Recent hybrids recapitulate ancient hybrid outcomes

Genomic outcomes of hybridization depend on selection and recombination in hybrids. Whether these processes have similar effects on hybrid genome composition in contemporary hybrid zones versus ancient hybrid lineages is unknown. Here we show that patterns of introgression in a contemporary hybrid zone in Lycaeides butterflies predict patterns of ancestry in geographically adjacent, older hybrid populations. We find a particularly striking lack of ancestry from one of the hybridizing taxa, Lycaeides melissa, on the Z chromosome in both the old and contemporary hybrids. The same pattern of reduced L. melissa ancestry on the Z chromosome is seen in two other ancient hybrid lineages. More generally, we find that patterns of ancestry in old or ancient hybrids are remarkably predictable from contemporary hybrids, which suggests selection and recombination affect hybrid genomes in a similar way across disparate time scales and during distinct stages of speciation and species breakdown.

Methods
We analyzed partial genome sequences from 835 Lycaeides butterflies from 23 populations in western North America. The sequence data from 643 of these butterflies was previously described in a study of admixture across the Lycaeides species complex (Gompert et al. 2014). Data from 192 of the butterflies were generated for the current study, and this includes many (but not all) of the Dubois individuals. Specific locations (latitude and longitude) and sample sizes for each population are provided in the manuscript. DNA sequence data were generated by  on an Illumina HiSeq 2500 (100 bp, single-end reads) by the Genome Sequencing and Analysis Facility at the University of Texas (Austin, TX).