Phylogeographic analysis of shrubby beardtongues reveals range expansions during the Last Glacial Maximum and implicates the Klamath Mountains as a hotspot for hybridization

Quaternary glacial cycles often altered species’ geographic distributions,
which in turn altered the geographic structure of species’ genetic
diversity. In many cases, glacial expansion forced species in temperate
climates to contract their ranges and reside in small pockets of suitable
habitat (refugia), where they were likely to interact closely with other
species, setting the stage for potential gene exchange. These
introgression events, in turn, would have degraded species boundaries,
making the inference of phylogenetic relationships challenging. Using
high-throughput sequence data, we employ a combination of species
distribution models and hybridization tests to assess the effect of
glaciation on the geographic distributions, phylogenetic relationships,
and patterns of gene flow of five species of Penstemon subgenus
Dasanthera, long-lived shrubby angiosperms distributed throughout the
Pacific Northwest of North America. Surprisingly, we find that rather than
reducing their ranges to small refugia, most Penstemon subgenus Dasanthera
species experienced increased suitable habitat during the Last Glacial
Maximum relative to the present day. We also find substantial evidence for
gene exchange between species, with the bulk of introgression events
occurring in or near the Klamath Mountains of southwestern Oregon and
northwestern California. Subsequently, our phylogenetic inference reveals
blurred taxonomic boundaries in the Klamath Mountains, where introgression
is most prevalent. Our results question the classical paradigm of
temperate species’ responses to glaciation and highlight the importance of
contextualizing phylogenetic inference with species’ histories of
introgression.