Inferring recent migration rates from individual genotypes

Molecular Ecology

Volumn 18, Issue 6, 2009, Pages 1048-1060

  Broquet, Thomas ^a   Yearsley, Jonathan ^a   Hirzel, Alexandre H ^a   Goudet, Jérôme ^a   Perrin, Nicolas ^a  

^a UNIVERSITY OF LAUSANNE   (Switzerland)

Author keywords

Backwards migration; Genetic inference; Immigration; Mixture model; Philopatry

Indexed keywords

ANIMAL; ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENETICS; GENOTYPE; GEOGRAPHY; METHODOLOGY; POPULATION DYNAMICS; POPULATION GENETICS; POPULATION MIGRATION; SHREW;

ANIMAL MIGRATION; ANIMALS; COMPUTER SIMULATION; GENETICS, POPULATION; GENOTYPE; GEOGRAPHY; MODELS, BIOLOGICAL; POPULATION DYNAMICS; SHREWS;

BASIDIOMYCOTA; CROCIDURA; CROCIDURA RUSSULA;

EID: 61649084999     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2008.04058.x     Document Type: Article

References (47)

1. Aitchison J (1986) The Statistical Analysis of Compositional Data. Blackburn Press, Caldwell, New Jersey.
2. Balding DJ, Nichols RA (1995) A method for quantifying differentiation between populations at multi-allelic loci and its implications for investigating identity and paternity. Genetica, 96, 3 12.
3. Beerli P (2004) Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Molecular Ecology, 13, 827 836.
4. Beerli P, Felsenstein J (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proceedings of the National Academy of Sciences, USA, 98, 4563 4568.
5. Berry O, Tocher MD, Sarre SD (2004) Can assignment tests measure dispersal? Molecular Ecology, 13, 551 561.
6. Billheimer D (2001) Compositional receptor modeling. Environmetrics, 12, 451 467.
7. Bouteiller C, Perrin N (2000) Individual reproductive success and effective population size in the greater white-toothed shrew Crocidura russula. Proceedings of the Royal Society B: Biological Sciences, 267, 701 705.
8. Brooks SP (2001) On Bayesian analyses and finite mixtures for proportions. Statistics and Computing, 11, 179 190.
9. Churchfield S (1990) The Natural History of Shrews. Cornell University Press, New York.
10. Duarte LC, Bouteiller C, Fontanillas P, Petit E, Perrin N (2003) Inbreeding in the greater white-toothed shrew, Crocidura russula. Evolution, 57, 638 645.
11. Ehinger M, Fontanillas P, Petit E, Perrin N (2002) Mitochondrial DNA variation along an altitudinal gradient in the greater white-toothed shrew, Crocidura russula. Molecular Ecology, 11, 939 945.
12. Erwing G, Nicholls G, Rodrigo A (2004) Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations. Genetics, 168, 2407 2420.
13. Faubet P, Waples RS, Gaggiotti OE (2007) Evaluating the performance of a multilocus Bayesian method for the estimation of migration rates. Molecular Ecology, 16, 1149 1166.
14. Favre L, Balloux F, Goudet J, Perrin N (1997) Female biased dispersal in the monogamous mammal Crocidura russula: evidence from field data and microsatellite patterns. Proceedings of the Royal Society B: Biological Sciences, 264, 127 132.
15. Fontanillas P, Petit E, Perrin N (2004) Estimating sex-specific dispersal rates with autosomal markers in hierarchically structured populations. Evolution, 58, 886 894.
16. Frankham R, Ballou JD, Briscoe DA (2002) Introduction to Conservation Genetics. Cambridge University Press, Cambridge, UK.
17. Gelman A, Rubin DB (1992) Inference from iterative simulation using multiple sequences. Statistical Science, 7, 457 511.
18. Gelman A, Carlin JB, Stearn HS, Rubin DB (2004) Bayesian Data Analysis, 2nd edn. Chapman & Hall/CRC, New York.
19. Genoud M, Perrin N (1994) Fecundity versus offspring size in the greater white-toothed shrew, Crocidura russula. Journal of Animal Ecology, 63, 328 336.
20. Ghosh JK, Delampady M, Samanta T (2006) An Introduction to Bayesian Analysis. Springer, New York.
