Data from: An integrative approach to phylogeography: investigating the effects of ancient seaways, climate, and historical geology on multi-locus phylogeographic boundaries of the arboreal salamander (Aneides lugubris)

Background: Phylogeography is an important tool that can be used to reveal
cryptic biodiversity and to better understand the processes that promote
lineage diversification. We studied the phylogeographic history of the
Arboreal Salamander (Aneides lugubris), a wide-ranging species endemic to
the California floristic province. We used multi-locus data to reconstruct
the evolutionary history of A. lugubris and to discover the geographic
location of major genetic breaks within the species. We also used species
distribution modeling and comparative phylogeography to better understand
the environmental factors that have shaped the genetic history of A.
lugubris. Results: We found six major mitochondrial clades in A. lugubris.
Nuclear loci supported the existence of at least three genetically
distinct groups, corresponding to populations north of the San Francisco
Bay and in the Sierra Nevada, in the Santa Cruz Mountains, and in the
central coast and southern California. All of the genetic breaks in
mitochondrial and nuclear loci corresponded to regions where historical
barriers to dispersal have been observed in other species. Geologic or
water barriers likely were the most important factors restricting gene
flow among clades. Climatic unsuitability during glacial maximum may have
contributed to the isolation of the mitochondrial clades in the central
coast and southern California. A projection of our species distribution
model to a future scenario with a moderate amount of climate change
suggests that most of the range of A. lugubris will remain climatically
suitable, but climatic conditions in the Sierra Nevada and low elevation
areas in Southern California are likely to deteriorate. Conclusions:
Aneides lugubris contains substantial cryptic genetic diversity as a
result of historical isolation of populations. At least two (and perhaps
three) evolutionarily significant units in A. lugubris merit protection;
all six mitochondrial clades should be considered as management units
within the species.