Data from: Adaptive evolution and segregating load contribute to the genomic landscape of divergence in two tree species connected by episodic gene flow

Speciation often involves repeated episodes of genetic contact between
divergent populations before reproductive isolation (RI) is complete.
Whole-genome sequencing (WGS) holds great promise for unravelling the
genomic bases of speciation. We have studied two ecologically divergent,
hybridizing species of the ‘model tree’ genus Populus (poplars, aspens,
cottonwoods), Populus alba and P. tremula, using >8.6 million
single nucleotide polymorphisms (SNPs) from WGS of population pools. We
used the genomic data to (i) scan these species’ genomes for regions of
elevated and reduced divergence, (ii) assess key aspects of their joint
demographic history based on genomewide site frequency spectra (SFS) and
(iii) infer the potential roles of adaptive and deleterious coding
mutations in shaping the genomic landscape of divergence. We identified
numerous small, unevenly distributed genome regions without fixed
polymorphisms despite high overall genomic differentiation. The joint SFS
was best explained by ancient and repeated gene flow and allowed
pinpointing candidate interspecific migrant tracts. The direction of
selection (DoS) differed between genes in putative migrant tracts and the
remainder of the genome, thus indicating the potential roles of adaptive
divergence and segregating deleterious mutations on the evolution and
breakdown of RI. Genes affected by positive selection during divergence
were enriched for several functionally interesting groups, including
well-known candidate ‘speciation genes’ involved in plant innate immunity.
Our results suggest that adaptive divergence affects RI in these
hybridizing species mainly through intrinsic and demographic processes.
Integrating genomic with molecular data holds great promise for revealing
the effects of particular genetic pathways on speciation.