recodeBi: Transform a multi-allelic Arlequin datafile to a bi-allelic datafile

Description

This function transforms a dataset with multi-allelic markers (e.g. microsatellites) to a bi-allelic dataset, where all alleles but one (usually the most frequent) are pooled together to form a second allelic class.

Usage

recodeBi(datafile, major.alleles)

Arguments

datafile

Name of the file to recode, with the extension (e.g. 'glyptemys3.arp').

major.alleles

A vector listing which allele to retain for each locus. Length of this vector should be equal to the number of markers in datafile.

Value

The Arlequin file coded in bi-allelic format is saved in the working directory.

Details

Because several population genetics parameter estimates are affected by the level of polymorphism of loci (e.g. Fst), it may be useful to recode multi-allelic markers to a bi-allelic state. For instance, this could allow the comparison of Fst values for microsatellites and single nucleotide polymorphisms (SNPs). McDonald (1994) introduced this as F2st, and it has been used elsewhere (e.g. Allendorf and Seeb 2000). All alleles aside from the retained one at each locus are pooled together and designated as '300'. Thus, the allele retained at each locus should be different than 300. The function popgen provides a quick way to obtain allele frequencies in order to determine which alleles are the most frequent, within populations or overall. To transform multiple files, use batchrecodeBi instead. Some .arp files might not be imported correctly depending on which software was used to generate them. If this is the case, start from the Genepop file and convert it first with convert.

References

Allendorf, F.W. and L.W. Seeb (2000) Concordance of genetic divergence among sockeye salmon populations at allozyme, nuclear DNA, and mitochondrial DNA markers. Evolution 54: 640-651. Excoffier, L. and H.E.L. Lischer (2010). Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Mol. Ecol. Res. 10: 564-567. McDonald, J.H. (1994) Detecting natural selection by comparing geographic variation in protein and DNA polymorphisms. Pages 88-100 in Golding B, ed. Non-neutral evolution: theories and molecular data. New York: Chapman and Hall. Rousset, F. (2008). Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Res. 8: 103-106.