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Population Structure and Migration

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Abstract

We begin with a discussion of how population structure is commonly modeled, including island, stepping-stone, and isolation-by-distance models. The structured coalescent is used as an intuitive model for thinking about the fate of alleles in a population whose demes are connected by appreciable gene flow. The migration rate m is defined and its importance to genetic population structure is emphasized. Modifications to the code of forward-simulation program FORTUNA add the ability to simulate gene flow using a single, symmetric value of m or a fully specified migration matrix among demes. An R script that allows visualization of a summary statistic across time and across sequence windows is introduced. Another important addition to FORTUNA is the ability to print out samples of haplotypes on specified generations. These files can be used to compare independent runs of evolution from the same starting point or to examine the molecular evolutionary process at greater resolution. The fixation index, F ST, is introduced and used to assess genetic connectivity between pairs of demes; the index is calculated using simulated data and an R script. The final addition to FORTUNA in this chapter allows the user to output the basic history of every allele generated during a simulation; this history includes the position of the derived allele, the generation it originated, and the deme in which it originated. These data are then used to explore the fate of alleles as they flow among demes via migration. A curious result is explored in detail to emphasize the importance of confirming that unexpected results have naturally emerged from the simulated model and are not due to an overlooked coding error.

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Notes

  1. 1.

    Quoted with permission. 2000, Zone Books, Brooklyn, NY.

  2. 2.

    Throughout this text (and in the extended version of FORTUNA developed in this chapter), I will use the term deme and population interchangeably; my justification for this sloppy nomenclature is that you could model networks of populations (metapopulations) or semi-isolated subdivisions of one population (demes) using different parameter values in the same program, FORTUNA.

  3. 3.

    matrix.h defines Matrix objects and the functions used to access and change their cell values; see online code for the file if interested in its details.

References

  • Nordborg M (1997) Structured coalescent process on different time scales. Genetics 146:1501–1514

    Article  CAS  Google Scholar 

  • Reich D, Thangaraj K, Patterson N, Price A, Singh L (2009) Reconstructing Indian population history. Nature 461:489–494

    Article  CAS  Google Scholar 

  • Rice SH (2004) Evolutionary theory: mathematical and conceptual foundations, 1st edn. Sinauer Associates, Sunderland

    Google Scholar 

  • Spieth PT (1974) Gene flow and genetic differentiation. Genetics 78:961–965

    Article  CAS  Google Scholar 

  • Wakeley J (2008) Coalescent theory: an introduction. Roberts and Company Publishers, Greenwood Village

    Google Scholar 

  • Whitlock MC, McCauley DE (1999) Indirect measures of gene flow and migration: fST 1∕(4nm + 1). Heredity 82:117–125

    Article  Google Scholar 

  • Wright S (1931) Evolution in mendelian populations. Genetics 16:97–159

    Article  CAS  Google Scholar 

  • Wright S (1951) The genetical structure of populations. Ann Eugenics 15:323–354

    Article  CAS  Google Scholar 

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Haasl, R. (2022). Population Structure and Migration. In: Nature in Silico. Springer, Cham. https://doi.org/10.1007/978-3-030-97381-0_6

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