genet.dist | R Documentation |
Estimates one of several genetic distances among all pairs of populations.
genet.dist(dat,diploid=TRUE,method="Dch")
dat |
A data frame containing population of origin as the first column and multi-locus genotypes in following columns |
diploid |
whether the data is from a diploid (default) or haploid organism. |
method |
One of “Dch”,“Da”,“Ds”,“Fst”,“Dm”,“Dr”,“Cp” or “X2”, all described in Takezaki and Nei (1996). Additionally “Nei87” and “WC84” return pairwise FSTs estimated following Nei (1987) pairwise.neifst and Weir & Cockerham (1984) pp.fst respectively |
the method argument specify which genetic distance to use, among eight, all briefly described in Takezaki and Nei (1996)
“Dch” By default, Cavalli-Sforza and Edwards Chord distance (eqn 6 in the reference) is returned. This distance is used as default since Takezaki & Nei (1996) found that it was the best to retrieve the relation among samples.
“Da” This is Nei's et al genetic distance (eqn 7), performing nearly as well as “Dch”
“Ds” Nei's standard genetic distance (eqn 1). Increases linearly with diverence time but has larger variance
“Fst” Latter's and also approximately Reynolds et al Genetic distance (eqn 3)
“Dm” Nei's minimum distance (eqn 2)
“Dr” Rogers's distance (eqn 4)
“Cp” Prevosti et al's distance (eqn 5)
“X2” Sanghvi's distance (eqn 8)
“Nei87” see pairwise.neifst
“WC84” see pairwise.WCfst
A matrix of pairwise genetic distance
Jerome Goudet jerome.goudet@unil.ch
Takezaki & Nei (1996) Genetic distances and reconstruction of Phylogenetic trees from microsatellite DNA. Genetics 144:389-399
Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press
Weir B.S. and Cockerham C.C. (1984) Estimating F-Statistics for the Analysis of Population Structure. Evolution 38:1358
pairwise.WCfst
pairwise.neifst
data(gtrunchier) genet.dist(gtrunchier[,-1]) genet.dist(gtrunchier[,-1],method="Dr")
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