereoglou F, Lindenmayer DB, MacGregor C, Ford F, Wood J, Banks SC. Landscape genetics of an early successional specialist in a disturbance-prone environment. Mol Ecol 2013; 22:1267-81. [PMID: 23379886 DOI: 10.1111/mec.12172] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 10/20/2012] [Accepted: 11/04/2012] [Indexed: 11/29/2022]
Abstract
Species that specialize in disturbed habitats may have considerably different dispersal strategies than those adapted to more stable environments. However, little is known of the dispersal patterns and population structure of such species. This information is important for conservation because many postfire specialists are at risk from anthropogenic changes to natural disturbance regimes. We used microsatellite markers to assess the effect of landscape variation and recent disturbance history on dispersal by a small mammal species that occupies the early seral stage of vegetation regeneration in burnt environments. We predicted that a postfire specialist would be able to disperse over multiple habitat types (generalist) and not exhibit sex-biased dispersal, as such strategies should enable effective colonization of spatially and temporally variable habitat. We found significant differentiation between sites that fitted an isolation-by-distance pattern and spatial autocorrelation of multilocus genotypes to a distance of 2-3 km. There was no consistent genetic evidence for sex-biased dispersal. We tested the influence of different habitat- and fire-specific landscape resistance scenarios on genetic distance between individuals and found a significant effect of fire. Our genetic data supported recently burned vegetation having greater conductance for gene flow than unburnt habitat, but variation in habitat quality between vegetation types and occupied patches had no effect on gene flow. Postfire specialists must evolve an effective dispersal ability to move over distances that would ensure access to early successional stage vegetation. Natural disturbance and natural heterogeneity may therefore not influence population genetic structure as negatively as expected.
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Affiliation(s)
- F Pereoglou
- Fenner School of Environment and Society, The Australian National University, Canberra, ACT, Australia.
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255
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Léger E, Vourc'h G, Vial L, Chevillon C, McCoy KD. Changing distributions of ticks: causes and consequences. EXPERIMENTAL & APPLIED ACAROLOGY 2013; 59:219-244. [PMID: 23015121 DOI: 10.1007/s10493-012-9615-0] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 09/15/2012] [Indexed: 05/28/2023]
Abstract
Today, we are witnessing changes in the spatial distribution and abundance of many species, including ticks and their associated pathogens. Evidence that these changes are primarily due to climate change, habitat modifications, and the globalisation of human activities are accumulating. Changes in the distribution of ticks and their invasion into new regions can have numerous consequences including modifications in their ecological characteristics and those of endemic species, impacts on the dynamics of local host populations and the emergence of human and livestock disease. Here, we review the principal causes for distributional shifts in tick populations and their consequences in terms of the ecological attributes of the species in question (i.e. phenotypic and genetic responses), pathogen transmission and disease epidemiology. We also describe different methodological approaches currently used to assess and predict such changes and their consequences. We finish with a discussion of new research avenues to develop in order to improve our understanding of these host-vector-pathogen interactions in the context of a changing world.
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Affiliation(s)
- Elsa Léger
- MIVEGEC (UMR UM2-UM1-CNRS 5290, UR IRD 224), Centre IRD, BP 64501, 911 avenue Agropolis, 34394 Montpellier Cedex 5, France.
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256
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Vergnes A, Kerbiriou C, Clergeau P. Ecological corridors also operate in an urban matrix: A test case with garden shrews. Urban Ecosyst 2013. [DOI: 10.1007/s11252-013-0289-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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257
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Barbu CM, Hong A, Manne JM, Small DS, Quintanilla Calderón JE, Sethuraman K, Quispe-Machaca V, Ancca-Juárez J, Cornejo del Carpio JG, Málaga Chavez FS, Náquira C, Levy MZ. The effects of city streets on an urban disease vector. PLoS Comput Biol 2013; 9:e1002801. [PMID: 23341756 PMCID: PMC3547802 DOI: 10.1371/journal.pcbi.1002801] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 10/12/2012] [Indexed: 11/18/2022] Open
Abstract
With increasing urbanization vector-borne diseases are quickly developing in cities, and urban control strategies are needed. If streets are shown to be barriers to disease vectors, city blocks could be used as a convenient and relevant spatial unit of study and control. Unfortunately, existing spatial analysis tools do not allow for assessment of the impact of an urban grid on the presence of disease agents. Here, we first propose a method to test for the significance of the impact of streets on vector infestation based on a decomposition of Moran's spatial autocorrelation index; and second, develop a Gaussian Field Latent Class model to finely describe the effect of streets while controlling for cofactors and imperfect detection of vectors. We apply these methods to cross-sectional data of infestation by the Chagas disease vector Triatoma infestans in the city of Arequipa, Peru. Our Moran's decomposition test reveals that the distribution of T. infestans in this urban environment is significantly constrained by streets (p<0.05). With the Gaussian Field Latent Class model we confirm that streets provide a barrier against infestation and further show that greater than 90% of the spatial component of the probability of vector presence is explained by the correlation among houses within city blocks. The city block is thus likely to be an appropriate spatial unit to describe and control T. infestans in an urban context. Characteristics of the urban grid can influence the spatial dynamics of vector borne disease and should be considered when designing public health policies.
