Calculate Phi_st from a genind object

Usage

Phi_st_Meirmans(x)

Arguments

x
genind object (from package adegenet)

Value

per.locus Phi_st estimate for each locus

global Phi_st estimate across all loci

Description

This function calculates Meirmans' corrected version of Phi_st, an Fst analog produced using the AMOVA framework. Note, the global estimate produced by this function is calculated as the mean distance between individuals across all loci, and this exlcuded individuals with one or more missing value.

References

Meirmans, PW. (2005), Using the AMOVA framework to estimate a standardized genetic differentiation measure. Evolution 60: 2399-402.

Excoffier, L., Smouse, P., Quattro, J. (1992), Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-91

Examples

data(nancycats) Phi_st_Meirmans(nancycats[1:26,])
Warning message: removing all individuals with NAs for global estimate
$per.locus fca8 fca23 fca43 fca45 fca77 fca78 fca90 fca96 0.3464402 0.4958678 0.6646293 0.6920874 0.3623217 0.5086112 0.2249415 0.3297373 fca37 0.7383496 $global [1] 0.538533

See also

Other diffstat: D_Jost, Gst_Hedrick, Gst_Nei, diff_stats