Optimizing the trade-off between spatial and genetic sampling efforts in patchy populations: Towards a better assessment of functional connectivity using an individual-based sampling scheme

Molecular Ecology

Volumn 22, Issue 22, 2013, Pages 5516-5530

  Prunier, J G ^a,b   Kaufmann, B ^b   Fenet, S ^c   Picard, D ^d   Pompanon, F ^e   Joly, P ^b   Lena, J P ^b  

^a Ecosphère ^*  (France)

^b UMR5023 Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés   (France)

^c UNIVERSITÉ LYON 1   (France)

^d UNIVERSITÉ D'ANGERS   (France)

^e UNIV GRENOBLE ALPES   (France)

Author keywords

CDPOP; Ichthyosaura alpestris; landscape genetics; Mantel tests; pairwise genetic distances; restricted permutations

Indexed keywords

MICROSATELLITE DNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CDPOP; COMPUTER SIMULATION; ENVIRONMENT; GENETICS; GENOTYPE; ICHTHYOSAURA ALPESTRIS; LANDSCAPE GENETICS; MANTEL TESTS; PAIRWISE GENETIC DISTANCES; POPULATION GENETICS; RESTRICTED PERMUTATIONS; SALAMANDRIDAE;

CDPOP; ICHTHYOSAURA ALPESTRIS; LANDSCAPE GENETICS; MANTEL TESTS; PAIRWISE GENETIC DISTANCES; RESTRICTED PERMUTATIONS;

ANIMALS; COMPUTER SIMULATION; ENVIRONMENT; GENETICS, POPULATION; GENOTYPE; MICROSATELLITE REPEATS; MODELS, GENETIC; SALAMANDRIDAE;

EID: 84887319258     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/mec.12499     Document Type: Article

References (77)