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Affiliation(s)
- Corentin M. Barbu
- Center for Clinical Epidemiology & Biostatistics - Department of Biostatistics & Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (CMB); (MZL)
| | - Andrew Hong
- Department of Statistics, The Wharton School University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jennifer M. Manne
- Department of Global Health and Population, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Dylan S. Small
- Department of Statistics, The Wharton School University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | | | - Karthik Sethuraman
- Center for Clinical Epidemiology & Biostatistics - Department of Biostatistics & Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
| | | | - Jenny Ancca-Juárez
- Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | | | - César Náquira
- Facultad de Ciencias y Filosofia, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Michael Z. Levy
- Center for Clinical Epidemiology & Biostatistics - Department of Biostatistics & Epidemiology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail: (CMB); (MZL)
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258
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Krueger-Hadfield SA, Roze D, Mauger S, Valero M. Intergametophytic selfing and microgeographic genetic structure shape populations of the intertidal red seaweedChondrus crispus. Mol Ecol 2013; 22:3242-60. [DOI: 10.1111/mec.12191] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 11/27/2012] [Accepted: 11/29/2012] [Indexed: 12/28/2022]
Affiliation(s)
- S. A. Krueger-Hadfield
- UPMC Univ Paris 06; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
- CNRS; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
- Departamento de Ecología; Facultad de Ciencias Biológicas; Center for Advanced Studies in Ecology and Biodiversity; Pontificia Universidad Católica de Chile; 6513677 Santiago Chile
| | - D. Roze
- UPMC Univ Paris 06; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
- CNRS; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
| | - S. Mauger
- UPMC Univ Paris 06; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
- CNRS; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
| | - M. Valero
- UPMC Univ Paris 06; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
- CNRS; UMR7144; Adaptation et Diversité en Milieu Marin; Station Biologique de Roscoff; Place Georges Teissier 29682 Roscoff France
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259
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Jeltsch F, Bonte D, Pe'er G, Reineking B, Leimgruber P, Balkenhol N, Schröder B, Buchmann CM, Mueller T, Blaum N, Zurell D, Böhning-Gaese K, Wiegand T, Eccard JA, Hofer H, Reeg J, Eggers U, Bauer S. Integrating movement ecology with biodiversity research - exploring new avenues to address spatiotemporal biodiversity dynamics. MOVEMENT ECOLOGY 2013; 1:6. [PMID: 25709820 PMCID: PMC4337763 DOI: 10.1186/2051-3933-1-6] [Citation(s) in RCA: 107] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 06/03/2013] [Indexed: 05/03/2023]
Abstract
Movement of organisms is one of the key mechanisms shaping biodiversity, e.g. the distribution of genes, individuals and species in space and time. Recent technological and conceptual advances have improved our ability to assess the causes and consequences of individual movement, and led to the emergence of the new field of 'movement ecology'. Here, we outline how movement ecology can contribute to the broad field of biodiversity research, i.e. the study of processes and patterns of life among and across different scales, from genes to ecosystems, and we propose a conceptual framework linking these hitherto largely separated fields of research. Our framework builds on the concept of movement ecology for individuals, and demonstrates its importance for linking individual organismal movement with biodiversity. First, organismal movements can provide 'mobile links' between habitats or ecosystems, thereby connecting resources, genes, and processes among otherwise separate locations. Understanding these mobile links and their impact on biodiversity will be facilitated by movement ecology, because mobile links can be created by different modes of movement (i.e., foraging, dispersal, migration) that relate to different spatiotemporal scales and have differential effects on biodiversity. Second, organismal movements can also mediate coexistence in communities, through 'equalizing' and 'stabilizing' mechanisms. This novel integrated framework provides a conceptual starting point for a better understanding of biodiversity dynamics in light of individual movement and space-use behavior across spatiotemporal scales. By illustrating this framework with examples, we argue that the integration of movement ecology and biodiversity research will also enhance our ability to conserve diversity at the genetic, species, and ecosystem levels.
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Affiliation(s)
- Florian Jeltsch
- Department of Plant Ecology and Nature Conservation, Intitute of Biochemistry and Biology, University of Potsdam, Maulbeerallee 2, 14469 Potsdam, Germany ; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, D-14195 Germany
| | - Dries Bonte
- Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Gent, 9000 Belgium
| | - Guy Pe'er
- Department of Conservation Biology, UFZ - Helmholtz Centre for Environmental Research, Permoserstr 15, Leipzig, 04318 Germany
| | - Björn Reineking
- Biogeographical Modelling, BayCEER, University of Bayreuth, Universitätsstr. 30, Bayreuth, 95447 Germany ; Irstea, UR EMGR Écosystèmes Montagnards, 2 rue de la Papeterie-BP 76, St-Martin-d'Hères, F-38402 France
| | - Peter Leimgruber
- National Zoological Park, Smithsonian, Conservation Biology Institute, 1500 Remount Road, Front Royal, VA 22630 USA
| | - Niko Balkenhol
- Department of Forest Zoology and Forest Conservation, University of Göttingen, Buesgenweg 3, Göttingen, 37077 Germany
| | - Boris Schröder
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, D-14195 Germany ; Landscape Ecology, Technische Universität München, Emil-Ramann-Str. 6, 85354 Freising-Weihenstephan, Germany ; Environmental Systems Analysis, Institute of Geoecology, Technical University of Braunschweig, Langer Kamp 19c, Braunschweig, 38106 Germany
| | - Carsten M Buchmann
- Department of Landscape Ecology, UFZ - Helmholtz Centre for Environmental Research, Permoserstr. 15, Leipzig, 04318 Germany
| | - Thomas Mueller
- National Zoological Park, Smithsonian, Conservation Biology Institute, 1500 Remount Road, Front Royal, VA 22630 USA ; Department of Biology, University of Maryland, College Park, MD 20742 USA
| | - Niels Blaum
- Department of Plant Ecology and Nature Conservation, Intitute of Biochemistry and Biology, University of Potsdam, Maulbeerallee 2, 14469 Potsdam, Germany
| | - Damaris Zurell
- Department of Plant Ecology and Nature Conservation, Intitute of Biochemistry and Biology, University of Potsdam, Maulbeerallee 2, 14469 Potsdam, Germany
| | - Katrin Böhning-Gaese
- Biodiversity and Climate Research Centre (BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, Frankfurt (Main), 60325 Germany ; Department of Biological Sciences, Goethe Universität, Max-von-Laue-Straße 9, Frankfurt (Main), 60438 Germany
| | - Thorsten Wiegand
- Department of Ecological Modelling, Helmholz Centre for Environmental Research (UFZ), Permoserstr. 15, Leipzig, 04318 Germany
| | - Jana A Eccard
- Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, D-14195 Germany ; Department of Animal Ecology, Institute of Biochemistry and Biology, Universität Potsdam, Maulbeerallee 1, Potsdam, 14469 Germany
| | - Heribert Hofer
- Department of Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin e.V., Alfred-Kowalke-Str. 17, Berlin, 10315 Germany
| | - Jette Reeg
- Department of Plant Ecology and Nature Conservation, Intitute of Biochemistry and Biology, University of Potsdam, Maulbeerallee 2, 14469 Potsdam, Germany
| | - Ute Eggers
- Department of Plant Ecology and Nature Conservation, Intitute of Biochemistry and Biology, University of Potsdam, Maulbeerallee 2, 14469 Potsdam, Germany
| | - Silke Bauer
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), P.O. Box 50, Wageningen, AB 6700 The Netherlands ; Swiss Ornithological Institute, Seerose 1, Sempach, 6204 Switzerland
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260
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Abstract
Whether they are used to describe fitness, genome architecture or the spatial distribution of environmental variables, the concept of a landscape has figured prominently in our collective reasoning. The tradition of landscapes in evolutionary biology is one of fitness mapped onto axes defined by phenotypes or molecular sequence states. The characteristics of these landscapes depend on natural selection, which is structured across both genomic and environmental landscapes, and thus, the bridge among differing uses of the landscape concept (i.e. metaphorically or literally) is that of an adaptive phenotype and its distribution across geographical landscapes in relation to selective pressures. One of the ultimate goals of evolutionary biology should thus be to construct fitness landscapes in geographical space. Natural plant populations are ideal systems with which to explore the feasibility of attaining this goal, because much is known about the quantitative genetic architecture of complex traits for many different plant species. What is less known are the molecular components of this architecture. In this issue of Molecular Ecology, Parchman et al. (2012) pioneer one of the first truly genome-wide association studies in a tree that moves us closer to this form of mechanistic understanding for an adaptive phenotype in natural populations of lodgepole pine (Pinus contorta Dougl. ex Loud.).
