Data from: Selection against recombinant hybrids maintains reproductive isolation in hybridizing Populus species despite F1 fertility and recurrent gene flow

Natural hybrid zones have proven to be precious tools for understanding
the origin and maintenance of reproductive isolation (RI) and therefore
species. Most available genomic studies of hybrid zones using whole- or
partial-genome resequencing approaches have focused on comparisons of the
parental source populations involved in genome admixture, rather than
exploring fine-scale patterns of chromosomal ancestry across the full
admixture gradient present between hybridizing species. We have studied
three well-known European ‘replicate’ hybrid zones of Populus alba and P.
tremula, two widespread, ecologically divergent forest trees, using up to
432 505 single-nucleotide polymorphisms (SNPs) from restriction
site-associated DNA (RAD) sequencing. Estimates of fine-scale chromosomal
ancestry, genomic divergence and differentiation across all 19 poplar
chromosomes revealed strikingly contrasting results, including an
unexpected preponderance of F1 hybrids in the centre of genomic clines on
the one hand, and genomically localized, spatially variable shared
variants consistent with ancient introgression between the parental
species on the other. Genetic ancestry had a significant effect on
survivorship of hybrid seedlings in a common garden trial, pointing to
selection against early-generation recombinants. Our results indicate a
role for selection against recombinant genotypes in maintaining RI in the
face of apparent F1 fertility, consistent with the intragenomic
‘coadaptation’ model of barriers to introgression upon secondary contact.
Whole-genome resequencing of hybridizing populations will clarify the
roles of specific genetic pathways in RI between these model forest trees
and may reveal which loci are affected most strongly by its cyclic
breakdown.