1. Anderson CD, Epperson BK, Fortin MJ, et al,. (2010) Considering spatial and temporal scale in landscape-genetic studies of gene flow. Molecular Ecology, 19, 3565-3575.
2. Austin JD, Gorman TA, Bishop D, (2011) Assessing fine-scale genetic structure and relatedness in the micro-endemic Florida bog frog. Conservation Genetics, 12, 833-838.
3. Baguette M, (2004) The classical metapopulation theory and the real, natural world: a critical appraisal. Basic and Applied Ecology, 5, 213-224.
4. Beerli P, (2004) Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Molecular Ecology, 13, 827-836.
5. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F, (2004) GENETIX 4.03, logiciel sous WindowsTM pour la génétique des populations. Laboratoire Génome, Populations, Interactions CNRS UMR 5000, Université de Montpellier II, Montpellier, France.
6. Blair C, Weigel DE, Balazik M, et al,. (2012) A simulation-based evaluation of methods for inferring linear barriers to gene flow. Molecular Ecology Resources, 12, 822-833.
7. Bonnet E, Van de Peer Y, (2002) zt: a software tool for simple and partial Mantel tests. Journal of Statistical software, 7, 1-12.
8. Borcard D, Legendre P, (2012) Is the Mantel correlogram powerful enough to be useful in ecological analysis? A simulation study. Ecology, 93, 1473-1481.
9. Bowcock AM, Ruizlinares A, Tomfohrde J, et al,. (1994) High-resolution of human evolutionary trees with polymorphic microsatellites. Nature, 368, 455-457.
10. Broquet T, Petit EJ, (2009) Molecular Estimation of Dispersal for Ecology and Population Genetics. Annual Review of Ecology Evolution and Systematics, pp. 193-216. Annual Reviews, Palo Alto.
11. Broquet T, Ray N, Petit E, Fryxell JM, Burel F, (2006) Genetic isolation by distance and landscape connectivity in the American marten (Martes americana). Landscape Ecology, 21, 877-889.
12. Broquet T, Berset-Braendli L, Emaresi G, Fumagalli L, (2007) Buccal swabs allow efficient and reliable microsatellite genotyping in amphibians. Conservation Genetics, 8, 509-511.
13. Cavalli-Sforza LL, Edwards AWF, (1967) Phylogenetic analysis: models and estimation procedures. American Journal of Human Genetics, 19, 233-257.
14. Chen C, Durand E, Forbes F, Francois O, (2007) Bayesian clustering algorithms ascertaining spatial population structure: a new computer program and a comparison study. Molecular Ecology Notes, 7, 747-756.
15. Clarke RT, Rothery P, Raybould AF, (2002) Confidence limits for regression relationships between distance matrices: estimating gene flow with distance. Journal of Agricultural Biological and Environmental Statistics, 7, 361-372.
16. Crida A, Manel S, (2007) WOMBSOFT: an R package that implements the Wombling method to identify genetic boundary. Molecular Ecology Notes, 7, 588-591.
17. Cushman SA, (2006) Effects of habitat loss and fragmentation on amphibians: a review and prospectus. Biological Conservation, 128, 231-240.
18. Cushman SA, Landguth EL, (2010a) Scale dependent inference in landscape genetics. Landscape Ecology, 25, 967-979.
19. Cushman SA, Landguth EL, (2010b) Spurious correlations and inference in landscape genetics. Molecular Ecology, 19, 3592-3602.
20. Cushman SA, McKelvey KS, Hayden J, Schwartz MK, (2006) Gene flow in complex landscapes: testing multiple hypotheses with causal modeling. American Naturalist, 168, 486-499.
21. Cushman SA, Wasserman TN, Landguth EL, Shirk AJ, (2013) Re-evaluating causal modeling with Mantel tests in landscape genetics. Diversity, 5, 51-72.
22. Efron B, Tibshirani R, (1993) An Introduction to the Bootstrap. Chapman & Hall, New York, London.
23. Emaresi G, Pellet J, Dubey S, Hirzel A, Fumagalli L, (2011) Landscape genetics of the Alpine newt (Mesotriton alpestris) inferred from a strip-based approach. Conservation Genetics, 12, 41-50.
24. Epperson BK, (2003) Geographical Genetics. Princeton University Press, Princeton and Oxford.
25. Epps CW, Palsboll PJ, Wehausen JD, et al,. (2005) Highways block gene flow and cause a rapid decline in genetic diversity of desert bighorn sheep. Ecology Letters, 8, 1029-1038.
26. 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). Molecular Ecology, 17, 1905-1917.
27. Funk WC, Blouin MS, Corn PS, et al,. (2005) Population structure of Columbia spotted frogs (Rana luteiventris) is strongly affected by the landscape. Molecular Ecology, 14, 483-496.
28. Garner TWJ, Schmidt BR, Hoeck P, Van Buskirk J, (2003) Di- and tetranucleotide microsatellite markers for the Alpine newt (Triturus alpestris): characterization and cross-priming in five congeners. Molecular Ecology Notes, 3, 186-188.
29. Goldberg CS, Waits LP, (2010) Comparative landscape genetics of two pond-breeding amphibian species in a highly modified agricultural landscape. Molecular Ecology, 19, 3650-3663.
30. Goudet J, (2001) FSTAT, a Program to Estimate and Test Gene Diversities and Fixation Indices (Version 2.9.3). University of Lausanne, Dorigny.
31. Graham MH, (2003) Confronting multicollinearity in ecological multiple regression. Ecology, 84, 2809-2815.
32. Graves T, Beier P, Royle JA, (2013) Current approaches using genetic distances produce poor estimates of landscape resistance to interindividual dispersal. Molecular Ecology, 22, 3888-3903.
33. Guillot G, Rousset F, (2013) Dismantling the Mantel tests. Methods in Ecology and Evolution, 4, 336-344.
34. Hanski I, (1999) Metapopulation Ecology. Oxford University Press, Oxford.
35. Harrison S, (1991) Local extinction in a metapopulation context: an empirical evaluation. Biological Journal of the Linnean Society, 42, 73-88.
36. Holderegger R, Wagner HH, (2008) Landscape genetics. BioScience, 58, 199-207.
37. Jaquiéry J, Broquet T, Hirzel AH, Yearsley J, Perrin N, (2011) Inferring landscape effects on dispersal from genetic distances: how far can we go? Molecular Ecology, 20, 692-705.
38. Jombart T, Devillard S, Dufour AB, Pontier D, (2008) Revealing cryptic spatial patterns in genetic variability by a new multivariate method. Heredity, 101, 92-103.
39. Kalinowski ST, (2005) Do polymorphic loci require large sample sizes to estimate genetic distances? Heredity, 94, 33-36.