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Affiliation(s)
- Andrew J Eckert
- Department of Biology, Virginia Commonwealth University, Richmond, VA 23284, USA.
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261
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Human introductions create opportunities for intra-specific hybridization in an alien lizard. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0353-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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262
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Buskirk J. Permeability of the landscape matrix between amphibian breeding sites. Ecol Evol 2012; 2:3160-7. [PMID: 23301180 PMCID: PMC3539008 DOI: 10.1002/ece3.424] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2012] [Revised: 10/10/2012] [Accepted: 10/13/2012] [Indexed: 12/02/2022] Open
Abstract
For organisms that reproduce in discrete habitat patches, land cover between patches (known as the matrix) is important for dispersal among breeding sites. Models of patchy populations often incorporate information on the permeability of the matrix to dispersal, sometimes based on expert opinion. I estimated the relative resistance to gene flow of land cover types and barriers using F(ST) calculated from microsatellite markers in two amphibians, within an 800-km(2) area in northern Switzerland. The species included a frog (Rana temporaria: 996 individuals, 48 populations, seven markers) and a newt (Triturus alpestris: 816 individuals, 41 populations, seven markers). Open fields and urban areas were more resistant to gene flow than forested land; roads and highways also reduced permeability. Results were similar for the two species. However, differences in resistance among matrix elements were relatively low: gene flow through urban areas was reduced by only 24-42% relative to forest; a divided highway reduced gene flow by 11-40% and was 7-8 times more resistant than a secondary road. These data offer an empirically based alternative to expert opinion for setting relative resistance values in landscape models.
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Affiliation(s)
- Josh Buskirk
- Institute of Evolutionary Biology & Environmental Studies, University of Zürich CH-8057, Zürich, Switzerland
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263
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Herrmann M, Holderegger R, Van Strien MJ. Influence of parameter settings in automated scoring of AFLPs on population genetic analysis. Mol Ecol Resour 2012; 13:128-34. [PMID: 23176344 DOI: 10.1111/1755-0998.12033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2012] [Revised: 09/28/2012] [Accepted: 10/07/2012] [Indexed: 11/28/2022]
Abstract
The use of procedures for the automated scoring of amplified fragment length polymorphisms (AFLP) fragments has recently increased. Corresponding software does not only automatically score the presence or absence of AFLP fragments, but also allows an evaluation of how different settings of scoring parameters influence subsequent population genetic analyses. In this study, we used the automated scoring package rawgeno to evaluate how five scoring parameters influence the number of polymorphic bins and estimates of pairwise genetic differentiation between populations (F(st)). Steps were implemented in r to automatically run the scoring process in rawgeno for a set of different parameter combinations. While we found the scoring parameters minimum bin width and minimum number of samples per bin to have only weak influence on pairwise F(st) values, maximum bin width and bin reproducibility had much stronger effects. The minimum average bin fluorescence scoring parameter affected F(st) values in an only moderate way. At a range of scoring parameters around the default settings of rawgeno, the number of polymorphic bins as well as pairwise F(st) values stayed rather constant. This study thus shows the particularities of AFLP scoring, be it either manual or automatical, can have profound effects on subsequent population genetic analysis.
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Affiliation(s)
- Marc Herrmann
- Swiss Federal Research Institute WSL, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland
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264
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Baguette M, Blanchet S, Legrand D, Stevens VM, Turlure C. Individual dispersal, landscape connectivity and ecological networks. Biol Rev Camb Philos Soc 2012; 88:310-26. [DOI: 10.1111/brv.12000] [Citation(s) in RCA: 385] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 10/18/2012] [Accepted: 10/25/2012] [Indexed: 11/28/2022]
Affiliation(s)
| | - Simon Blanchet
- USR CNRS 2936; Station d'Ecologie Expérimentale du CNRS à Moulis; 2 route du CNRS; F-09200; Saint Girons; France
| | - Delphine Legrand
- USR CNRS 2936; Station d'Ecologie Expérimentale du CNRS à Moulis; 2 route du CNRS; F-09200; Saint Girons; France
| | - Virginie M. Stevens
- USR CNRS 2936; Station d'Ecologie Expérimentale du CNRS à Moulis; 2 route du CNRS; F-09200; Saint Girons; France
| | - Camille Turlure
- F.R.S.-FNRS; Universite Catholique de Louvain, Earth and Life Institute, Biodiversity Research Centre; Croix du Sud 4; B-1348; Louvain-la-Neuve; Belgium
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265
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266
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Wang IJ, Glor RE, Losos JB. Quantifying the roles of ecology and geography in spatial genetic divergence. Ecol Lett 2012; 16:175-82. [DOI: 10.1111/ele.12025] [Citation(s) in RCA: 190] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 07/18/2012] [Accepted: 10/04/2012] [Indexed: 12/01/2022]
Affiliation(s)
- Ian J. Wang
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge; MA; 02138; USA
| | - Richard E. Glor
- Department of Biology; University of Rochester; Rochester; NY; 14627; USA
| | - Jonathan B. Losos
- Department of Organismic and Evolutionary Biology; Harvard University; Cambridge; MA; 02138; USA
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267
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Pérez-Espona S, McLeod JE, Franks NR. Landscape genetics of a top neotropical predator. Mol Ecol 2012; 21:5969-85. [PMID: 23110496 DOI: 10.1111/mec.12088] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Revised: 08/31/2012] [Accepted: 09/12/2012] [Indexed: 11/30/2022]
Abstract
Habitat loss and fragmentation as a consequence of human activities is a worldwide phenomenon and one of the major threats to global biodiversity. Habitat loss and fragmentation is particularly a concern in the biodiverse tropics, where deforestation is occurring at unprecedented rates. Although insects are one of the most diverse and functionally important groups in tropical ecosystems, the quantitative effect of landscape features on their gene flow remains unknown. Here, we used a robust landscape genetics approach to quantify the effect of ten landscape features (deforestation, mature forests, other forest types, the River Chagres, streams, stream banks, roads, sea, lakes and swamps) and interactions between them, on the gene flow of a neotropical forest keystone species, the army ant Eciton burchellii. The influence of landscape on E. burchellii's gene flow reflected the different dispersal capability of its sexes; aerial for males and pedestrian for females, and the different depths of population history inferred from microsatellites and mitochondrial DNA. In contrast to the gene flow-facilitating effect of mature forests, deforested areas were found to be strong barriers for E. burchellii's gene flow. Other forest types were found to be gene flow facilitators but only when interacting with mature secondary forests, therefore indicating the importance of mature forests for the survival of E. burchelii and its associate species. The River Chagres was identified as a major historical gene flow barrier for E. burchellii, suggesting that an important loss of connectivity may occur because of large artificial waterways such as the Panama Canal.
