Computer programs for population genetics data analysis: A survival guide

Nature Reviews Genetics

Volumn 7, Issue 10, 2006, Pages 745-758

  Excoffier, Laurent ^a   Heckel, Gerald ^a  

^a UNIVERSITY OF BERN   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PROTEIN;

AMINO ACID SEQUENCE; BAYES THEOREM; COMPUTER GRAPHICS; COMPUTER PROGRAM; DATA ANALYSIS; DNA SEQUENCE; GENE LINKAGE DISEQUILIBRIUM; GENETIC VARIABILITY; GENOTYPE; HUMAN; IMMIGRANT; MAXIMUM LIKELIHOOD METHOD; MIGRATION; MONTE CARLO METHOD; POPULATION GENETICS; POPULATION SIZE; PRIORITY JOURNAL; PROBABILITY; REVIEW; SHORT TANDEM REPEAT; STATISTICAL ANALYSIS;

COMPUTERS; GENETICS, POPULATION; HUMANS; SOFTWARE; STATISTICS;

EID: 33748762488     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg1904     Document Type: Review

References (65)

1. Schaffner, S. F. et al. Calibrating a coalescent simulation of human genome sequence variation. Genome Res. 15, 1576-1583 (2005).
2. Akey, J. M. et al. Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol. 2, e286 (2004).
3. Williamson, S. H. et al. Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc. Natl Acad. Sci. USA 102, 7882-7887 (2005). One of the first and more elaborate attempts to correct for the effect of past demography when inferring patterns of selection at the sequence level.
4. Fernandez, J., Villanueva, B., Pong-Wong, R. & Toro, M. A. Efficiency of the use of pedigree and molecular marker information in conservation programs. Genetics 170, 1313-1321 (2005).
5. Labate, J. A. Software for population genetics analyses of molecular marker data. Crop Sci. 40, 1521-1528 (2000).
6. Stephens, M. & Scheet, P. Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am. J. Hum. Genet. 76, 449-462 (2005).
7. Felsenstein, J. Inferring Phylogenies (Sinauer Associates, Sunderland, 2003).
8. Knowles, L. L. The burgeoning field of statistical phylogeography. J. Evol. Biol. 17, 1-10 (2004).
9. Morrison, D. A. Networks in phylogenetic analysis: new tools for population biology. Int. J. Parasitol. 35, 567-582 (2005).
10. Jones, A. G. & Ardren, W. R. Methods of parentage analysis in natural populations. Mol. Ecol. 12, 2511-2523 (2003).
11. Dudbridge, F. A survey of current software for linkage analysis. Hum. Genomics 1, 63-65 (2003).
12. Beaumont, M. A. & Rannala, B. The Bayesian revolution in genetics. Nature Rev. Genet. 5, 251-261 (2004). A necessary read presenting a broad overview of the use of Bayesian approaches in population genetics.
13. Beerli, P. Comparison of Bayesian and maximum-likelihood inference of population genetic parameters. Bioinformatics 22, 341-345 (2006).
14. Rosenberg, N. A. et al. Genetic structure of human populations. Science 298, 2381-2385 (2002).
15. Valdes, A. M., Slatkin, M. & Freimer, N. B. Allele frequencies at microsatellite loci: the stepwise mutation model revisited. Genetics 133, 737-749 (1993).
16. Slatkin, M. A measure of population subdivision based on microsatellite allele frequencies. Genetics 139, 457-462 (1995).
17. Goldstein, D. B., Ruiz Linares, A., Cavalli-Sforza, L. L. & Feldman, M. W. An evaluation of genetic distances for use with microsatellite loci. Genetics 139, 463-471 (1995).
18. Balloux, F., Brunner, H., Lugon-Moulin, N., Hausser, J. & Goudet, J. Microsatellites can be misleading: an empirical and simulation study. Evolution Int. J. Org. Evolution 54, 1414-1422 (2000).
19. Raymond, M. & Rousset, F. An exact test for population differentiation. Evolution 49, 1280-1283 (1995).
20. Lewontin, R. C. The interaction of selection and linkage. II. Optimum models. Genetics 50, 757-782 (1964).
21. Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595 (1989).
22. Evanno, G., Regnaut, S. & Goudet, J. Detecting the number of clusters of individuals using the software Structure: a simulation study. Mol. Ecol. 14, 2611-2620 (2005).
