Data from: Genomic and functional approaches reveal a case of adaptive introgression from Populus balsamifera (balsam poplar) in P. trichocarpa (black cottonwood)

Natural hybrid zones in forest trees provide systems to study the transfer
of adaptive genetic variation by introgression. Previous landscape genomic
studies in Populus trichocarpa, a keystone tree species, indicated genomic
footprints of admixture with its sister species P. balsamifera and
identified candidate genes for local adaptation. Here, we explored
patterns of introgression and signals of local adaptation in P.
trichocarpa and P. balsamifera, employing genome resequencing data from
three chromosomes in pure species and admixed individuals from wild
populations. Local ancestry analysis in admixed P. trichocarpa revealed a
telomeric region in chromosome 15 with P. balsamifera ancestry, containing
several candidate genes for local adaptation. Genomic analyses revealed
signals of selection in certain genes in this region (e.g. PRR5, COMT1),
and functional analyses based on gene expression variation and
correlations with adaptive phenotypes suggest distinct functions of the
introgressed alleles. In contrast, a block of genes in chromosome 12
paralogous to the introgressed region showed no signs of introgression or
signatures of selection. We hypothesize that the introgressed region in
chromosome 15 has introduced modular, or cassette-like variation into P.
trichocarpa. These linked adaptive mutations are associated with a block
of genes in chromosome 15 that appear to have undergone neo- or
sub-functionalization relative to paralogs in a duplicated region on
chromosome 12 that show no signatures of adaptive variation. The
association between P. balsamifera introgressed alleles with the
expression of adaptive traits in P. trichocarpa supports the hypothesis
that this is a case of adaptive introgression in an ecologically important
foundation species.