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Affiliation(s)
- S Pérez-Espona
- School of Biological Sciences, The University of Bristol, Bristol, BS8 1UG, UK.
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268
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Development of microsatellite loci for the western slimy salamander (Plethodon albagula) using 454 sequencing. CONSERV GENET RESOUR 2012. [DOI: 10.1007/s12686-012-9784-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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269
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270
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Coscia I, Robins PE, Porter JS, Malham SK, Ironside JE. Modelled larval dispersal and measured gene flow: seascape genetics of the common cockle Cerastoderma edule in the southern Irish Sea. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0404-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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271
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272
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Pavlova A, Amos JN, Goretskaia MI, Beme IR, Buchanan KL, Takeuchi N, Radford JQ, Sunnucks P. Genes and song: genetic and social connections in fragmented habitat in a woodland bird with limited dispersal. Ecology 2012; 93:1717-27. [PMID: 22919917 DOI: 10.1890/11-1891.1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Understanding the processes leading to population declines in fragmented landscapes is essential for successful conservation management. However, isolating the influence of disparate processes, and dispersal in particular, is challenging. The Grey Shrike-thrush, Colluricincla harmonica, is a sedentary woodland-dependent songbird, with learned vocalizations whose incidence in suitable habitat patches falls disproportionally with decline in tree cover in the landscape. Although it has been suggested that gaps in tree cover might act as barriers to its dispersal, the species remains in many remnants of native vegetation in agricultural landscapes, suggesting that it may have responded to habitat removal and fragmentation by maintaining or even increasing dispersal distances. We quantified population connectivity of the Grey Shrike-thrush in a system fragmented over more than 120 years using genetic (microsatellites) and acoustic (song types) data. First, we tested for population genetic and acoustic structure at regional and local scales in search of barriers to dispersal or gene flow and signals of local spatial structuring indicative of restricted dispersal or localized acoustic similarity. Then we tested for effects of habitat loss and fragmentation on genetic and acoustic connectivity by fitting alternative models of mobility (isolation-by-distance [the null model] and reduced and increased movement models) across treeless vs. treed areas. Birds within -5 km of each other had more similar genotypes and song types than those farther away, suggesting that dispersal and song matching are limited in the region. Despite restricted dispersal detected for females (but not males), populations appeared to be connected by gene flow and displayed some cultural (acoustic) connectivity across the region. Fragmentation did not appear to impact greatly the dispersal of the Grey Shrike-thrush: none of the mobility models fit the genetic distances of males, whereas for females, an isolation-by-distance model could not be rejected in favor of the models of reduced or increased movement through treeless gaps. However, dissimilarities of the song types were more consistent with the model of reduced cultural connectivity through treeless areas, suggesting that fragmentation impedes song type sharing in the Grey Shrike-thrush. Our paper demonstrates that habitat fragmentation hinders important population processes in an Australian woodland bird even though its dispersal is not detectably impacted.
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Affiliation(s)
- Alexandra Pavlova
- School of Biological Sciences and Australian Centre for Biodiversity, Monash University, Melbourne, Clayton Campus, Clayton, VIC 3800, Australia.
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273
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Andreasen AM, Stewart KM, Longland WS, Beckmann JP, Forister ML. Identification of source-sink dynamics in mountain lions of the Great Basin. Mol Ecol 2012; 21:5689-701. [DOI: 10.1111/j.1365-294x.2012.05740.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2011] [Revised: 06/21/2011] [Accepted: 07/02/2012] [Indexed: 11/28/2022]
Affiliation(s)
- Alyson M. Andreasen
- Program in Ecology, Evolution and Conservation Biology; University of Nevada; 1664 N. Virginia Street, Stop 314; Reno; NV; 89557; USA
| | - Kelley M. Stewart
- Department of Natural Resources and Environmental Sciences; University of Nevada; 1664 N. Virginia Street, Stop 186; Reno; NV; 89503; USA
| | - William S. Longland
- Agricultural Research Service; USDA, University of Nevada; 920 Valley Road; Reno; NV; 89512; USA
| | - Jon P. Beckmann
- North America Program; Wildlife Conservation Society; 301 N. Willson Ave.; Bozeman; MT; 59715; USA
| | - Matthew L. Forister
- Biology Department; University of Nevada; 1664 N. Virginia Street, Stop 314; Reno; NV; 89557; USA
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274
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Blair ME, Melnick DJ. Scale-dependent effects of a heterogeneous landscape on genetic differentiation in the Central American squirrel monkey (Saimiri oerstedii). PLoS One 2012; 7:e43027. [PMID: 22905197 PMCID: PMC3419685 DOI: 10.1371/journal.pone.0043027] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2012] [Accepted: 07/16/2012] [Indexed: 11/30/2022] Open
Abstract
Landscape genetic studies offer a fine-scale understanding of how habitat heterogeneity influences population genetic structure. We examined population genetic structure and conducted a landscape genetic analysis for the endangered Central American Squirrel Monkey (Saimiri oerstedii) that lives in the fragmented, human-modified habitats of the Central Pacific region of Costa Rica. We analyzed non-invasively collected fecal samples from 244 individuals from 14 groups for 16 microsatellite markers. We found two geographically separate genetic clusters in the Central Pacific region with evidence of recent gene flow among them. We also found significant differentiation among groups of S. o. citrinellus using pairwise FST comparisons. These groups are in fragments of secondary forest separated by unsuitable “matrix” habitats such as cattle pasture, commercial African oil palm plantations, and human residential areas. We used an individual-based landscape genetic approach to measure spatial patterns of genetic variance while taking into account landscape heterogeneity. We found that large, commercial oil palm plantations represent moderate barriers to gene flow between populations, but cattle pastures, rivers, and residential areas do not. However, the influence of oil palm plantations on genetic variance was diminished when we restricted analyses to within population pairs, suggesting that their effect is scale-dependent and manifests during longer dispersal events among populations. We show that when landscape genetic methods are applied rigorously and at the right scale, they are sensitive enough to track population processes even in species with long, overlapping generations such as primates. Thus landscape genetic approaches are extremely valuable for the conservation management of a diverse array of endangered species in heterogeneous, human-modified habitats. Our results also stress the importance of explicitly considering the heterogeneity of matrix habitats in landscape genetic studies, instead of assuming that all matrix habitats have a uniform effect on population genetic processes.
