introgress-package: introgress

Description Details Author(s) References

Description

introgress provides functions for analyzing introgression of genotypes between divergent, hybridizing lineages, including estimating genomic clines from multi-locus genotype data and testing for deviations from neutral expectations. Functions are also provided for maximum likelihood estimation of molecular hybrid index and graphical analysis.

Details

introgress includes several core functions that are needed to implement the genomic clines method of Gompert and Buerkle (2009a). prepare.data estimates the counts of alleles inherited from each of two parental population at each locus for admixed individuals. These estimates are based on genotype data from admixed population(s) and specified parental populations. The function est.h uses the list output returned from prepare.data and the raw genotype data for the admixed population(s) to compute maximum likelihood estimates of hybrid index. The list output returned by prepare.data and the data.frame output returned by est.h are used to estimate genomic clines, which is accomplished with the function genomic.clines. The genomic.clines function includes arguments specifying whether significance testing is performed and the procedure used to generate null expectations for significance testing. The clines.plot function provides graphical output for genomic clines analysis similar to Gompert and Buerkle (2009a, 2009b). In addition, the introgress package includes the compare.clines function to contrast patterns of introgression between hybrid zones.

introgress implements additional functions for graphical analysis of hybrid zones. triangle.plot plots the relationship between hybrid index and inter-class heterozygosity (calc.intersp.het) for an admixed population. The mk.image function produces a graphical representation of marker ancestry allowing visual inspection of variation in patterns of introgression among markers.

For further information regarding the above functions and additional introgress functions, please see the appropriate function help pages.

Author(s)

Zachariah Gompert [email protected], C. Alex Buerkle [email protected]

References

Gompert Z. and Buerkle C. A. (2009) A powerful regression-based method for admixture mapping of isolation across the genome of hybrids. Molecular Ecology, 18, 1207-1224.

Gompert Z. and Buerkle C. A. (2009) introgress: a software package for mapping components of isolation in hybrids. Molecular Ecology Resources, in preparation.


introgress documentation built on May 29, 2017, 9:07 p.m.