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Inferring Patterns of Migration

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Book cover Bioinformatics

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 452))

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Abstract

The historical movement of organisms, whether recent or in the distant past, forms a central aspect of evolutionary studies. Inferring patterns of migration can be difficult and requires reliance on a large suite of bioinformatic tools. As it is primarily the movement of groups of related individuals or populations that are of interest, population genetic and phylogeographic methods form the core of tools used to decipher migration patterns. Following a description of these tools, we discuss the most critical—and potentially most difficult—aspect of these studies: the inference process used. Designing a study, determining which data to collect, how to analyze the data, and how to coordinate these results into a coherent narrative are all a part of this inference process. Furthermore, using different types of data (e.g., genotypic and DNA sequence) from different types of sources (direct, or from the organisms of interest; and indirect, from symbiotic organisms) produces a powerful suite of techniques that are used to infer patterns of migration.

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References

  1. Crandall, K. A., Templeton, A. R. (1993) Empirical tests of some predictions from coa-lescent theory with applications to intraspe-cific phylogeny reconstruction. Genetics 134, 959–969.

    PubMed  CAS  Google Scholar 

  2. Nickerson, D. M., Brunell, A. (1998) Power analysis for detecting trends in the presence of concomitant variables. Ecology 79, 1442–1447.

    Article  Google Scholar 

  3. Brumfield, R. T., Beerli, P., Nickerson, D. A., et al. (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends Ecol Evol 18, 249–256.

    Article  Google Scholar 

  4. Ewing, B., Hillier, L., Wendl, M. C., et al. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8, 175–185.

    PubMed  CAS  Google Scholar 

  5. Stephens, M., Smith, N., Donnelly, P. (2001) A new statistical method for haplo-type reconstruction from population data. Am J Hum Genet 68, 978–989.

    Article  PubMed  CAS  Google Scholar 

  6. Nielsen, R., Signorovitch, J. (2003) Correcting for ascertainment biases when analyzing SNP data: applications to the estimation of linkage disequilibrium. Theor Popul Biol 63, 245–255.

    Article  PubMed  Google Scholar 

  7. Zhang, D.-X., Hewitt, G. M. (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol Ecol 12, 563–584.

    Article  PubMed  CAS  Google Scholar 

  8. Bensch, S., Akesson, M. (2005) Ten years of AFLP in ecology and evolution: why so few animals? Mol Ecol 14, 2899–2914.

    Article  PubMed  CAS  Google Scholar 

  9. Wright, S. (1965) The interpretation of population structure by F-statistics with special regard to system of mating. Evolution 19, 395–420.

    Article  Google Scholar 

  10. Balloux, F., Lugon-Moulin, N. (2002) The estimation of population differentiation with microsatellite markers. Mol Ecol 11, 155–165.

    Article  PubMed  Google Scholar 

  11. Beerli, P., Felsenstein, J. (2001) Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopu-lations by using a coalescent approach. Proc Natl Acad Sci U S A 98, 4563–4568.

    Article  PubMed  CAS  Google Scholar 

  12. Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.

    Google Scholar 

  13. Hauser, L., Adcock, G. J., Smith, P. J., et al. (2002) Loss of microsatellite diversity and low effective population size in an overex-ploited population of New Zealand snapper (Pagrus auratus). Proc Natl Acad Sci U S A 99, 11742–11747.

    Article  PubMed  CAS  Google Scholar 

  14. Goudet, J. (2002) FSTAT: A Program to Estimate and Test Gene Diversities and Fixation Indices. Institut d'Ecologie, Université de Lausanne, Switzerland.

    Google Scholar 

  15. Schneider, S., Roessli, D., Excoffier, L. (2000) Arlequin. A Software for Population Genetics Data Analysis. Genetics and Biometry Laboratory, University of Geneva.

    Google Scholar 

  16. Excoffier, L., Smouse, P. E., Quattro, J. M. (1992) Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochon-drial DNA restriction data. Genetics 131, 479–491.

