Determining the factors promoting speciation and adaptation is paramount to our understanding of biogeography and, ultimately, conservation and management of subterranean biodiversity. Speciation in subterranean organisms is generally thought to follow one of two main models: the climate-relict model which invokes allopatric speciation, and the adaptive-shift model where parapatric speciation occurs in the face of gene flow. I have tested both models in detail in cave salamanders and cavefishes. These studies include examining ecological speciation in Gyrinophilus salamanders and the role of selection in the evolution of eye loss and potential for re-evolution of eye functionality in amblyopsid cavefishes. In addition, I have examined the effect of climatic and geological factors on the colonization and subterranean evolution of cavefishes, resulting in the first robust molecular phylogeny of this fascinating clade of fishes. This phylogenetic framework also has allowed me to test hypotheses of the tempo and mode of diversification.
Many important questions remain to be addressed, such as whether similar ecological and evolutionary mechanisms as well as genetic loci underlie the evolution of troglomorphy (subterranean phenotypes) and subterranean adaptation in disparate taxonomic groups. I am currently examining rates and modes of speciation combining next-generation sequencing (NGS) with multilocus phylogenetic and species-tree approaches in two diverse groups of subterranean organisms: crangonyctid amphipods and carabid cave beetles. Unlike amblyopsid cavefishes, both of these groups represent large subterranean radiations (>150 species) throughout the Ozark Highlands, Interior Low Plateau, and Appalachian Valley of the eastern United States that also include many surface- and spring-dwelling species. Many species in both groups are restricted to single cave systems while others are widespread. Some caves only contain a single species of each group, though up to six species may inhabit the same cave in some cases. Consequently, these groups are ideal to study the factors that promote or constrain diversification and that facilitate syntopy and community structure of related species in subterranean habitats. Equipped with these robust phylogenies that provide phylogenetic frameworks of subterranean ecological and morphological divergence, I have unparalleled comparative systems to develop and test hypotheses regarding the genetic, morphological, and behavioral characters underlying subterranean adaptation, as well as responses to both anthropogenic and natural environmental change.