40. Kelly RP, Oliver TA, Sivasundar A, Palumbi SR, (2010) A method for detecting population genetic structure in diverse, high gene-flow species. Journal of Heredity, 101, 423-436.
41. Kimura M, Weiss GH, (1964) The stepping stone model of population structure and the decrease of genetic correlation with distance. Genetics 49, 561-576.
42. Kovar R, Brabec M, Vita R, Bocek R, (2009) Spring migration distances of some Central European amphibian species. Amphibia-Reptilia, 30, 367-378.
43. Landguth EL, Cushman SA, (2010) CDPOP: a spatially explicit cost distance population genetics program. Molecular Ecology Resources, 10, 156-161.
44. Landguth EL, Cushman SA, Schwartz MK, et al,. (2010) Quantifying the lag time to detect barriers in landscape genetics. Molecular Ecology, 19, 4179-4191.
45. Landguth EL, Fedy BC, Oyler-McCance SJ, et al,. (2012) Effects of sample size, number of markers, and allelic richness on the detection of spatial genetic pattern. Molecular Ecology Resources, 12, 276-284.
46. Legendre P, (2000) Comparison of permutation methods for the partial correlation and partial Mantel tests. Journal of Statistical Computation and Simulation, 67, 37-73.
47. Legendre P, Fortin MJ, (2010) Comparison of the Mantel test and alternative approaches for detecting complex multivariate relationships in the spatial analysis of genetic data. Molecular Ecology Resources, 10, 831-844.
48. Legendre L, Legendre P, (1998) Numerical Ecology, 2nd edn. Elsevier, Amsterdam.
49. Lowe WH, Allendorf FW, (2010) What can genetics tell us about population connectivity? Molecular Ecology, 19, 3038-3051.
50. Manel S, Schwartz MK, Luikart G, Taberlet P, (2003) Landscape genetics: combining landscape ecology and population genetics. Trends in Ecology & Evolution, 18, 189-197.
51. Manel S, Gaggiotti OE, Waples RS, (2005) Assignment methods: matching biological questions techniques with appropriate techniques. Trends in Ecology & Evolution, 20, 136-142.
52. Manel S, Joost S, Epperson BK, et al,. (2010) Perspectives on the use of landscape genetics to detect genetic adaptive variation in the field. Molecular Ecology, 19, 3760-3772.
53. Manly BFJ, (2007) Randomization, Bootstrap and Monte Carlo Methods in Biology, 3rd edn. Chapman & Hall/CRC, Boca Raton.
54. Manni F, Guerard E, Heyer E, (2004) Geographic patterns of (genetic, morphologic, linguistic) variation: how barriers can be detected by using Monmonier's algorithm. Human Biology, 76, 173-190.
55. Mantel N, (1967) Detection of disease clustering and a generalized regression approach. Cancer Research 27, 209-220.
56. Mayer C, Schiegg K, Pasinelli G, (2009) Patchy population structure in a short-distance migrant: evidence from genetic and demographic data. Molecular Ecology, 18, 2353-2364.
57. Nei M, Tajima F, Tateno Y, (1983) Accuracy of estimated phylogenetic trees from molecular data. Journal of Molecular Evolution, 19, 153-170.
58. Olivieri I, Michalakis Y, Gouyon PH, (1995) Metapopulation genetics and the evolution of dispersal. American Naturalist, 146, 202-228.
59. Perret N, Pradel R, Miaud C, Grolet O, Joly P, (2003) Transience, dispersal and survival rates in newt patchy populations. Journal of Animal Ecology, 72, 567-575.
60. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
61. Prunier J, Kaufmann B, Grolet O, et al,. (2012) Skin swabbing as a new efficient DNA sampling technique in amphibians, and 14 new microsatellite markers in the alpine newt (Ichthyosaura alpestris). Molecular Ecology Resources, 12, 524-531.
62. Rousset F, (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145, 1219-1228.
63. Rousset F, (2000) Genetic differentiation between individuals. Journal of Evolutionary Biology, 13, 58-62.
64. Ruzzante DE, (1998) A comparison of several measures of genetic distance and population structure with microsatellite data: bias and sampling variance. Canadian Journal of Fisheries and Aquatic Sciences, 55, 1-14.
65. Safner T, Miaud C, Gaggiotti O, et al,. (2011a) Combining demography and genetic analysis to assess the population structure of an amphibian in a human-dominated landscape. Conservation Genetics, 12, 161-173.
66. Safner T, Miller MP, McRae BH, Fortin M-J, Manel S, (2011b) Comparison of Bayesian clustering and edge detection methods for inferring boundaries in landscape genetics. International Journal of Molecular Sciences, 12, 865-889.
67. Schwartz MK, McKelvey KS, (2009) Why sampling scheme matters: the effect of sampling scheme on landscape genetic results. Conservation Genetics, 10, 441-452.
68. Segelbacher G, Cushman SA, Epperson BK, et al,. (2010) Applications of landscape genetics in conservation biology: concepts and challenges. Conservation Genetics, 11, 375-385.
69. Selkoe KA, Watson JR, White C, et al,. (2010) Taking the chaos out of genetic patchiness: seascape genetics reveals ecological and oceanographic drivers of genetic patterns in three temperate reef species. Molecular Ecology, 19, 3708-3726.
70. Smith MA, Green DM, (2005) Dispersal and the metapopulation paradigm in amphibian ecology and conservation: are all amphibian populations metapopulations? Ecography, 28, 110-128.
71. Smouse PE, Peakall R, (1999) Spatial autocorrelation analysis of individual multiallele and multilocus genetic structure. Heredity, 82, 561-573.
72. Smouse PE, Long JC, Sokal RR, (1986) Multiple-regression and correlation extensions of the mantel test of matrix correspondence. Systematic Zoology, 35, 627-632.
73. Van Strien MJ, Keller D, Holderegger R, (2012) A new analytical approach to landscape genetic modelling: least-cost transect analysis and linear mixed models. Molecular Ecology, 21, 4010-4023.
74. Weir BS, Cockerham CC, (1984) Estimating F-Statistics for the analysis of population structure. Evolution, 38, 1358-1370.
75. Wright S, (1931) Evolution in Mendelian populations. Genetics, 16, 0097-0159.
76. Wright S, (1943) Isolation by distance. Genetics, 28, 114-138.
77. Wright S, (1951) The genetical structure of populations. Annals of Eugenics, 15, 323-354.