Data from: Inferring phylogeny and introgression using RADseq data: an example from flowering plants (Pedicularis: Orobanchaceae)

Phylogenetic relationships among recently diverged species are often
difficult to resolve due to insufficient phylogenetic signal in available
markers and/or conflict among gene trees. Here we explore the use of
reduced-representation genome sequencing, specifically in the form of
restriction-site associated DNA (RAD), for phylogenetic inference and the
detection of ancestral hybridization in non-model organisms. As a case
study, we investigate Pedicularis section Cyathophora, a systematically
recalcitrant clade of flowering plants in the broomrape family
(Orobanchaceae). Two methods of phylogenetic inference, maximum likelihood
and Bayesian concordance, were applied to data sets that included as many
as 40,000 RAD loci. Both methods yielded similar topologies that included
two major clades: a “rex-thamnophila” clade, composed of two species and
several subspecies with relatively low floral diversity, and
geographically widespread distributions at lower elevations, and a
“superba” clade, composed of three species characterized by relatively
high floral diversity and isolated geographic distributions at higher
elevations. Levels of molecular divergence between subspecies in the
rex-thamnophila clade are similar to those between species in the superba
clade. Using Patterson’s D-statistic test, including a novel extension of
the method that enables finer-grained resolution of introgression among
multiple candidate taxa by removing the effect of their shared ancestry,
we detect significant introgression among nearly all taxa in the
rex-thamnophila clade, but not between clades or among taxa within the
superba clade. These results suggest an important role for geographic
isolation in the emergence of species barriers, by facilitating local
adaptation and differentiation in the absence of homogenizing gene flow.