23. Nielsen, R. & Wakeley, J. Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics 158, 885-896 (2001).
24. Nielsen, R. & Slatkin, M. Likelihood analysis of ongoing gene flow and historical association. Evolution Int. J. Org. Evolution 54, 44-50 (2000).
25. Felsenstein, J. How can we infer geography and history from gene frequencies? J. Theor. Biol. 96, 9-20 (1982).
26. Wakeley, J. Distinguishing migration from isolation using the variance of pairwise differences. Theor. Popul. Biol. 49, 369-386 (1996).
27. Mountain, J. L. et al. SNPSTRs: empirically derived, rapidly typed, autosomal haplotypes for inference of population history and mutational processes. Genome Res. 12, 1766-1772 (2002).
28. Brooks, S. & Giudici, P. in Bayesian Statistics (eds Bernardo, J., Berger, J., Dawid, A. P. & Smith, A. F. M.) 733-742 (Oxford Univ. Press, Oxford, 1999).
29. Gaggiotti, O. E. et al. Patterns of colonization in a metapopulation of grey seals. Nature 416, 424-427 (2002). One of the first applications of RJ-MCMC in population and conservation genetics. The method allowed the authors to integrate non-genetic data such as demographic or environmental information directly in the inference process.
30. Gaggiotti, O. E., Brooks, S. P., Amos, W. & Harwood, J. Combining demographic, environmental and genetic data to test hypotheses about colonization events in metapopulations. Mol. Ecol. 13, 811-825 (2004).
31. Beaumont, M. A. & Nichols, R. A. Evaluating loci for use in the genetic analysis of population structure. Proc. R. Soc. Lond. B 263, 1619-1626 (1996). The first description of how genome scans that were performed in several populations can be used to detect loci under selection.
32. Beaumont, M. A. & Balding, D. J. Identifying adaptive genetic divergence among populations from genome scans. Mol. Ecol. 13, 969-980 (2004).
33. Slatkin, M. Seeing ghosts: the effect of unsampled populations on migration rates estimated for sampled populations. Mol. Ecol. 14, 67-73 (2005).
34. Beerli, P. Effect of unsampled populations on the estimation of population sizes and migration rates between sampled populations. Mol. Ecol. 13, 827-836 (2004).
35. Nielsen, R. Population genetic analysis of ascertained SNP data. Hum. Genomics 1, 218-224 (2004). A lucid description of the effect of SNP ascertainment bias on parameter inference and ways to correct it.
36. Nielsen, R. et al. Genomic scans for selective sweeps using SNP data. Genome Res. 15, 1566-1575 (2005).
37. Hey, J. & Nielsen, R. 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 (2004). A comprehensive presentation of the elaborate methodology underlying the IM program, which can simultaneously estimate gene flow and divergence time between two populations.
38. Beaumont, M. A., Zhang, W. & Balding, D. J. Approximate Bayesian computation in population genetics. Genetics 162, 2025-2035 (2002). A fundamental paper presenting the principles of ABC computations. It shows how genetic simulations can be used to accurately estimate parameters of arbitrarily complex demographic models, for which the likelihood is impossible or too costly to compute.
39. Marjoram, P., Molitor, J., Plagnol, V. & Tavare, S. Markov chain Monte Carlo without likelihoods. Proc. Natl Acad. Sci. USA 100, 15324-15328 (2003).
40. Excoffier, L., Estoup, A. & Cornuet, J.-M. Bayesian analysis of an admixture model with mutations and arbitrarily linked markers. Genetics 169, 1727-1738 (2005).
41. Zhao, J. H. & Tan, Q. Integrated analysis of genetic data with R. Hum. Genomics 2, 258-265 (2006).
42. Goudet, J. Hierfstat, a package for R to compute and test hierarchical F-statistics. Mol. Ecol. Notes 5, 184-186 (2005).
