recluster.fst: Compute some indexes of genetic differentiation

Description Usage Arguments Details Value Author(s) References Examples

View source: R/recluster.fst.R

Description

This function computes some indexes of genetic differentiation based on a distance matrix and on a vector for populations.

Usage

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recluster.fst(dist,vect,setzero=F,setnazero=F)

Arguments

dist

A distance matrix.

vect

A vector indicating population membership. Cases must be in the some order of the distance matrix.

setzero

A logical indicating if negative values should be set to zero

setnazero

A logical indicating if NA values should be set to zero

Details

There has been a large dabate around FST like indexes. Two main indexes are culcalated by this function: the absolute differentiation (Dst) and the standardized differentiation (Gst) (Nei, 1987) .Dst is calculated as: Dst = Ht - Hs where Ht represents the average distances among all the specimens in the sample, and Hs is the average of the intra-area (or intra-sub-area) distances. Thus, Dst represents the average genetic differentiation among areas in p-distance units. Gst is a standardized index defined as: Gst = Dst/Ht representing the fraction of the total genetic differentiation encompassed by the differentiation among areas (Nei, 1987). This index ranges from negative values to 1 (complete differentiation). Negative values in Gst and Dst (intra-area differentiation higher than inter-area differentiation) can have different subtle meanings, but are most often generated as bias due to relatively small sample sizes; usually they are set to zero (Meirmans & Hedrick, 2011) and we applied this solution. In the species showing no mutations in the sample, Gst returns a NA value (while Dst equals to zero). These cases can be also set to zero The use of Dst and Gst has been debated as a measure of population diversification for extremely variable markers (as micro-satellites) as it tends to underestimate differentiation among populations and to strongly depend on intra-population variability (Jost, 2008; Whitlock, 2011). D and G-st indices are less affected by high values of Hs

Value

Ht

The average distances among all the specimens in the sample.

lengthHt

The number of distances among all the specimens in the sample.

Hs

The average distances among the specimens of the same populations.

lengthHs

The number of distances among the specimens of the same populations.

Dst

The Dst value.

Gst

The Gst value.

D

The D value.

G1st

The G'st value.

Author(s)

Leonardo Dapporto

References

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

Meirmans P. G., Hedrick P. W. "Assessing population structure: FST and related measures: Invited Technical Reviwev." Mol Ecol Res (2011), 11: 5-18.

Nei M. Molecular evolutionary genetics (1987), Columbia University Press.

Whitlock M.C. "G'ST and D do not replace FST." Mol Ecol (2011), 20: 1083-1091.

Examples

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datavirtual<-data.frame(replicate(10,sample(0:1,30,rep=TRUE)))
dist<-recluster.dist(datavirtual)
population<-c(rep(1,20),rep(2,20),rep(3,20))
recluster.fst(dist,population)

recluster documentation built on July 27, 2020, 1:15 a.m.