The trouble with isolation by distance

Molecular Ecology

Volumn 21, Issue 12, 2012, Pages 2839-2846

  Meirmans, Patrick G ^a  

^a UNIVERSITY OF AMSTERDAM   (Netherlands)

Author keywords

amova; fdist; Mantel test; null model; population structure; spatial autocorrelation

Indexed keywords

ANIMAL; BIOLOGICAL MODEL; GENE FREQUENCY; GENETIC VARIABILITY; REPRODUCTIVE ISOLATION; REVIEW; SPATIAL ANALYSIS; STATISTICAL MODEL;

ANIMALS; GENE FREQUENCY; GENETIC VARIATION; MODELS, GENETIC; MODELS, STATISTICAL; REPRODUCTIVE ISOLATION; SPATIAL ANALYSIS;

EID: 84861998927     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2012.05578.x     Document Type: Review

References (47)

1. Barrett RDH, Hoekstra H, (2011) Molecular spandrels: tests of adaptation at the genetic level. Nature Reviews Genetics, 12, 767-780.
2. Beaumont MA, Nichols RA, (1996) Evaluating loci for use in the genetic analysis of population structure. Proceedings of the Royal Society of London Series B-Biological Sciences, 263, 1619-1626.
3. Borcard D, Gillet F, Legendre P, (2011) Numerical Ecology with R. Springer Verlag, New York, pp. 1-319.
4. Coop G, Witonsky D, Di Rienzo A, Pritchard J, (2010) Using environmental correlations to identify loci underlying local adaptation. Genetics, 185, 1411-1423.
5. Drummond CS, Hamilton MB, (2007) Hierarchical components of genetic variation at a species boundary: population structure in two sympatric varieties of Lupinus microcarpus (Leguminosae). Molecular Ecology, 16, 753-769.
6. Dyer R, Nason J, Garrick RC, (2010) Landscape modelling of gene flow: improved power using conditional genetic distance derived from the topology of population networks. Molecular Ecology, 19, 3746-3759.
7. Eckert A, Van Heervaarden J, Wegrzyn J, et al. (2010) Patterns of population structure and environmental associations to aridity across the range of loblolly pine (Pinustaeda L., Pinaceae). Genetics, 185, 969-982.
8. Excoffier L, Lischer H, (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources, 10, 564-567.
9. Excoffier L, Smouse PE, Quattro JM, (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial-DNA restriction data. Genetics, 131, 479-491.
10. Excoffier L, Hofer T, Foll M, (2009) Detecting loci under selection in a hierarchically structured population. Heredity, 103, 285-298.
11. Foll M, Gaggiotti OE, (2006) Identifying the environmental factors that determine the genetic structure of populations. Genetics, 174, 875-891.
12. Foll M, Gaggiotti OE, (2008) A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics, 180, 977-993.
13. François O, Ancelet S, Guillot G, (2006) Bayesian clustering using hidden Markov random fields in spatial population genetics. Genetics, 174, 805-816.
14. Frantz AC, Cellina S, Krier A, Schley L, Burke T, (2009) Using spatial Bayesian methods to determine the genetic structure of a continuously distributed population: clusters or isolation by distance? Journal of Applied Ecology, 46, 493-505.
15. Greenwood PJ, (1980) Mating systems, philopatry and dispersal in birds and mammals. Animal Behaviour, 28, 1140-1162.
16. Guillot G, Leblois R, Coulon A, Frantz A, (2009) Statistical methods in spatial genetics. Molecular Ecology, 18, 4734-4756.
17. Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A, (2005) Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology, 25, 1965-1978.
18. Holliday J, Yuen M, Ritland K, Aitken S, (2010) Postglacial history of a widespread conifer produces inverse clines in selective neutrality tests. Molecular Ecology, 19, 3857-3864.
19. Jaramillo-Correa J, Grivet D, Terrab A, et al. (2010) The Strait of Gibraltar as a major biogeographic barrier in Mediterranean conifers: a comparative phylogeographic survey. Molecular Ecology, 19, 5452-5468.
20. Joost S, Bonin A, Bruford M, et al. (2007) A spatial analysis method (SAM) to detect candidate loci for selection: towards a landscape genomics approach to adaptation. Molecular Ecology, 16, 3955-3969.
