Hydrologic and geologic history of the Ozark Plateau drive phylogenomic patterns in a cave‐obligate salamander

Abstract

Aim: Habitat specialization can constrain patterns of dispersal and drive allopatric speciation in organisms with limited dispersal ability. Herein, we tested biogeographic patterns and dispersal in a salamander with surface-dwelling larvae and obligate cave-dwelling adults.Location: Ozark Plateau, eastern North America. Methods:A population-level phylogeny of grotto salamanders (Eurycea spelaea complex) was reconstructed using mitochondrial (mtDNA) and multi-locus nuclear DNA (nucDNA), primarily derived from anchored hybrid enrichment (AHE). We tested patterns of molecular variance among populations and associations between genetic distance and geographic features. Results: Divergence time estimates suggest rapid formation of three major lineages in the Middle Miocene. Contemporary gene flow among divergent lineages appears negligible, and mtDNA suggests that most populations are isolated. There is a significant association between phylogenetic distance and palaeodrainages, contemporary drainages and sub-plateaus of the Ozarks, as all features explain a proportion of genetic variation. However, the greatest proportion of genetic variation is explained by the combined effects of palaeodrainages and sub-plateaus.Main conclusions: The geologic and hydrologic history of the Ozark Plateau has influenced lineage diversification in the grotto salamander, leading to genetic isolation among populations. Limited gene flow and strong phylogeographic structure in this complex may result from the restriction of highly specialized adults to caves.

Post‐Pleistocene differentiation in a Central Interior Highlands endemic salamander

“…Further, we observed significant pairwise F ST values between our northern and southern CIH clusters (Table 2 and Table S4) and low migration rates among populations (Table S2) we found concordance in the approximate location of the A. annulatum phylogeographic break with those of aquatic and terrestrial fauna that exist between the northern and southern Ozarks (Hardy et al, 2002;Hutchison & Templeton, 1999;Phillips, Fenolio, Emel, & Bonett, 2017;Ray, Wood, & Simons, 2006;Routman et al, 1994).…”

“…For each color, the proportion of the pie corresponds to the frequency of the haplotype in that population as outlined in Note: Bias estimates for the root of the relative mean integrated square error (RRMISE), average relative bias, and the factor 2 score of the mode of the posterior distribution are also included. spelaea), show similar phylogeographic breaks between the northern and southern Ozarks that were attributed to the palaeodrainages, contemporary drainages, and subplateaus in the Ozarks (Phillips et al, 2017). Similarly, some terrestrial taxa exhibit similar patterns of genetic diversity despite these organisms not being constrained to riparian networks (Hutchison & Templeton, 1999).…”

Extreme Adaptation in Caves

“…Salamanders are the only tetrapods that exhibit exclusive inhabitation in caves. More than 700 salamanders in 10 families have been described (AmphibiaWeb ), but only 14 species in two families are considered true subterranean obligates (Gorički et al, ; Phillips et al, ). Eleven subterranean‐obligate species in the lungless salamander family Plethodontidae have been described, all from karst regions of central and eastern North America in the genera Eurycea (eight species) and Gyrinophilus (three species).…”

Rapid phenotypic evolution following shifts in life cycle complexity

“…We used anchored hybrid enrichment [28][29][30] to isolate 190 nuclear genomic regions from representative individuals of each of the 28 populations (lineages) of E. tynerensis. Our anchored sequence capture protocol was described in detail in [30]. Briefly, genomic DNA was extracted using Qiagen DNeasy extraction kits, and sheared using a Covaris M220 focused-ultrasonicator.…”