21. Hey J, Nielsen R (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics, 167, 747 760.
22. Hirzel AH, Jaquiéry J (2007) Ecogenetics Computer Program. University of Lausanne, Lausanne, Switzerland. URL : http://www.unil.ch/ biomapper/ecogenetics/.
23. Jain S, Neal RM (2004) A split-merge Markov chain Monte Carlo procedure for the Dirichlet process mixture model. Journal of Computational and Graphical Statistics, 13, 158 182.
24. Kass RE, Wasserman L (1996) The selection of prior distributions by formal rules. Journal of the American Statistical Association, 91, 1343 1370.
25. Koenig W, Van Vuren D, Hooge P (1996) Detectability, philopatry, and the distribution of dispersal distances in vertebrates. Trends in Ecology & Evolution, 11, 514 517.
26. Lande R (1993) Risks of population extinction from demographic and environmental stochasticity and random catastrophes. The American Naturalist, 142, 911 927.
27. Manel S, Gaggiotti OE, Waples RS (2005) Assignment methods: matching biological questions with appropriate techniques. Trends in Ecology & Evolution, 20, 136 142.
28. Neal RM (2000) Markov chain sampling methods for Dirichlet process mixture. Journal of Computational and Graphical Statistics, 9, 249 265.
29. Neigel JE (1997) A comparison of alternative strategies for estimating gene flow from genetic markers. Annual Review of Ecology and Systematics, 28, 105 128.
30. Paetkau D, Slade R, Burdens M, Estoup A (2004) Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Molecular Ecology, 13, 55 65.
31. Pella J, Masuda M (2001) Bayesian methods for analysis of stock mixtures from genetic characters. Fisheries Bulletin, 99, 151 167.
32. Plummer M, Best N, Cowles K, Vines K (2006) CODA: convergence diagnosis and output analysis for MCMC. R News, 6, 7 11. http://CRAN.R-project.org/doc.
33. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics, 155, 945 959.
34. R Development Core Team (2005) r: A Language and Environment for Statistical Computing. 2.2.1 edn. r Foundation for Statistical Computing, Vienna, Austria.
35. Reynolds JH, Tremplin WD (2004) Detecting specific populations in mixtures. Environmental Biology of Fishes, 69, 233 243.
36. Rousset F (2001) Genetic approaches to the estimation of dispersal rates. In : Dispersal (eds Clobert J, Danchin E, Dhondt AA, Nichols JD pp. 18 28. Oxford University Press, New York.
37. Slatkin M (2005) Seeing ghosts: the effect of unsampled populations on migration rates estimated for sampled populations. Molecular Ecology, 14, 67 73.
38. Slatkin M, Barton NH (1989) A comparison of three indirect methods for estimating average levels of gene flow. Evolution, 43, 1349 1368.
39. Sork VL, Nason J, Campbell DR, Fernandez JF (1999) Landscape approaches to historical and contemporary gene flow in plants. Trends in Ecology & Evolution, 14, 219 224.
40. Thomas A, Hara BO, Ligges U, Sturtz S (2006) Making BUGS open. R News, 6, 12 17.
41. Vitalis R (2002) Sex-specific genetic differentiation and coalescence times: estimating sex-biased dispersal rates. Molecular Ecology, 11, 125 138.
42. Vitalis R, Couvet D (2001) Estimation of effective population size and migration rate from one- and two-locus identity measures. Genetics, 157, 911 925.
43. Vogel P (1999) Colonisation capacity of the greater white-toothed shrew Crocidura russula: an experimental study. Säugetierkundliche Mitteilungen, 44, 37 47.
44. Wang J, Whitlock MC (2003) Estimating effective population size and migration rates from genetic samples over space and time. Genetics, 163, 429 446.
45. ST ≠ 1/(4Nm + 1). Heredity, 82, 117 125.
46. Wilson GA, Rannala B (2003) Bayesian inference of recent migration rates using multilocus genotypes. Genetics, 163, 1177 1191.
47. Wright S (1931) Evolution in Mendelian populations. Genetics, 16, 97 159.