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Affiliation(s)
- Mary E Blair
- Department of Ecology, Evolution and Environmental Biology, Columbia University, New York, New York, United States of America.
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275
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Temunović M, Franjić J, Satovic Z, Grgurev M, Frascaria-Lacoste N, Fernández-Manjarrés JF. Environmental heterogeneity explains the genetic structure of Continental and Mediterranean populations of Fraxinus angustifolia Vahl. PLoS One 2012; 7:e42764. [PMID: 22905171 PMCID: PMC3414449 DOI: 10.1371/journal.pone.0042764] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Accepted: 07/12/2012] [Indexed: 11/18/2022] Open
Abstract
Tree species with wide distributions often exhibit different levels of genetic structuring correlated to their environment. However, understanding how environmental heterogeneity influences genetic variation is difficult because the effects of gene flow, drift and selection are confounded. We investigated the genetic variation and its ecological correlates in a wind-pollinated Mediterranean tree species, Fraxinus angustifolia Vahl, within a recognised glacial refugium in Croatia. We sampled 11 populations from environmentally divergent habitats within the Continental and Mediterranean biogeographical regions. We combined genetic data analyses based on nuclear microsatellite loci, multivariate statistics on environmental data and ecological niche modelling (ENM). We identified a geographic structure with a high genetic diversity and low differentiation in the Continental region, which contrasted with the significantly lower genetic diversity and higher population divergence in the Mediterranean region. The positive and significant correlation between environmental and genetic distances after controlling for geographic distance suggests an important influence of ecological divergence of the sites in shaping genetic variation. The ENM provided support for niche differentiation between the populations from the Continental and Mediterranean regions, suggesting that contemporary populations may represent two divergent ecotypes. Ecotype differentiation was also supported by multivariate environmental and genetic distance analyses. Our results suggest that despite extensive gene flow in continental areas, long-term stability of heterogeneous environments have likely promoted genetic divergence of ashes in this region and can explain the present-day genetic variation patterns of these ancient populations.
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Affiliation(s)
- Martina Temunović
- Department of Forest Genetics, Faculty of Forestry, University of Zagreb, Zagreb, Croatia.
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276
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ROBINSON STACIEJ, SAMUEL MICHAELD, LOPEZ DAVINL, SHELTON PAUL. The walk is never random: subtle landscape effects shape gene flow in a continuous white-tailed deer population in the Midwestern United States. Mol Ecol 2012; 21:4190-205. [DOI: 10.1111/j.1365-294x.2012.05681.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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277
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Wagner HH, Fortin MJ. A conceptual framework for the spatial analysis of landscape genetic data. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0391-5] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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278
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Lee CR, Mitchell-Olds T. Environmental adaptation contributes to gene polymorphism across the Arabidopsis thaliana genome. Mol Biol Evol 2012; 29:3721-8. [PMID: 22798389 DOI: 10.1093/molbev/mss174] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The level of within-species polymorphism differs greatly among genes in a genome. Many genomic studies have investigated the relationship between gene polymorphism and factors such as recombination rate or expression pattern. However, the polymorphism of a gene is affected not only by its physical properties or functional constraints but also by natural selection on organisms in their environments. Specifically, if functionally divergent alleles enable adaptation to different environments, locus-specific polymorphism may be maintained by spatially heterogeneous natural selection. To test this hypothesis and estimate the extent to which environmental selection shapes the pattern of genome-wide polymorphism, we define the "environmental relevance" of a gene as the proportion of genetic variation explained by environmental factors, after controlling for population structure. We found substantial effects of environmental relevance on patterns of polymorphism among genes. In addition, the correlation between environmental relevance and gene polymorphism is positive, consistent with the expectation that balancing selection among heterogeneous environments maintains genetic variation at ecologically important genes. Comparison of the gene ontology annotations shows that genes with high environmental relevance are enriched in unknown function categories. These results suggest an important role for environmental factors in shaping genome-wide patterns of polymorphism and indicate another direction of genomic study.
