popgen: Compute allele frequencies, population genetic parameters, and pairwise Fst values from a Arlequin (.arp) input file

Description

This function does not do anything that other population genetic software could not do, but provides a quick way to obtain allele frequencies in a table format (overall and within each population), and it can calculate allelic richness, number of private alleles, expected and observed heterozygosity (He and Ho), and population pairwise Fst values, for each locus and across all markers.

Usage

popgen(datafile, ndigit = 3, freq.overall = T, freq.by.pop = T, genetic.stats = T, pairwise.fst = T)

Arguments

datafile

Name of the input Arlequin file, with extension (e.g. 'glyptemys3.arp').

ndigit

Number of digits per allele in input file. Can be 2 or 3. (Default is 3).

freq.overall

Obtain a table of overall allele frequencies?

freq.by.pop

Obtain a table of allele frequencies in each population?

genetic.stats

Obtain a table listing number of alleles, allelic richness, private alleles, Ho and He?

pairwise.fst

Obtain a table of population pairwise Fst values, for each marker and overall?

Value

Results will be saved in tab-delimited text files in the working directory.

Details

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. All output files will be saved to the working directory. Allelic richness is calculated by jackknife resampling (1000 replicates), and the sample size for each locus is determined as the smallest number of individuals sampled among all populations for that specific locus. Thus, the sample size may vary between markers. Pairwise Fst values are calculated according to Wright's formula (Wright 1931; 1951). This option is provided as a data exploration tool. Numerous software allow the computation of Fst indices that integrate sampling effects, such as Weir and Cockerham's theta (1984), and these indices should be preferably reported. See Holsinger and Weir (2009) for more details.

References

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. Holsinger, K.E. and B.S. Weir (2009) Genetics in geographically structured populations: defining, estimating and interpreting Fst. Nat. Rev. Genet. 10:639-650. Rousset, F. (2008). Genepop'007: a complete reimplementation of the Genepop software for Windows and Linux. Mol. Ecol. Res. 8: 103-106. Weir, B.S. and C.C. Cockerham (1984) Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370. Wright, S. (1931) Evolution in Mendelian populations. Genetics 16: 97-159. Wright, S. (1951) The genetical structure of populations. Annals of Eugenics 15: 323-354.