Genome-scale data reveal deep lineage divergence and a complex
demographic history in the Texas horned lizard (Phrynosoma cornutum)
throughout the southwestern and central US
Abstract
The southern US and northern Mexico serve as an ideal region to test
alternative hypotheses regarding biotic diversification. Genomic data
can now be combined with sophisticated computational models to quantify
the impacts of paleoclimate change, geographic features, and habitat
heterogeneity on spatial patterns of genetic diversity. In this study we
combine thousands of genotyping-by-sequencing (GBS) loci with mtDNA
sequences (ND1) from the Texas Horned Lizard (Phrynosoma cornutum) to
quantify relative support for different catalysts of diversification.
Phylogenetic and clustering analyses of the GBS data indicate support
for at least three primary populations with evidence of recent
admixture. The spatial distribution of populations appears concordant
with habitat type, with desert populations in Arizona and New Mexico
showing the largest genetic divergence. The mtDNA data also support a
divergent desert population, but other relationships differ and suggest
mtDNA introgression. Genotype-environmental association analyses support
divergence along environmental axes. Demographic analyses support a
model of allopatric divergence during the Pleistocene followed by
secondary contact and gene flow. These results are consistent with
inferred paleo-species distribution models. Our results also indicate
that caution is warranted when fitting a multispecies coalescent model
without introgression to populations that have exchanged genes
throughout their diversification history. In sum, our results support
allopatric divergence due to Pleistocene climate change, which was
followed by secondary contact and widespread genomic introgression.
Results also suggest that populations are continuing to diverge along
habitat gradients. Finally, the strong evidence of admixture, gene flow,
and mtDNA introgression among populations suggests that P. cornutum
should be considered a single widespread species.