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279
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Vernesi C, Rocchini D, Pecchioli E, Neteler M, Vendramin GG, Paffetti D. A landscape genetics approach reveals ecological-based differentiation in populations of holm oak (Quercus ilex L.) at the northern limit of its range. Biol J Linn Soc Lond 2012. [DOI: 10.1111/j.1095-8312.2012.01940.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Cristiano Vernesi
- Department of Biodiversity and Molecular Ecology-Centre for Research and Innovation; Fondazione Edmund Mach; via E. Mach 1; 38010; S. Michele all'Adige; Italy
| | - Duccio Rocchini
- Department of Biodiversity and Molecular Ecology-Centre for Research and Innovation; Fondazione Edmund Mach; via E. Mach 1; 38010; S. Michele all'Adige; Italy
| | - Elena Pecchioli
- Department of Biodiversity and Molecular Ecology-Centre for Research and Innovation; Fondazione Edmund Mach; via E. Mach 1; 38010; S. Michele all'Adige; Italy
| | - Markus Neteler
- Department of Biodiversity and Molecular Ecology-Centre for Research and Innovation; Fondazione Edmund Mach; via E. Mach 1; 38010; S. Michele all'Adige; Italy
| | - Giovanni G. Vendramin
- IGV; Consiglio Nazionale delle Ricerche; via Madonna del Piano, 10; 50019; Sesto Fiorentino; Italy
| | - Donatella Paffetti
- DEISTAF; University of Florence; via S. Bonaventura 13; 50145; Firenze; Italy
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280
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VAN Strien MJ, Keller D, Holderegger R. A new analytical approach to landscape genetic modelling: least-cost transect analysis and linear mixed models. Mol Ecol 2012; 21:4010-23. [PMID: 22738667 DOI: 10.1111/j.1365-294x.2012.05687.x] [Citation(s) in RCA: 142] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Landscape genetics aims to assess the effect of the landscape on intraspecific genetic structure. To quantify interdeme landscape structure, landscape genetics primarily uses landscape resistance surfaces (RSs) and least-cost paths or straight-line transects. However, both approaches have drawbacks. Parameterization of RSs is a subjective process, and least-cost paths represent a single migration route. A transect-based approach might oversimplify migration patterns by assuming rectilinear migration. To overcome these limitations, we combined these two methods in a new landscape genetic approach: least-cost transect analysis (LCTA). Habitat-matrix RSs were used to create least-cost paths, which were subsequently buffered to form transects in which the abundance of several landscape elements was quantified. To maintain objectivity, this analysis was repeated so that each landscape element was in turn regarded as migration habitat. The relationship between explanatory variables and genetic distances was then assessed following a mixed modelling approach to account for the nonindependence of values in distance matrices. Subsequently, the best fitting model was selected using the statistic. We applied LCTA and the mixed modelling approach to an empirical genetic dataset on the endangered damselfly, Coenagrion mercuriale. We compared the results to those obtained from traditional least-cost, effective and resistance distance analysis. We showed that LCTA is an objective approach that identifies both the most probable migration habitat and landscape elements that either inhibit or facilitate gene flow. Although we believe the statistical approach to be an improvement for the analysis of distance matrices in landscape genetics, more stringent testing is needed.
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Affiliation(s)
- Maarten J VAN Strien
- WSL Swiss Federal Research Institute, Zürcherstrasse 111, CH-8903 Birmensdorf, Switzerland.
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281
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GALPERN PAUL, MANSEAU MICHELINE, WILSON PAUL. Grains of connectivity: analysis at multiple spatial scales in landscape genetics. Mol Ecol 2012; 21:3996-4009. [DOI: 10.1111/j.1365-294x.2012.05677.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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282
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Dudaniec RY, Spear SF, Richardson JS, Storfer A. Current and historical drivers of landscape genetic structure differ in core and peripheral salamander populations. PLoS One 2012; 7:e36769. [PMID: 22590604 PMCID: PMC3349670 DOI: 10.1371/journal.pone.0036769] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2012] [Accepted: 04/12/2012] [Indexed: 11/18/2022] Open
Abstract
With predicted decreases in genetic diversity and greater genetic differentiation at range peripheries relative to their cores, it can be difficult to distinguish between the roles of current disturbance versus historic processes in shaping contemporary genetic patterns. To address this problem, we test for differences in historic demography and landscape genetic structure of coastal giant salamanders (Dicamptodon tenebrosus) in two core regions (Washington State, United States) versus the species' northern peripheral region (British Columbia, Canada) where the species is listed as threatened. Coalescent-based demographic simulations were consistent with a pattern of post-glacial range expansion, with both ancestral and current estimates of effective population size being much larger within the core region relative to the periphery. However, contrary to predictions of recent human-induced population decline in the less genetically diverse peripheral region, there was no genetic signature of population size change. Effects of current demographic processes on genetic structure were evident using a resistance-based landscape genetics approach. Among core populations, genetic structure was best explained by length of the growing season and isolation by resistance (i.e. a ‘flat’ landscape), but at the periphery, topography (slope and elevation) had the greatest influence on genetic structure. Although reduced genetic variation at the range periphery of D. tenebrosus appears to be largely the result of biogeographical history rather than recent impacts, our analyses suggest that inherent landscape features act to alter dispersal pathways uniquely in different parts of the species' geographic range, with implications for habitat management.
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Affiliation(s)
- Rachael Y Dudaniec
- Department of Forest Sciences, University of British Columbia, Vancouver, British Columbia, Canada.
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283
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Blair C, Weigel DE, Balazik M, Keeley ATH, Walker FM, Landguth E, Cushman S, Murphy M, Waits L, Balkenhol N. A simulation-based evaluation of methods for inferring linear barriers to gene flow. Mol Ecol Resour 2012; 12:822-33. [PMID: 22551194 DOI: 10.1111/j.1755-0998.2012.03151.x] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Different analytical techniques used on the same data set may lead to different conclusions about the existence and strength of genetic structure. Therefore, reliable interpretation of the results from different methods depends on the efficacy and reliability of different statistical methods. In this paper, we evaluated the performance of multiple analytical methods to detect the presence of a linear barrier dividing populations. We were specifically interested in determining if simulation conditions, such as dispersal ability and genetic equilibrium, affect the power of different analytical methods for detecting barriers. We evaluated two boundary detection methods (Monmonier's algorithm and WOMBLING), two spatial Bayesian clustering methods (TESS and GENELAND), an aspatial clustering approach (STRUCTURE), and two recently developed, non-Bayesian clustering methods [PSMIX and discriminant analysis of principal components (DAPC)]. We found that clustering methods had higher success rates than boundary detection methods and also detected the barrier more quickly. All methods detected the barrier more quickly when dispersal was long distance in comparison to short-distance dispersal scenarios. Bayesian clustering methods performed best overall, both in terms of highest success rates and lowest time to barrier detection, with GENELAND showing the highest power. None of the methods suggested a continuous linear barrier when the data were generated under an isolation-by-distance (IBD) model. However, the clustering methods had higher potential for leading to incorrect barrier inferences under IBD unless strict criteria for successful barrier detection were implemented. Based on our findings and those of previous simulation studies, we discuss the utility of different methods for detecting linear barriers to gene flow.
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Affiliation(s)
- Christopher Blair
- Department of Ecology and Evolutionary Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.
