Identification of hybrid individuals and direction of
backcrossing
In order to determine whether individuals with intermediate ancestry
were progeny of recent interbreeding or historical events, we used
Faststructure (Raj et al. 2014) with k = 2 to estimate pusillusand extoni ancestry (i.e., hybrid index) based on all loci, and
separately for loci on scaffolds that aligned to the zebra finch Z
chromosome. We estimated interspecific heterozygosity of each individual
based on a genome-wide subset of 1,723 SNPs with allele frequency
difference > 0.95 between allopatric pusillus andextoni populations, and compared this to the hybrid index across
the whole genome and the Z chromosome to identify F1 hybrids, first
generation backcrosses and the direction of backcrossing for early and
later-generation backcrosses.
To illustrate the relationship between hybrid index and interspecific
heterozygosity, we produced triangle plots, which would reveal F1
hybrids as individuals with intermediate hybrid index and the highest
levels of interspecific heterozygosity at loci diagnostic for each
species. F2 hybrids and backcrosses would be expected to have
intermediate levels of interspecific heterozygosity and fall in the
middle and sides of the triangle respectively, in accordance with
simulations (Toews et al., 2018), with non-admixed individuals falling
in the lower corners of the triangle.