43. Price, E. W. & Carbone, I. SNAP: workbench management tool for evolutionary population genetic analysis. Bioinformatics 21, 402-404 (2005).
44. Altshuler, D. et al. A haplotype map of the human genome. Nature 437, 1299-1320 (2005).
45. Gilks, W. R., Richardson, S. & Spiegelhalter, D. J. Markov Chain Monte Carlo in Practice (Chapman and Hall/CRC, London, 1996).
46. Guillot, G., Mortier, F. & Estoup, A. Geneland: a computer package for landscape genetics. Mol. Ecol. Notes 5, 712-715 (2005).
47. Guillot, G., Estoup, A., Mortier, F. & Cosson, J. F. A spatial statistical model for landscape genetics. Genetics 170, 1261-1280 (2005). An extension of the Structure approach that explicitly uses spatial information to infer the genetic structure of populations and to detect recent immigrants.
48. Cegelski, C. C., Waits, L. P. & Anderson, N. J. Assessing population structure and gene flow in Montana wolverines (Gulo gulo) using assignment-based approaches. Mol. Ecol. 12, 2907-2918 (2003).
49. Excoffier, L., Laval, G. & Schneider, S. Arlequin ver. 3. 0: an integrated software package for population genetics data analysis. Evolutionary Bioinformatics Online 1, 47-50 (2005).
50. Rozas, J., Sanchez-DelBarrio, J. C., Messeguer, X. & Rozas, R. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496-2497 (2003).
51. Goudet, J. FSTAT (version 1.2): a computer program to calculate F-statistics. J. Hered. 86, 485-486 (1995).
52. Raymond, M. & Rousset, F. Genepop (version 1.2): population genetics software for exact tests and ecumenicism. J. Hered. 86, 248-249 (1995).
53. Kumar, S., Tamura, K. & Nei, M. MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief. Bioinform. 5, 150-163 (2004).
54. Dieringer, D. & Schlötterer, C. Microsatellite Analyser (MSA): a platform independent analysis tool for large microsatellite data sets. Mol. Ecol. Notes 3, 167-169 (2003).
55. Hardy, O. J. & Vekemans, X. SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol. Ecol. Notes 2, 618-620 (2002).
56. Wilson, G. A. & Rannala, B. Bayesian inference of recent migration rates using multilocus genotypes. Genetics 163, 1177-1191 (2003).
57. Corander, J., Waldmann, P., Marttinen, P. & Sillanpaa, M. J. BAPS 2: enhanced possibilities for the analysis of genetic population structure. Bioinformatics 20, 2363-2369 (2004).
58. Piry, S. et al. GeneClass2: A software for genetic assignment and first-generation migrant detection. J. Hered. 95, 536-539 (2004).
59. Anderson, E. C. & Thompson, E. A. A model-based method for identifying species hybrids using multilocus genetic data. Genetics 160, 1217-1229 (2002). A powerful Bayesian method that uses multilocus genotype information to identify the different types of hybrid individual present in a population.
60. Pritchard, J. K., Stephens, M. & Donnelly, P. Inference of population structure using multilocus genotype data. Genetics 155, 945-959 (2000). A highly influential and innovative paper that uses multilocus genotype information to assign individuals to populations, and to identify recent immigrants and admixed individuals.
61. Falush, D., Stephens, M. & Pritchard, J. K. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164, 1567-1587 (2003).
62. Wilson, I. J., Weale, M. E. & Balding, D. J. Inferences from DNA data: population histories, evolutionary processes and forensic match probabilities. J. R. Stat. Soc. A 166, 155-188 (2003).
63. Foll, M. & Gaggiotti, O. E. Colonise: a computer program to study colonization processes in metapopulations. Mol. Ecol. Notes 5, 705-707 (2005).
64. Beaumont, M. A. Detecting population expansion and decline using microsatellites. Genetics 153, 2013-2029 (1999).
65. Glaubitz, J. C. Convert: a user-friendly program to reformat diploid genotypic data for commonly used population genetic software packages. Mol. Ecol. Notes 4, 309-310 (2004)