Date of Graduation

5-2021

Document Type

Dissertation

Degree Name

Doctor of Philosophy in Biology (PhD)

Degree Level

Graduate

Department

Biological Sciences

Advisor

Marlis R. Douglas

Committee Member

Michael E. Douglas

Second Committee Member

John S. Placyk, Jr.

Third Committee Member

Andrew J. Alverson

Keywords

Introgression, Phylogenetics, Phylogeography, Sistrurus, Speciation, Terrapene

Abstract

Hybridization has traditionally been viewed as a happenstance that negatively impacts populations, but is now recognized as an important evolutionary mechanism that can substantially impact the evolutionary trajectories of gene pools, influence adaptive capacity, and contravene or reinforce divergence. Physiographic processes are important drivers of dispersal, alternately funneling populations into isolation, promoting divergence, or facilitating secondary contact of diverged populations, increasing the potential for hybridization. In North America, glacial-interglacial cycles and geomorphological changes have provided a dynamic backdrop over the last two million years that promoted such oscillations of population contraction and expansion. These biogeographic processes have resulted in regional hybrid zones where hybridization spans generations

Herein, I explored hybrid zones in two species complexes of reptiles across Eastern, Central, and Southwestern North America. Hybrid zones can influence evolutionary trajectories, and understanding the mechanisms underlying their formation is important for defining appropriate management strategies and can help avoid actions that would inadvertently lead to new hybrid zones.

Chapter I assessed differential introgression in a complex of terrestrial turtles, the American Box Turtles (Terrapene spp.), from a contemporary hybrid zone in the southeastern United States. Transcriptomic loci were correlated with environmental predictors to evaluate mechanisms engendering maladapted hybrids and adaptive introgression. Selection against hybrids predominated for inter-specifics but directional introgression did so in conspecifics. Outlier loci also primarily correlated with temperature, reflecting the temperature dependency of ectotherms and underscoring their vulnerability to climate change.

Chapter II performed a robust assessment of recently developed machine learning (M-L) approaches to delimit four Terrapene species and evaluate the impact of data filtering and M-L parameter choices. Parameter selections were varied to determine their effects in resolving clusters. The results provide necessary recommendations on using M-L for species delimitation in species complexes defined by secondary contact. These data exemplify usage of M-L software in a phylogenetically complex group.

Chapter III describes an R package to visualize some of the analyses from Chapter I. Current software to generate genomic clines does not include functions to visualize the results. Thus, I wrote an API (application programming interface) that does so and also performs other genomic and geographic cline-related tasks.

Chapter IV examines historical and contemporary phylogeographic patterns in the Massasaugas (Sistrurus spp.), a type of dwarf rattlesnake found across the Southwest and Central Great Plains. In the Southwest, S. tergeminus tergeminus and S. t. edwardsii putatively diverged in the absence of strong physiographic barriers and physical glaciers, suggesting primary divergence. In contrast, a disjunct population of S. t. tergeminus in Missouri reflects potentially historical secondary contact with S. catenatus. These taxa represent contrasting examples of divergence resulting from alternative phylogeographic processes and contextualizes evolutionarily significant and management units.

Combined, the four chapters present population genomic data to elucidate impacts of phylogeographic processes on hybrid zones at a continental scale. The data will promote effective conservation management strategies, as many species in the focal regions have been affected by anthropogenic pressures. In this sense, the results can be extrapolated to co-distributed taxa with similar phylogeographic histories.

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