Data from: Genotyping by sequencing reveals contrasting patterns of population structure, ecologically mediated divergence and long-distance dispersal in North American palms

Comparative studies can provide powerful insights into processes that
affect population divergence and thereby help to elucidate the mechanisms
by which contemporary populations may respond to environmental change.
Furthermore, approaches such as genotyping by sequencing (GBS) provide
unprecedented power for resolving genetic differences among species and
populations. We therefore used GBS to provide a genome-wide perspective on
the comparative population structure of two palm genera, Washingtonia and
Brahea, on the Baja California peninsula, a region of high landscape and
ecological complexity. First, we used phylogenetic analysis to address
taxonomic uncertainties among five currently recognised species. We
resolved three main clades, the first corresponding to W. robusta and W.
filifera, the second to B. brandegeei and B. armata, and the third to B.
edulis from Guadalupe Island. Focusing on the first two clades, we then
delved deeper by investigating the underlying population structure.
Striking differences were found, with GBS uncovering four distinct
Washingtonia populations and identifying a suite of loci associated with
temperature, consistent with ecologically mediated divergence. By
contrast, individual mountain ranges could be resolved in Brahea and few
loci were associated with environmental variables, implying a more
prominent role of neutral divergence. Finally, evidence was found for
long-distance dispersal events in Washingtonia but not Brahea, in line
with knowledge of the dispersal mechanisms of these palms including the
possibility of human-mediated dispersal. Overall, our study demonstrates
the power of GBS together with a comparative approach to elucidate
markedly different patterns of genome-wide divergence mediated by multiple
effectors.