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284
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STELKENS RIKEB, JAFFUEL GEOFFREY, ESCHER MATTHIAS, WEDEKIND CLAUS. Genetic and phenotypic population divergence on a microgeographic scale in brown trout. Mol Ecol 2012; 21:2896-915. [DOI: 10.1111/j.1365-294x.2012.05581.x] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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285
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Landguth EL, Balkenhol N. Relative sensitivity of neutral versus adaptive genetic data for assessing population differentiation. CONSERV GENET 2012. [DOI: 10.1007/s10592-012-0354-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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286
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Landscape configuration determines gene flow and phenotype in a flightless forest-edge ground-dwelling bush-cricket, Pholidoptera griseoaptera. Evol Ecol 2012. [DOI: 10.1007/s10682-012-9571-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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287
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Spear SF, Crisafulli CM, Storfer A. Genetic structure among coastal tailed frog populations at Mount St. Helens is moderated by post-disturbance management. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2012; 22:856-869. [PMID: 22645816 DOI: 10.1890/11-0627.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Catastrophic disturbances often provide "natural laboratories" that allow for greater understanding of ecological processes and response of natural populations. The 1980 eruption of the Mount St. Helens volcano in Washington, USA, provided a unique opportunity to test biotic effects of a large-scale stochastic disturbance, as well as the influence of post-disturbance management. Despite severe alteration of nearly 600 km2 of habitat, coastal tailed frogs (Ascaphus truei) were found within a portion of the blast area five years after eruption. We investigated the genetic source of recolonization within the blast area and tested whether post-eruption salvage logging and subsequent tree planting influenced tailed frog movement patterns. Our results support widespread recolonization across the blast area from multiple sources, as all sites are grouped into one genetic cluster. Landscape genetic models suggest that gene flow through the unmanaged portion of the blast area is influenced only by distance between sites and the frost-free period (r2 = 0.74). In contrast, gene flow pathways within the blast area where salvage logging and replanting occurred post-eruption are strongly limited (r2 = 0.83) by the physiologically important variables of heat load and precipitation. These data suggest that the lack of understory and coarse wood (downed and standing dead tree boles) refugia in salvaged areas may leave frogs more susceptible to desiccation and mortality than those frogs moving through the naturally regenerated area. Simulated populations based on the landscape genetic models show an increase in the inbreeding coefficient in the managed area relative to the unmanaged blast area. In sum, we show surprising resilience of an amphibian species to a catastrophic disturbance, and we suggest that, at least for this species, naturally regenerating habitat may better maintain long-term genetic diversity of populations than actively managed habitat.
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Affiliation(s)
- Stephen F Spear
- The Orianne Society, 579 Highway 441 S, Clayton, Georgia 30525, USA.
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288
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ANDREW ROSEL, OSTEVIK KATHERINEL, EBERT DANIELP, RIESEBERG LORENH. Adaptation with gene flow across the landscape in a dune sunflower. Mol Ecol 2012; 21:2078-91. [DOI: 10.1111/j.1365-294x.2012.05454.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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289
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Wang IJ. Environmental and topographic variables shape genetic structure and effective population sizes in the endangered Yosemite toad. DIVERS DISTRIB 2012. [DOI: 10.1111/j.1472-4642.2012.00897.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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290
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Cyr F, Angers B. Historical process lead to false genetic signal of current connectivity among populations. Genetica 2012; 139:1417-28. [PMID: 22388987 DOI: 10.1007/s10709-012-9640-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 02/20/2012] [Indexed: 10/28/2022]
Abstract
Identification of the effects of historical processes on spatial genetic variation is of major importance in landscape genetics, especially in recent systems where the signal of recent isolation is often hardly perceptible. The goal of this study was to assess how differences in colonization patterns could influence spatial genetic variation using two centrarchidae species, the pumpkinseed sunfish (Lepomis gibbosus) and the rock bass (Ambloplites rupestris), from two adjacent drainage systems. The striking difference between the spatial genetic variations of the two species suggests completely opposite patterns of colonization. Rock bass colonized the drainage system from a downstream source, which resulted in a loss of diversity in upstream populations and a strong differentiation between drainage systems. In contrast, the reduction of genetic diversity and increase of differentiation toward downstream populations that were observed among sunfish populations suggest colonization from upstream to downstream. The colonization pattern observed in sunfish, which result in low differentiation between upstream most sites of the two drainages, leads to a false genetic signal of current inter-drainage gene flow. The present study demonstrates through empirical evidence that colonization patterns may impede the capacity to estimate current connectivity.
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Affiliation(s)
- Frédéric Cyr
- Group for Interuniversity Research in Limnology and Aquatic Environment, Département de Sciences Biologiques, Université de Montréal, 90 Vincent d'Indy, Montreal, QC, Canada.
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291
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MUNSHI-SOUTH JASON. Urban landscape genetics: canopy cover predicts gene flow between white-footed mouse (Peromyscus leucopus) populations in New York City. Mol Ecol 2012; 21:1360-78. [DOI: 10.1111/j.1365-294x.2012.05476.x] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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292
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Amaral AR, Beheregaray LB, Bilgmann K, Boutov D, Freitas L, Robertson KM, Sequeira M, Stockin KA, Coelho MM, Möller LM. Seascape genetics of a globally distributed, highly mobile marine mammal: the short-beaked common dolphin (genus Delphinus). PLoS One 2012; 7:e31482. [PMID: 22319634 PMCID: PMC3271111 DOI: 10.1371/journal.pone.0031482] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Accepted: 01/09/2012] [Indexed: 02/04/2023] Open
Abstract
Identifying which factors shape the distribution of intraspecific genetic diversity is central in evolutionary and conservation biology. In the marine realm, the absence of obvious barriers to dispersal can make this task more difficult. Nevertheless, recent studies have provided valuable insights into which factors may be shaping genetic structure in the world's oceans. These studies were, however, generally conducted on marine organisms with larval dispersal. Here, using a seascape genetics approach, we show that marine productivity and sea surface temperature are correlated with genetic structure in a highly mobile, widely distributed marine mammal species, the short-beaked common dolphin. Isolation by distance also appears to influence population divergence over larger geographical scales (i.e. across different ocean basins). We suggest that the relationship between environmental variables and population structure may be caused by prey behaviour, which is believed to determine common dolphins' movement patterns and preferred associations with certain oceanographic conditions. Our study highlights the role of oceanography in shaping genetic structure of a highly mobile and widely distributed top marine predator. Thus, seascape genetic studies can potentially track the biological effects of ongoing climate-change at oceanographic interfaces and also inform marine reserve design in relation to the distribution and genetic connectivity of charismatic and ecologically important megafauna.
