Calculate differentiation statistics for a genind object

Usage

diff_stats(x, phi_st = FALSE)

Arguments

x
genind object (from package adegenet)
phi_st
Boolean Calculate Phi_st (default is FALSE)

Value

per.locus values for each statistic for each locus in the dataset

global estimtes for these statistics across all loci in the dataset

Description

By default this function calculates three different statistics of differentiation for a genetic dataset. Nei's Gst, Hedrick's G''st and Jost's D. Optionally, it can also calculate Phi'st, which is not calculated by default as it can take somewhat more time to run.

Details

See individual functions (listed below) for more details.

References

Hedrick, PW. (2005), A Standardized Genetic Differentiation Measure. Evolution 59: 1633-1638.

Jost, L. (2008), GST and its relatives do not measure differentiation. Molecular Ecology, 17: 4015-4026.

Meirmans PG, Hedrick PW (2011), Assessing population structure: FST and related measures. Molecular Ecology Resources, 11:5-18

Nei M. (1973) Analysis of gene diversity in subdivided populations. PNAS: 3321-3323.

Nei M, Chesser RK. (1983). Estimation of fixation indices and gene diversities. Annals of Human Genetics. 47: 253-259.

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) diff_stats(nancycats)
$per.locus Hs Ht Gst Gprime_st D fca8 0.7708277 0.8614311 0.10517782 0.4844461 0.42006021 fca23 0.7415102 0.7992621 0.07225650 0.2956688 0.23738411 fca43 0.7416796 0.7935120 0.06532017 0.2675766 0.21319208 fca45 0.7273320 0.7641204 0.04814486 0.1870423 0.14335289 fca77 0.7766369 0.8655618 0.10273670 0.4855829 0.42300076 fca78 0.6316202 0.6772045 0.06731245 0.1933327 0.13147655 fca90 0.7369587 0.8141591 0.09482221 0.3807578 0.31183460 fca96 0.6699736 0.7654561 0.12473941 0.3984843 0.30740024 fca37 0.5623259 0.6024354 0.06657894 0.1609576 0.09737005 $global Hs Ht Gst_est Gprime_st D_het D_mean 0.70654052 0.77146027 0.08415178 0.30308603 0.23504860 0.20017978

See also

Other diffstat: D_Jost, Gst_Hedrick, Gst_Nei, Phi_st_Meirmans