Sample design effects in landscape genetics

Springer Science and Business Media LLC - Tập 14 Số 2 - Trang 275-285 - 2013
Sara J. Oyler‐McCance1, Bradley C. Fedy2,1, Erin L. Landguth3
1U.S. Geological Survey, Fort Collins Science Center, Fort Collins, USA
2Department of Environment and Resource Studies, University of Waterloo, Waterloo, Canada
3Division of Biological Sciences, University of Montana, Missoula, USA

Tóm tắt

Từ khóa


Tài liệu tham khảo

Aarts G, MacKenzie M, McConnell B, Fedak M, Matthiopoulos J (2008) Estimating space-use and habitat preference from wildlife telemetry data. Ecography 31:140–160

Agee JK, Johnson DR (1987) Ecosystem management for parks and wilderness. University of Washington Press, Seattle

Anderson CD, Epperson BK, Fortin M-J, Holdregger R, James PM, Rosenberg M, Scriber KT, Spear ST (2010) Considering spatial and temporal scale in landscape-genetic studies of gene flow. Mol Ecol 19:3565–3575

Balkenhol N, Landguth EL (2011) Simulation modeling in landscape genetics: on the need to go further. Mol Ecol 20:667–670

Balkenhol N, Gugerli F, Cushman SA, Waits LP, Coulon A, Arntzen JW, Holderegger R, Wagner HH (2009) Identifying future research needs in landscape genetics: where to from here? Landsc Ecol 24:455–463

Barba MD, Waits LP, Genovesi P, Randi E, Chirichella R, Cetto E (2010) Comparing opportunistic and systematic sampling methods for non-invasive genetic monitoring of a small translocated brown bear population. J Appl Ecol 47:172–181

Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL (1994) High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368:455–457

Bruggeman DJ, Wiegand T, Fernandez N (2010) The relative effects of habitat loss and fragmentation on population genetic variation in the red-cockaded woodpecker (Picoides borealis). Mol Ecol 19:3679–3691

Castoe TA, Poole AW, de Koning APJ, Jones KL, Tomback DF, Oyler-McCance SJ, Fike JA, Lance SL, Streicher JW, Smith EN, Pollock DD (2012) Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. PLoS ONE 7(2):e30953. doi: 10.1371/journal.pone.0030953

Cegelski CC, Waits LP, Anderson NJ, Flagstad O, Strobeck C, Kyle CJ (2006) Genetic diversity and population structure of wolverine (Gulo gulo) populations at the southern edge of their current distribution in North America with implications for genetic viability. Conserv Genet 7:197–211

Chapin S, Kofinas GP, Folke C (2009) Principles of ecosystem stewardship: resilience-based natural resource management in a changing world. Springer Science and Business Media, New York

Coe PK, Johnson BK, Wisdom MJ, Cook JG, Vavra M, Nielson RM (2011) Validation of elk resource selection models with spatially independent data. J Wildl Manage 75:159–170

Coulon A, Cosson JF, Angibault JM, Cargnelutti B, Galan M, Morellet N, Petit E, Aulagnier S, Hewison AJM (2004) Landscape connectivity influences gene flow in a roe deer population inhabiting a fragmented landscape: an individual-based approach. Mol Ecol 13:2841–2850

Cushman SA, Landguth EL (2010) Spurious correlations and inference in landscape genetics. Mol Ecol 19:3592–3602

Cushman SA, McKelvey KS, Hayden J, Schwartz MK (2006) Gene-flow in complex landscapes: testing multiple models with causal modeling. Am Natur 168:486–499

Dupanloup I, Schneider S, Excoffier L (2002) A simulated annealing approach to define the genetic structure of populations. Mol Ecol 11:2571–2581

Dyer RJ, Nason JD, Garrick RC (2010) Landscape modelling of gene flow: improved power using conditional genetic distance derived from the topology of population networks. Mol Ecol 19:3746–3759

Eckert AJ, Bower AD, González-Martínez SC, Wegrzyn JL, Coop G, Neale DB (2010) Back to nature: ecological genomics of loblolly pine (Pinus taeda, Pinaceae). Mol Ecol 19:3789–3805

