Molecular evolution of subterranean adaptation
The repeated degeneration or loss of traits has long been of interest to evolutionary biologists. Despite the broad recognition of regressive evolution, the developmental and molecular mechanisms underlying character loss remain poorly understood. Cave animals are popular examples of regressive evolution, as many lineages have independently lost their eyes and pigmentation. However, few studies have demonstrated that loss of eyes is associated with loss of selective constraint in vision-related genes at the molecular level. In particular, no studies have demonstrated loss of function of the visual photoreceptor gene rhodopsin, one of the best-studied retinal proteins. A study of molecular evolution of rhodopsin in amblyopsid cavefishes (Niemiller et al. 2013), a small family of North American fishes that occur in both surface and cave habitats (Niemiller & Poulson 2010), revealed repeated loss of functional constraint in this gene, with at least three cave lineages having independently accumulated unique loss-of-function mutations. Although several cave lineages still possess a functional rhodopsin, they exhibit increased rates of mutations that have greater effects on the structure and function of the protein compared to mutations in surface lineages. Retention of functionality may be related to recent subterranean colonization rather than possible pleiotropic roles.
Many genes likely are gained and lost during the transition from living on the surface to underground. To identify candidate genes underlying loss of eyes and other cave-related changes, I am conducting comparative genomic analyses of the transcriptomes of surface and cave amblyopsids. My aim is to develop a large-scale genomic approach to the study of adaptation in subterranean organisms. With the genomic tools generated from this project, I am screening for genes involved in development, function, and regulation of cave-related traits. Preliminary analyses have discovered several candidate loci that are differentially expressed between surface and cave species, including several associated with eyes and metabolism.
Primary Collaborators: Benjamin M. Fitzpatrick (University of Tennessee), Thomas J. Near (Yale University)
Genetic and functional diversity of cavefishes
Subterranean aquatic habitats are among the most poorly known environments on the planet. In collaboration with Daphne Soares (University of Maryland), Prosanta Chakrabarty (Louisiana State University) and Dante Fenolio (San Antonio Zoo), we seek to understand how adaptation to extreme conditions is facilitated or constrained by variation in genetic and functional diversity during ecological transition into subterranean environments using cavefishes as a model. Specifically, we aim to: (1) determine the relationship among cavefishes with their surface relatives, and to study their mode of diversification and biogeographic origins, (2) quantify genetic diversity among cavefish species and populations, (3) examine the link between neuroecology and evolutionary changes that are constructive or regressive. Specifically, we aim to determine whether genetic diversity and diversity in sensory adaptations in surface ancestors promote or constrain speciation in subterranean ecosystems?, and how does variation in subterranean environmental conditions impact genetic, functional and taxonomic diversity? We will incorporate comparative genomics and transcriptomics to provide an evolutionary framework for understanding genetic and taxonomic diversity and to identify functional genes important for ecological transitions from surface to cave habitats; (2) qualitative and quantitative approaches to identify and assay anatomical, behavioral and physiological mechanisms underlying sensory adaptation; and (3) a rigorous neuroecological program that will characterize and relate unique aquatic cave habitats to cavefish behavior and function.
Primary Collaborators: Daphne Soares (University of Maryland), Prosanta Chakrabarty (Louisiana State University), Dante B. Fenolio (San Antonio Zoo)