    PubMed  CAS  Google Scholar 

  17. Rogers, A.R., Harpending, H. (1992) Population growth makes waves in the distribution of pairwise genetic differences. Mol Biol Evol 9, 552–569.

    PubMed  CAS  Google Scholar 

  18. Slatkin, M., Hudson, R. R. (1991) Pair-wise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129, 555–562.

    PubMed  CAS  Google Scholar 

  19. Nee, S., Holmes, E. C., Rambaut, A., et al. (1995) Inferring population history from molecular phylogenies. Philos Trans Roy Soc B 349, 25–31.

    Article  CAS  Google Scholar 

  20. Pybus, O. G., Rambaut, A., Holmes, E. C., et al. (2002) New inferences from tree shape: numbers of missing taxa and population growth rates. Syst Biol 51, 881–888.

    Article  PubMed  CAS  Google Scholar 

  21. Pybus, O. G., Rambaut, A. (2002) GENIE: estimating demographic history from molecular phylogenies. Bioinformatics 18, 1404–1405.

    Article  PubMed  CAS  Google Scholar 

  22. Pybus, O. G., Rambaut, A., Harvey, P. H. (2000) An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155, 1429–1437.

    PubMed  CAS  Google Scholar 

  23. Strimmer, K., Pybus, O. G. (2001) Exploring the demographic history of DNA sequences using the generalized skyline plot. Mol Biol Evol 18, 2298–2305.

    PubMed  CAS  Google Scholar 

  24. Drummond, A., Strimmer, K. (2001) PAL: an object-oriented programming library for molecular evolution and phylogenetics. Bio-informatics 17, 662–663.

    CAS  Google Scholar 

  25. Holsinger, K. E. (1999) Analysis of genetic diversity in geographically structured populations: a Bayesian perspective. Hereditas 130, 245–255.

    Article  Google Scholar 

  26. Drummond, A. J., Nicholls, G. K., Rodrigo A. G., et al. (2002) Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161, 1307–1320.

    PubMed  CAS  Google Scholar 

  27. Wilson, G. A., Rannala, B. (2003) Bayesian inference of recent migration rates using mul-tilocus genotypes. Genetics 163, 1177–1191.

    PubMed  Google Scholar 

  28. Reeve, J., Rannala, B. (2002) DMLE+: Bayesian linkage disequilibrium gene mapping. Bioinformatics 18, 894–895.

    Article  PubMed  CAS  Google Scholar 

  29. Pritchard, J. K., Stephens, M., Donnelly, P. (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945–959.

    PubMed  CAS  Google Scholar 

  30. Wirth, T., Meyer, A., Achtman, M. (2005) Deciphering host migrations and origins by means of their microbes. Mol Ecol 14, 3289–3306.

    Article  PubMed  CAS  Google Scholar 

  31. Swofford, D. L. (2003) PAUP*: Phyloge-netic Analyses Using Parsimony and other methods, Version 4.0. Sinauer, Sunderland, MA.

    Google Scholar 

  32. Felsenstein, J. (2005) PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.

    Google Scholar 

  33. Posada, D., Crandall, K. A. (1998) Model-test: testing the model of DNA substitution. Bioinformatics 14, 817–818.

    Article  PubMed  CAS  Google Scholar 

  34. Nylander, J. A. A. (2004) MrModeltest v2. Program distributed by the author. Evolutionary Biology Centre, Uppsala University.

    Google Scholar 

  35. Huelsenbeck, J. P., Ronquist, F. (2001) MRBAYES: Bayesian inference of phylog-eny. Bioinformatics 17, 754–755.

    Article  PubMed  CAS  Google Scholar 

  36. Templeton, A. R. (1998) Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Mol Ecol 7, 381–397.

    Article  PubMed  CAS  Google Scholar 

  37. Clement, M., Posada, D., Crandall, K. A. (2000) TCS: a computer program to estimate gene genealogies. Mol Ecol 9, 1657–1659.

    Article  PubMed  CAS  Google Scholar 

  38. Templeton, A. R., Boerwinkle, E., Sing, C. F. (1987) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of Alcohol Dehydro-genase activity in Drosophila. Genetics 117, 343–351.

