Selection shapes the genomic landscape of introgressed ancestry in a pair of sympatric sea urchin species

A growing number of recent studies have demonstrated that introgression is
common across the tree of life. However, we still have a limited
understanding of the fate and fitness consequence of introgressed
variation at the whole-genome scale across diverse taxonomic groups. Here,
we implemented a phylogenetic hidden Markov model to identify and
characterize introgressed genomic regions in a pair of well-diverged,
non-sister sea urchin species: Strongylocentrotus pallidus and S.
droebachiensis. Despite the old age of introgression, a sizable fraction
of the genome (1% - 5%) exhibited introgressed ancestry, including
numerous genes showing signals of historical positive selection that may
represent cases of adaptive introgression. One striking result was the
overrepresentation of hyalin genes in the identified introgressed regions
despite observing considerable overall evidence of selection against
introgression. There was a negative correlation between introgression and
chromosome gene density, and two chromosomes were observed with
considerably reduced introgression. Relative to the non-introgressed
genome-wide background, introgressed regions had significantly reduced
nucleotide divergence (dXY) and overlapped fewer protein-coding genes,
coding bases, and genes with a history of positive selection.
Additionally, genes residing within introgressed regions showed slower
rates of evolution (dN, dS, dN/dS) than random samples of genes without
introgressed ancestry. Overall, our findings are consistent with
widespread selection against introgressed ancestry across the genome and
suggest that slowly evolving, low-divergence genomic regions are more
likely to move between species and avoid negative selection following
hybridization and introgression.