Speciation with gene flow in a narrow endemic West Virginia cave salamander (\u3ci\u3eGyrinophilus subterraneus\u3c/i\u3e)

Due to their limited geographic distributions and specialized ecologies, cave species are often highly endemic and can be especially vulnerable to habitat degradation within and surrounding the cave systems they inhabit. We investigated the evolutionary history of the West Virginia Spring Salamander (Gyrinophilus subterraneus), estimated the population trend from historic and current survey data, and assessed the current potential for water quality threats to the cave habitat. Our genomic data (mtDNA sequence and ddRADseq-derived SNPs) reveal two, distinct evolutionary lineages within General Davis Cave corresponding to G. subterraneus and its widely distributed sister species, Gyrinophilus porphyriticus, that are also differentiable based on morphological traits. Genomic models of evolutionary history strongly support asymmetric and continuous gene flow between the two lineages, and hybrid classification analyses identify only parental and first generation cross (F1) progeny. Collectively, these results point to a rare case of sympatric speciation occurring within the cave, leading to strong support for continuing to recognize G. subterraneus as a distinct and unique species. Due to its specialized habitat requirements, the complete distribution of G. subterraneus is unresolved, but using survey data in its type locality (and currently the only known occupied site), we find that the population within General Davis Cave has possibly declined over the last 45 years. Finally, our measures of cave and surface stream water quality did not reveal evidence of water quality impairment and provide important baselines for future monitoring. In addition, our unexpected finding of a hybrid zone and partial reproductive isolation between G. subterraneus and G. porphyriticus warrants further attention to better understand the evolutionary and conservation implications of occasional hybridization between the species

Supplementary_table_1

Supplementary table S1. Museum specimen catalog numbers, micro-CT scanning parameters, GenBank accession numbers, and Procrustes coordinate

tree_nexus

A phylogenetic tree of 53 species generated using maximum likelihood method of estimation and based on a concatenated sequence of 9 nuclear genes and 4 mitochondrial genes obtained from GenBank (see supplementary table S1)

Extratympanic hearing in salamanders: A comparative assessment of structural variation and terrestrial function of an atympanic ear

The auditory system mediates the detection of acoustic cues and enhances survival within complex environments by enabling organisms to construct an auditory scene of their surroundings. The tympanic middle ear evolved multiple times in all terrestrial tetrapod lineages to overcome the impedance mismatch encountered by sound pressure at the air-skin boundary, indicating its significance for aerial hearing; however, fossil evidence demonstrates that the earliest terrestrial tetrapods retained aquatically-adapted ears that were unspecialized for detecting airborne sound. How did these unspecialized ears function on land? Comparative study of extant atympanate vertebrates can provide key insights into the ancestral state and early evolution of the terrestrial tetrapod auditory system following the water-to-land transition. In this dissertation, I use atympanate salamanders as a model to investigate the structural and functional parameters underlying terrestrial hearing with unspecialized ears. In chapter one, I review the biology of the salamander auditory system. In chapter two, I characterized morphological variation of the salamander ear and found evidence for habitat-related specialization, suggesting underlying physiological variation. In chapter three, I measured auditory sensitivity to sound pressure and seismic vibration, and observed variation in sensitivity that corroborates the ecomorphological trends reported in chapter two. I assessed the contributions of hypothesized extratympanic pathways for hearing, including seismic sensitivity, cavity resonance, and bone conduction. I determined that aerial auditory sensitivity is mediated by bone conduction of sound as head vibrations that are detectable to the inner ear. In chapter four, I evaluated the sound localization capabilities of an atympanic ear. I found that bone conduction hearing in salamanders supports a figure-eight pattern of directional sensitivity to airborne sound. I contextualize my findings with other studies of tympanate and atympanate taxa and suggest that bone conduction may represent a general mechanism enabling aerial sound detection and localization in terrestrial species with atympanic ears

Data from: Bony labyrinth morphometry reveals hidden diversity in lungless salamanders (Family Plethodontidae): structural correlates of ecology, development, and vision in the inner ear

Lungless salamanders (Family Plethodontidae) form a highly speciose group that has undergone spectacular adaptive radiation to colonize a multitude of habitats. Substantial morphological variation in the otic region coupled with great ecological diversity within this clade make plethodontids an excellent model for exploring the ecomorphology of the inner ear. We examined the influence of habitat, development, and vision on inner ear morphology in 53 plethodontid species. We collected traditional and 3D geometric morphometric measurements to characterize variation in size and shape of the otic endocast and peripheral structures of the salamander ear. Phylogenetic comparative analyses demonstrate structural convergence in the inner ear across ecologically similar species. Species that dwell in spatially-complex microhabitats exhibit robust, highly curved semicircular canals suggesting enhanced vestibular sense, whereas species with reduced visual systems demonstrate reduced canal curvature indicative of relaxed selection on the vestibulo-ocular reflex. Cave specialists show parallel enlargement of auditory-associated structures. The morphological correlates of ecology among diverse species reveal underlying evidence of habitat specialization in the inner ear and suggest that there exists physiological variation in the function of the salamander ear even in the apparent absence of selective pressures on the auditory system to support acoustic behavior