Publication Date


Advisor(s) - Committee Chair

Keith Philips (Chair), Albert Meier, Matthew Niemiller

Degree Program

Department of Biology

Degree Type

Master of Science


The relationship between geographic distribution and phylogeny is pronounced in patchy, discontinuous habitats that limit gene flow, such as cave ecosystems. The isolating nature and selective pressures of cave environments can result in relatively high levels of endemism and cryptic speciation in cave faunas. Cryptic speciation exhibited in cave faunas is poorly studied, though it is an integral aspect to consider when discussing conservation efforts.

Our study employed the 3RAD genomic sequencing technique and robust population sampling across the distribution of a monotypic genus of cave beetle, Darlingtonea Valentine, that inhabits karst systems in a nearly 200 square mile range in south-central Kentucky and possibly northern Tennessee.

The 3RAD technique yielded tens of thousands of single nucleotide polymorphisms (SNPs) from homologous loci across the entire genome from 161 individuals that were analyzed through population structuring software packages Structure and a Discriminant Analysis of Principle Components (DAPC) to best fit the genetic diversity of the genus into distinct species clades and through a Bayesian analysis to hypothesize population relationships and estimate genetic divergence.

Significant barriers to gene flow were discovered throughout the distribution of Darlingtonea that separates populations into 11 distinct genetic species clades supported by Bayesian inference, Structure analyses, and DAPC. The substantial lack of gene flow between populations and extremely limited ability to disperse effectively is accompanied by overwhelming evidence that the genus should be represented by 11 independent species. Delineating cryptic species and defining their boundaries is integral in deciding how to direct conservation effort for the unique and fragile ecosystem found within karst ecosystems in eastern North America and other places in the world.


Biodiversity | Entomology | Genetics and Genomics | Life Sciences | Molecular Genetics