Predictors of genomic differentiation within a hybrid taxon

Hybridization is increasingly recognized as an important evolutionary
force. Novel genetic methods now enable us to address how the genomes of
parental species are combined in hybrid lineages. However, we still do not
know the relative importance of admixed proportions, genome architecture
and local selection in shaping hybrid genomes. Here, we take advantage of
the genetically divergent island populations of Italian sparrow on Crete,
Corsica and Sicily to investigate the predictors of genomic variation
within a hybrid taxon. We test if differentiation is affected by
recombination rate, selection, or variation in ancestry proportions. We
find that the relationship between recombination rate and differentiation
is less pronounced within hybrid lineages than between the parent species,
as expected if purging of minor parent ancestry in low recombination
regions reduces the variation available for differentiation. In addition,
we find that differentiation between islands is correlated with
differences in signatures of selection in two out of three comparisons.
Signatures of selection within islands are correlated across all islands,
suggesting that shared selection may mould genomic differentiation. The
best predictor of strong differentiation within islands is the degree of
differentiation from house sparrow, and hence loci with Spanish sparrow
ancestry may vary more freely. Jointly, this suggests that constraints and
selection interact in shaping the genomic landscape of differentiation in
this hybrid species.