    CAS  Google Scholar 

  39. Templeton, A. R., Sing, C. F. (1993) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics 134, 659–669.

    PubMed  CAS  Google Scholar 

  40. Posada, D., Crandall, K. A., Templeton, A. R. (2000) GeoDis: a program for the cladistic nested analysis of the geographical distribution of haplotypes. Mol Ecol 9, 487–488.

    Article  PubMed  CAS  Google Scholar 

  41. Knowles, L. L., Maddison, W. P. (2002) Statistical phylogeography. Mol Ecol 11, 2623–2635.

    Article  PubMed  Google Scholar 

  42. Templeton, A. R. (2004) Statistical phy-logeography: methods of evaluating and minimizing inference errors. Mol Ecol 13, 789–809.

    Article  PubMed  Google Scholar 

  43. Cavalli-Sforza, L. L. (1998) The DNA revolution in population genetics. Trends Genet 14, 60–65.

    Article  PubMed  CAS  Google Scholar 

  44. Diamond, J., Bellwood, P. (2003) Farmers and their languages: the first expansion. Science 300, 597–603.

    Article  PubMed  CAS  Google Scholar 

  45. Wirth, T., Wang, X., Linz, B., et al. (2004) Distinguishing human ethnic groups by means of sequences from Helicobacter pylori: lessons from the Ladakh. Proc Natl Acad Sci U S A 101, 4746–4751.

    Article  PubMed  CAS  Google Scholar 

  46. Falush, D., Wirth, T., Linz, B., et al. (2003) Traces of human migration in Helicobacter pylori. Science 299, 1582–1585.

    Article  PubMed  CAS  Google Scholar 

  47. Yang, Z., Nielsen, R. (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19, 908–917.

    PubMed  CAS  Google Scholar 

  48. McVean, G., Awadalla, P., Fearnhead, P. (2002) A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160, 1231–1241.

    PubMed  CAS  Google Scholar 

  49. Maynard Smith, J. (1999) The detection and measurement of recombination from sequence data. Genetics 153, 1021–1027.

    Google Scholar 

  50. Farris, J. S., Kallersjo, M., Kluge, A. G., et al (1995) Testing significance of incongru-ence. Cladistics 10, 315–319.

    Article  Google Scholar 

  51. Shimodaira, H., Hasegawa, M. (1999) Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 16, 1114–1116.

    CAS  Google Scholar 

  52. Buckley, T. R. (2002) Model misspecifica-tion and probabilistic tests of topology: evidence from empirical data sets. Syst Biol 51, 509–523.

    Article  PubMed  Google Scholar 

  53. Strimmer, K., von Haeseler, A. (1997) Likelihood-mapping: A simple method to visualize phylogenetic content of a sequence alignment. Proc Natl Acad Sci U S A 94, 6815–6819.

    Article  PubMed  CAS  Google Scholar 

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Acknowledgments

This work was supported by a Deutsche Forschungsgemein-schaft grant to Thierry Wirth (WI 2710/1) and the University of Konstanz.

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Authors and Affiliations

  1. Department of Biology, Lehrstuhl für Zoologie und Evolutionsbiologie, University of Konstanz, Konstanz, Germany

    Paul M.E. Bunje

  2. Department of Systematics and Evolution, Museum National d'Histoire Naturelle, Herbier, Paris, France

    Thierry Wirth

Authors
  1. Paul M.E. Bunje
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  2. Thierry Wirth
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Editor information

Editors and Affiliations

  1. School of Mathematical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia

    Jonathan M. Keith PhD

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© 2008 Humana Press, a part of Springer Science+Business Media, LLC

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Bunje, P.M., Wirth, T. (2008). Inferring Patterns of Migration. In: Keith, J.M. (eds) Bioinformatics. Methods in Molecular Biology™, vol 452. Humana Press. https://doi.org/10.1007/978-1-60327-159-2_23

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  • DOI: https://doi.org/10.1007/978-1-60327-159-2_23

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-707-5

  • Online ISBN: 978-1-60327-159-2

  • eBook Packages: Springer Protocols

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