21. Kimura M, (1968) Evolutionary rate at the molecular level. Nature, 217, 624-626.
22. Kimura M, (1983) The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK, pp. 1-193.
23. Kuchta S, Tan A, (2005) Isolation by distance and post-glacial range expansion in the rough-skinned newt, Taricha granulosa. Molecular Ecology, 14, 225-244.
24. Landguth E, Cushman S, Schwartz M, Mckelvey K, Murphy M, Luikart G, (2010) Quantifying the lag time to detect barriers in landscape genetics. Molecular Ecology, 19, 4179-4191.
25. Lee C, Mitchell-Olds T, (2011) Quantifying effects of environmental and geographical factors on patterns of genetic differentiation. Molecular Ecology, 20, 4631-4642.
26. Legendre P, (1993) Spatial autocorrelation:- trouble or new paradigm? Ecology, 74, 1659-1673.
27. Malécot G, (1948). Les mathématiques de l'hérédité. Masson, Paris, France.
28. Mantel N, (1967) The detection of disease clustering and a generalized regression approach. Cancer Research, 27, 209-220.
29. Meirmans PG, (2011) Marlin, software to create, run, and analyse spatially realistic simulations. Molecular Ecology Resources, 11, 146-150.
30. Meirmans PG, Van Tienderen PH, (2004) GenoType and GenoDive: two programs for the analysis of genetic diversity of asexual organisms. Molecular Ecology Notes, 4, 792-794.
31. Meirmans PG, Goudet J, Gaggiotti OE, (2011) Ecology and life history affect different aspects of the population structure of 27 high-alpine plants. Molecular Ecology, 20, 3144-3155.
32. Moran PAP, (1950) Notes on continuous stochastic phenomena. Biometrika, 37, 17-23.
33. Neuenschwander S, Hospital F, Guillaume F, Goudet J, (2008) quantinemo: an individual-based program to simulate quantitative traits with explicit genetic architecture in a dynamic metapopulation. Bioinformatics, 24, 1552-1553.
34. Oden NL, Sokal RR, (1986) Directional autocorrelation: an extension of spatial correlograms to two dimensions. Systematic Biology, 35, 608-617.
35. Oksanen J, Kindt R, Legendre P, et al. (2009). Vegan: Community ecology package. R package version 1.15-3.
36. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945-959.
37. Rousset F, (1997) Genetic differentiation and estimation of gene flow from F-statistics under isolation by distance. Genetics, 145, 1219-1228.
38. Smouse PE, Long JC, Sokal RR, (1986) Multiple regression and correlation extensions of the Mantel test of matrix correspondence. Systematic zoology, 35, 627-632.
39. Taberlet P, Fumagalli L, Wust-Saucy AG, Cosson JF, (1998) Comparative phylogeography and postglacial colonization routes in Europe. Molecular Ecology, 7, 453-464.
40. Tackenberg O, Poschlod P, Kahmen S, (2003) Dandelion seed dispersal: the horizontal wind speed does not matter for long-distance dispersal-it is updraft! Plant Biology, 5, 451-454.
41. Vasemägi A, (2006) The adaptive hypothesis of clinal variation revisited: single-locus clines as a result of spatially restricted gene flow. Genetics, 173, 2411-2414.
42. Vekemans X, Hardy OJ, (2004) New insights from fine-scale spatial genetic structure analyses in plant populations. Molecular Ecology, 13, 921-935.
43. Wasser SK, Shedlock AM, Comstock K, Ostrander EA, Mutayoba B, Stephens M, (2004) Assigning African elephant DNA to geographic region of origin: applications to the ivory trade. Proceedings of the National Academy of Sciences of the United States of America, 101, 14847-14852.
44. Whitlock MC, McCauley DE, (1999) Indirect measures of gene flow and migration: F-ST != 1/(4Nm+1). Heredity, 82, 117-125.
45. Wiegand T, Moloney KA, (2004) Rings, circles, and null-models for point pattern analysis in ecology. Oikos, 104, 209-229.
46. Wright S, (1931) Evolution in Mendelian populations. Genetics, 16, 97-159.
47. Wright S, (1943) Isolation by distance. Genetics, 28, 114- 138.