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Affiliation(s)
- Ana R Amaral
- Centro de Biologia Ambiental, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
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293
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Wagner HH, Murphy MA, Holderegger R, Waits L. Developing an Interdisciplinary, Distributed Graduate Course for Twenty-First Century Scientists. Bioscience 2012. [DOI: 10.1525/bio.2012.62.2.11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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294
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Niedziałkowska M, Fontaine M, Jędrzejewska B. Factors shaping gene flow in red deer (Cervus elaphus) in seminatural landscapes of central Europe. CAN J ZOOL 2012. [DOI: 10.1139/z11-122] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We studied gene flow and connectivity between three subpopulations and nine groups of red deer ( Cervus elaphus L., 1758) occurring in forests in northeastern Poland and western Belarus. The red deer in this region mostly originated from translocated individuals that were introduced primarily in the 19th and 20th centuries. The genetic structure of the population has been identified during the previous study. Using 14 microsatellite loci, we detected 14 first-generation migrants between the three subpopulations and 21 among the nine groups of deer. The number of effective migrants (Nm) was estimated to be 2.5 individuals/generation between the subpopulations and 6.2 individuals/generation between the groups. About 80% of first-generation migrants moved less than 150 km. The gene flow of hinds and stags was similar. A least cost path (LCP) analysis was performed using different habitat types: deciduous and mixed forests, coniferous forests, wetlands, meadows, arable lands, scarce settlements, dense settlements, and waters. No significant barriers to dispersal were detected, but individual dispersal was restricted in space by the significant isolation by distance. The best model, explaining the genetic distance (FST/1 – FST) between the forests, suggested that LCP corridor length limited gene flow and high forest cover within LCP corridors increased gene flow among the forests.
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Affiliation(s)
- M. Niedziałkowska
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | - M.C. Fontaine
- Institute of Integrative and Comparative Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
- Université Paris-Sud, Laboratoire Ecologie, Systématique et Evolution, UMR 8079, Orsay CEDEX, F-91405; CNRS, UMR 8079, Orsay CEDEX, F-91405
| | - B. Jędrzejewska
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
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295
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PRUNIER J, KAUFMANN B, GROLET O, PICARD D, POMPANON F, JOLY P. Skin swabbing as a new efficient DNA sampling technique in amphibians, and 14 new microsatellite markers in the alpine newt (
Ichthyosaura alpestris
). Mol Ecol Resour 2012; 12:524-31. [DOI: 10.1111/j.1755-0998.2012.03116.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. PRUNIER
- Ecosphère, 3bis rue des Remises, 94100 Saint Maur des Fossés, France
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, ENTPE, CNRS, Villeurbanne, F‐69622, France
| | - B. KAUFMANN
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, ENTPE, CNRS, Villeurbanne, F‐69622, France
| | - O. GROLET
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, ENTPE, CNRS, Villeurbanne, F‐69622, France
| | - D. PICARD
- Université d’Angers, Laboratoire d’Etudes Environnementales des Systèmes Anthropisés, 2 Boulevard Lavoisier, 49045 Angers Cedex 01, France
| | - F. POMPANON
- Université Joseph Fourier, Laboratoire d’Ecologie Alpine, CNRS, UMR 5553, 2233 Rue de la Piscine, 38041 Grenoble Cedex 9, France
| | - P. JOLY
- UMR5023 Ecologie des Hydrosystèmes Naturels et Anthropisés, Université de Lyon, Université Lyon 1, ENTPE, CNRS, Villeurbanne, F‐69622, France
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296
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Connectivity of prairie dog colonies in an altered landscape: inferences from analysis of microsatellite DNA variation. CONSERV GENET 2011. [DOI: 10.1007/s10592-011-0293-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
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297
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Rosales-Castillo JA, Vázquez-Garcidueñas MS, Álvarez-Hernández H, Chassin-Noria O, Varela-Murillo AI, Zavala-Páramo MG, Cano-Camacho H, Vázquez-Marrufo G. Genetic diversity and population structure of Escherichia coli from neighboring small-scale dairy farms. J Microbiol 2011; 49:693-702. [DOI: 10.1007/s12275-011-0461-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 04/21/2011] [Indexed: 10/15/2022]
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298
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Plants on the move: The role of seed dispersal and initial population establishment for climate-driven range expansions. ACTA OECOLOGICA-INTERNATIONAL JOURNAL OF ECOLOGY 2011. [DOI: 10.1016/j.actao.2011.05.001] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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299
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Lymbery AJ, Thompson RCA. The molecular epidemiology of parasite infections: tools and applications. Mol Biochem Parasitol 2011; 181:102-16. [PMID: 22027028 DOI: 10.1016/j.molbiopara.2011.10.006] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/10/2011] [Accepted: 10/12/2011] [Indexed: 10/16/2022]
Abstract
Molecular epidemiology, broadly defined, is the application of molecular genetic techniques to the dynamics of disease in a population. In this review, we briefly describe molecular and analytical tools available for molecular epidemiological studies and then provide an overview of how they can be applied to better understand parasitic disease. A range of new molecular tools have been developed in recent years, allowing for the direct examination of parasites from clinical or environmental samples, and providing access to relatively cheap, rapid, high throughput molecular assays. At the same time, new analytical approaches, in particular those derived from coalescent theory, have been developed to provide more robust estimates of evolutionary processes and demographic parameters from multilocus, genotypic data. To date, the primary application of molecular epidemiology has been to provide specific and sensitive identification of parasites and to resolve taxonomic issues, particularly at the species level and below. Population genetic studies have also been used to determine the extent of genetic diversity among populations of parasites and the degree to which this diversity is associated with different host cycles or epidemiologically important phenotypes. Many of these studies have also shed new light on transmission cycles of parasites, particularly the extent to which zoonotic transmission occurs, and on the prevalence and importance of mixed infections with different parasite species or intraspecific variants (polyparasitism). A major challenge, and one which is now being addressed by an increasing number of studies, is to find and utilize genetic markers for complex traits of epidemiological significance, such as drug resistance, zoonotic potential and virulence.
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Affiliation(s)
- A J Lymbery
- Fish Health Unit, School of Veterinary and Biomedical Sciences, Murdoch University, Murdoch WA 6150, Australia.
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300
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MORTIMER ELIZABETH, VAN VUUREN BETTINEJANSEN, MEIKLEJOHN KIAN, CHOWN STEVENL. Phylogeography of a mite, Halozetes fulvus, reflects the landscape history of a young volcanic island in the sub-Antarctic. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01770.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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