Date of Award

December 2019

Document Type


Degree Name

Master of Science (MS)


Biological Sciences

Committee Member

Christopher L Parkinson

Committee Member

Antonio Baeza

Committee Member

Vincent Richards


Understanding evolution is a key component in trying to decipher the processes generating global species diversity. The strength, direction, and interaction of gene flow and selection often determine diversification patterns and the process of speciation. The Nerodia fasciata/clarkii species complex, a lineage of water snakes, is thought to have high levels of both gene flow and selective pressures due to ecological constraint. Nerodia clarkii resides in salt marsh and estuarine habitats while Nerodia fasciata is typically found in fresh water. Salinity is a strong selective pressure and is thought to play a role in the diversification process. Currently, there are five described subspecies within the complex but their validity is in question, causing concerns about the conservation status of the federally threatened Atlantic Salt Marsh Snake (N. c. taeniata). To understand the diversification of the Nerodia fasciata/clarkii complex and to resolve the noted taxonomic issues, I generated the first population genomic dataset for this group using double digest restriction site-associated DNA sequencing (ddRADseq). I first used a Discriminate Analysis of Principal Components (DAPC) to identify population structure and SVDQuartets to generate a coalescent based phylogeny. With these data, I identified 4-6 populations that approximate subspecies designations although only one assigned subspecies, N. c. clarkii, was monophyletic. Second, I estimated migration among the best supported population clustering (k=5) using Estimated Effective Migration Surfaces (EEMS). EEMS revealed a migration corridor between the mostly N. fasciata populations and a reduction in gene flow at the coasts. Third, I used two selection scan analyses and one environmental association analysis to identify genes that are putatively under selection with an emphasis on local adaptation to saline water. I found 10 candidate genes that may be involved in osmoregulation and multiple correlations to temperature and precipitation. My results indicate that the two species are valid, and that four subspecies are also evolutionary lineages. Although gene flow and population assignment tests provided evidence that N. c. taeniata was isolated from other populations I could not unambiguously determine its validity. Both the candidate gene frequencies and EEMS indicate that majority N. fasciata populations mostly share a selection regime and gene flow patterns separate them from N. clarkii. This may demonstrate how a reduction in gene flow and a change in selection pressures can generate species diversity.



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