For each animal, the hybrid index S is the share of species-2 alleles at the diagnostic markers, and the interspecies heterozygosity H is the share of markers carrying one allele from each species. With markers that are fixed or nearly fixed, these simple counts match the maximum-likelihood estimates of Fitzpatrick (2012) closely.
Usage
hybrid_scores(geno, markers, method = c("count", "likelihood"))Arguments
- geno
Genotype matrix as in
diagnostic_markers().- markers
Output of
diagnostic_markers().- method
"count"(simple counts; for fixed or nearly fixed markers) or"likelihood"(maximum-likelihood estimates that use each marker's allele frequencies in the two reference groups, for markers that are not fixed; Fitzpatrick 2012).
References
Fitzpatrick BM (2012) Estimating ancestry and heterozygosity of hybrids using molecular markers. BMC Evolutionary Biology 12:131.
Examples
ex <- hybridclock_example()
mk <- diagnostic_markers(ex$genotypes, ex$groups, "species1", "species2", locus = ex$locus)
head(hybrid_scores(ex$genotypes, mk))
#> S H n_markers
#> species1_1 0 0 314
#> species1_2 0 0 314
#> species1_3 0 0 314
#> species1_4 0 0 314
#> species1_5 0 0 314
#> species1_6 0 0 314