Data from: Gene flow and isolation in the arid Nearctic revealed by genomic analyses of desert spiny lizards

The opposing forces of gene flow and isolation are two major processes
shaping genetic diversity. Understanding how these vary across space and
time is necessary to identify the environmental features that promote
diversification. The detection of considerable geographic structure in
taxa from the arid Nearctic has prompted research into the drivers of
isolation in the region. Several geographic features have been proposed as
barriers to gene flow, including the Colorado River, Western Continental
Divide, and a hypothetical Mid-Peninsular Seaway in Baja California.
However, recent studies suggest that the role of barriers in genetic
differentiation may have been overestimated when compared to other
mechanisms of divergence. In this study, we infer historical and spatial
patterns of connectivity and isolation in Desert Spiny Lizards (Sceloporus
magister) and Baja Spiny Lizards (S. zosteromus), which together form a
species complex composed of parapatric lineages with wide distributions in
arid western North America. Our analyses incorporate mitochondrial
sequences, genomic-scale data, and past and present climatic data to
evaluate the nature and strength of barriers to gene flow in the region.
Our approach relies on estimates of migration under the multispecies
coalescent to understand the history of lineage divergence in the face of
gene flow. Results show that the S. magister complex is geographically
structured, but we also detect instances of gene flow. The Continental
Divide is a strong barrier to gene flow, while the Colorado River is more
permeable. Analyses yield conflicting results for the catalyst of
differentiation of peninsular lineages in S. zosteromus. Our study shows
how large-scale genomic data for thoroughly sampled species can shed new
light on biogeography. Furthermore, our approach highlights the need for
the combined analysis of multiple sources of evidence to adequately
characterize the drivers of divergence.