divMigrate: An experimental function for the detection of directional differentiation from microsatellite data.

Description

divMigrate uses the method described in Sundqvist et al., 2013 to plot the relative migration levels between population samples, from microsatellite allele frequency data. The method is still in the experimental stages, and it is not clear how well it performs under most evolutionary scenarios. Caution should be exercised.

Usage

divMigrate(infile = NULL, outfile = NULL, boots = 0, stat = "all",  filter_threshold = 0, plot_network = FALSE,  plot_col = "darkblue", para = FALSE)

Arguments

infile

Input genepop file name or path.

outfile

String prefix to be added to the results directory. If left NULL, no networks will be written to file.

boots

The number of bootstrap iteration to carry out for calculating mean relative migration and 95% confidence intervals.

stat

A character string indicating which statistic should be used to estimate relative migration between populations. The argument accepts one of the following: "d" (Jost's D), "gst" (Nei's Gst), "Nm" (Alcala et al, 2014) or "all" (all of the preceeding statistics; default).

filter_threshold

The minimum relative migration value for which edges in the networks should be displayed.

plot_network

A logical argument, specifying whether migration results should be plotted in a network.

plot_col

Defines the colour of edges in networks. Default is set to "darkblue".

para

A logical argument, specifying if multiple CPUs should be used when available.

Value

Details

The function will except both Arlequin (.arp) genotype and genepop (.gen/.txt) files, containing co-dominant diploid data. Using the method outlined in Sundqvist et al., 2013, the relative migration levels between all pairs of populations is determined. A weighted network plot is returned, as well as four matrices containing the objects described below.

References

Lisa Sundqvist, M.Z. & Kleinhans, D., 2013. Directional genetic differentiation and asymmetric migration. arXiv pre-print: arXiv:1304.0118v2

Rousset, F., ``genepop'007: a complete re-implementation of the genepop software for Windows and Linux.,'' Molecular ecology resources, vol. 8, no. 1, pp. 103-6, (2008).

Alcala, N., Goudet, J., Vuilleumier, S., 2014, On the transition of genetic differentiation from isolation to panmixia: What we can learn from Gst and D, Theoretical Population Biology, Vol 93, pp75-84.