Phylogenomic analyses resolve relationships among garter snakes (Thamnophis: Natricinae: Colubridae) and elucidate biogeographic history and morphological evolution

Garter snakes (Thamnophis) are a successful group of natricines endemic to
North America.  They have become important natural models for
ecological and evolutionary research, yet prior efforts to resolve
phylogenetic relationships have resulted in conflicting topologies and
weak support for certain relationships.  Here, we use
phylogenomic data generated with a reduced representation double-digest
RADseq approach to reassess the evolutionary relationships across
Thamnophis.  We then use the resulting phylogeny to better
understand how biogeography and feeding ecology have influenced lineage
diversification and morphological evolution.  We recovered highly
congruent and strongly supported topologies from maximum likelihood and
Bayesian inference analyses, but some discordance with a multispecies
coalescent approach.  All phylogenomic estimates split Thamnophis
into two clades largely defined by northern and southern North American
species.  Divergence time estimates and biogeographic analyses
indicate a mid-Miocene origin of Thamnophis in Mexico.  In
addition, historical vicariant events thought to explain biogeographic
patterns in other lineages (e.g., Isthmus of Tehuantepec, Rocky Mountain
Range, and Trans-Mexican Volcanic Belt) appear to have influenced patterns
of diversification in Thamnophis as well.  Analyses of
morphological traits associated with feeding ecology showed degrees of
phylogenetic signal, and ancestral state reconstruction suggested some
association between head morphology and diet composition.  Our
new estimate of Thamnophis phylogeny yields an improved understanding of
the biogeographic history and morphological evolution of garter snakes,
and provides a robust framework for future research on these snakes.