Epperson BK, McRae BH, Scribner K, Cushman SA, Rosenberg MS, Fortin M-J, James PA, Murphy M, Manel S, Legendre P, Dale MRT (2010) Utility of computer simulations in landscape genetics. Mol Ecol 19:3549–3564

ESRI (1999–2008) Environmental System Research Institute, Redlands

Fedy BC, Martin K, Ritland C, Young J (2008) Genetic and ecological data provide incongruent interpretations of population structure and dispersal in naturally subdivided populations of white-tailed ptarmigan (Lagopus leucura). Mol Ecol 17:1905–1917

François O, Ancelet S, Guillot G (2006) Bayesian clustering using hidden markov random fields in spatial population genetics. Genetics 174:805–816

Freedman AH, Thomassen HA, Buermann W, Smith TB (2010) Genomic signals of diversification along ecological gradients in a tropical lizard. Mol Ecol 19:3773–3788

Galindo HM, Pfeiffer-Herbert AS, McManus MA, Chao Y, Chai F, Palumbi SR (2010) Seascape genetics along a steep cline: using genetic patterns to test predictions of marine larval dispersal. Mol Ecol 19:3692–3707

Gamache I, Jaramillo-Correa JP, Payette S, Bousquet J (2003) Diverging patterns of mitochondrial and nuclear DNA diversity in subartic black spruce: imprint of a founder effect associated with postglacial colonization. Mol Ecol 12:891–901

Gauffre B, Estoup A, Bretagnolle V, Cosson JF (2008) Spatial genetic structure of a small rodent in a heterogenous landscape. Mol Ecol 17:4619–4629

Goslee SC, Urban DL (2007) The ecodist package for dissimilarity-based analysis of ecological data. J Stat Software 22:1–19

Guillot G, Rousset F (2012) On the use of simple and partial Mantel tests in presence of spatial autocorrelation. arXiv:1112.0651v1 [q-bio.PE]

Holderegger R, Wagner HH (2008) Landscape genetics. Bioscience 58:199–207

Jacquemyn H, Brys R, Honnay O, Hermy M, Roldán-Ruiz I (2006) Sexual reproduction, clonal diversity and genetic differentiation in patchily distributed populations of the temperate forest herb Paris quadrifolia (Trilliacaea). Oecologia 147:434–444

Jaquie′ry J, Broquet T, Hirzel AH, Yearsley J, Perrin N (2011) Inferring landscape effects on dispersal from genetic distances: how far can we go? Mol Ecol 20:692–705

Kendall KC, Stetz JB, Roon DA, Waits LP, Boulanger JB, Paetkau D (2008) Grizzly bear density in Glacier National Park, Montana. J Wildl Manage 72:1693–1705

Knowles LL, Alvarado-Serrano DF (2010) Exploring the population genetic consequences of the colonization process with spatio-temporally explicit models: insights from coupled ecological, demographic and genetic models in montane grasshoppers. Mol Ecol 19:3727–3745

Landguth EL, Cushman SA (2010) CDPOP: a spatially explicit cost distance population genetics program. Mol Ecol Res 10:156–161

Landguth EL, Cushman SA, Schwartz MK, McKelvey KS, Murphy M, Luikart G (2010) Quantifying the lag time to detect barriers in landscape genetics. Mol Ecol 19:4179–4191

Landguth EL, Fedy BC, Oyler-McCance SJ, Garey AL, Emel SL, Mumma M, Wagner HH, Fortin M-J, Cushman SA (2011) Effects of sample size, number of markers, and allelic richness on the detection of spatial genetic pattern. Mol Ecol Res. doi: 10.1111/j.1755-0998.2011.03077.x

Legendre P, Fortin M-J (2010) Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Mol Ecol Res 10:831–844

Legendre P, Legendre L (1998) Numerical ecology, 2nd English edn. Elsevier, Amsterdam

Manel S, Schwartz MK, Luikart G, Taberlet P (2003) Landscape genetics: combining landscape ecology and population genetics. Trends Ecol Evol 18:189–197

Manel S, Poncet BN, Legendre P, Gugerli F, Holderegger R (2010) Common factors drive adaptive genetic variation at different spatial scales in Arabis alpina. Mol Ecol 19:3824–3835

