Compares the QST of a single phenotypic trait to the mean FST of series of marker loci. It calculates the distribution of QST - FST under a model assuming neutrality of both the phenotypic trait and the genetic markers from which FST is estimated. Returns the simulated estimates of Qst - Fst under neutrality following the procedure described in Gilbert and Whitlock (2014) and Whitlock & Guillaume (2009). Also returns the simulated estimates of Fst and Qst used to compute the null distribution.
A data frame with the first column indicating population of origin and
the following columns representing genotypes at loci; see the
README https://github.com/kjgilbert/QstFstComp/blob/master/README.md for further description.
If using AFLPs, this is a data frame of q-hat values, with pops in columns, loci in rows
and the corresponding q-hat variances in the following columns, and
the input table of the breeding data
number of populations in the sample
number of simulation replicates to perform to create the null distributions and bootstraps
@param AFLP whether or not to use AFLP data
@param breeding.design the breeding design used when collecting the trait data There are two options for breeding design:
@param dam.offspring.relatedness relatedness between offspring in the dam model, default is 1/4, i.e. half-sib
@param output whether to output full, concise, or without writing out vector of resampled Q-F values, see details below
Returns either a concise list of a subset of results or a full list with all possible results. Both output options write the vector of Qst-Fst values to a text file unless "_nowrite" is appended to the option, e.g. "concise_nowrite" returns only the concise output without writing output to a text file.
Concise list returns (default)
Full list returns
Be mindful of the fact that with a small number of loci, bootstrapped confidence intervals of Fst can be less accurate.
Kimberly J Gilbert & Michael C Whitlock
Gilbert KJ and MC Whitlock (2015) Qst Fst comparisons with unbalanced half-sib designs. Molecular Ecology Resources, 15(2), 262-267.
Whitlock MC and F Guillaume (2009) Testing for spatially divergent selection: Comparing Qst to Fst. Genetics, 183:1055-1063.
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## using balanced half-sib sire trait data and biallelic marker data data(hssire) # trait data data(biallelic) # marker data QstFstComp(biallelic, hssire, numpops=15, nsim=100, breeding.design="half.sib.sire", output="full") data(hsdam) data(aflp) QstFstComp(aflp, hsdam, numpops=15, nsim=100, AFLP=TRUE, breeding.design="half.sib.dam", output="concise")
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