Mantel N (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

Martinez JG, Carranza J, Fernandez-Garcia JL, Sanchez-Prieto CB (2002) Genetic variation of red deer populations under hunting exploitation in southwestern Spain. J Wildl Manage 66:1273–1282

McRae BH, Beier P (2007) Circuit theory predicts gene flow in plant and animal populations. Proc Natl Acad Sci USA 104:19885–19890

Miller JR, Turner MG, Smithwick AH, Dent CL, Stanley EH (2004) Spatial extrapolation: the science of predicting ecological patterns and processes. Bioscience 4:310–320

Mladenoff DJ, Sickley TA, Wydeven AP (1999) Predicting gray wolf landscape recolonization: logistic regression models vs. new field data. Ecol Appl 9:37–44

Murphy M, Evans J, Cushman S, Storfer A (2008) Representing genetic variation as continuous surfaces: an approach for identifying spatial dependency in landscape genetic studies. Ecography 31:685–697

Murphy MA, Dezzani R, Pilliod DS, Storfer A (2010) Landscape genetics of high mountain frog metapopulations. Mol Ecol 19:3634–3649

Oyler-McCance SJ, Taylor SE, Quinn TW (2005) A multilocus genetic survey of greater sage-grouse across their range. Mol Ecol 14:1293–1310

Pernetta AP, Allen JA, Beebee TJC, Reading CH (2011) Fine-scale population genetic structure and sex-biased dispersal in the smooth snake (Coronella austriaca) in southern England. Heredity 107:231–238

Pritchard JK, Stephens M, Donnelly PJ (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

Raufaste N, Rousset F (2001) Are partial mantel tests adequate? Evolution 55:1703–1705

R Development Core Team (2009) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0, URL http://www.R-project.org

Schwartz MK, McKelvey KS (2009) Why sampling scheme matters: the effect of sampling scheme on landscape genetic results. Conserv Genet 10:441–452

Schwartz MK, Copeland JP, Anderson NJ, Squires JR, Inman RM, McKelvey KS, Pilgrim KL, Waits LP, Cushman SA (2009) Wolverine gene flow across a narrow climatic niche. Ecology 90:3222–3232

Segelbacher G, Cushman SA, Epperson BK, Fortin M-J, Francois O, Hardy OJ, Holdregger R, Taberlet P, Waits LP, Manel S (2010) Applications of landscape genetics in conservation biology: concepts and challenges. Conserv Genet 11:375–385

Selkoe KA, Watson JR, White C, Horin TB, Iacchei M, Mitarai S, Siegel DA, Gaines SD, Toonen RJ (2010) Taking the chaos out of genetic patchiness: seascape genetics reveals ecological and oceanographic drivers of genetic patterns in three temperate reef species. Mol Ecol 19:3708–3726

Shirk AJ, Wallin DO, Cushman SA, Rice CG, Warheit KI (2010) Inferring landscape effects on gene flow: a new multi-scale model selection framework. Mol Ecol 19:3603–3619

Short Bull RA, Cushman SA, Mace R, Chilton T, Kendall KC, Landguth EL, Schwartz MK, McKelvey K, Allendorf F, Luikart G (2010) Why replication is important in landscape genetics: American black bears in the Rocky Mountains. Mol Ecol 20:1092–1107

Sork V, Waits L (2010) Contributions of landscape genetics—approaches, insights, and future potential. Mol Ecol 17:3489–3495

Spear S, Balkenhol N, Fortin M-J, McRae B, Scribner K (2010) Use of resistance surfaces for landscape genetic studies: considerations for parameterization and analysis. Mol Ecol 19:3576–3591

Storfer A, Murphy M, Evans J, Goldberg C, Robinson S, Spear S, Dezzani R, Delmelle E, Vierling L, Waits L (2007) Putting the landscape in landscape genetics. Heredity 98:128–142

Storfer A, Murphy MA, Spear SF, Holderegger R, Waits LP (2010) Landscape Genetics: where are we now? Mol Ecol 19:3496–3514

Thomassen HA, Cheviron ZA, Freedman AH, Harrigan RJ, Wayne RK, Smith TB (2010) Spatial modelling and landscape-level approaches for visualizing intra-specific variation. Mol Ecol 19:3532–3548

Trombulak S, Baldwin R (2010) Landscape-scale conservation planning. Springer, New York