Molecular phylogenetics of the North American snake tribe Thamnophiini

Abstract

Advancements in phylogenetic theory and methodology coupled with improvements in computational and sequencing technology facilitate study of the divergence and diversification patterns of life. I apply our current understanding to further explore the relationships and evolution of the North American snake tribe Thamnophiini, as well as to address current topics in phylogenetic and taxonomic methodology. There are two paradigms for the phylogenetic analysis of multi-locus sequence data: one which forces all genes to share the same underlying history, and another that allows genes to follow idiosyncratic patterns of descent from ancestral alleles. The first of these approaches (concatenation) is a simplified model of the actual process of genome evolution while the second (species-tree methods) may be overly complex for histories characterized by long divergence times between cladogenesis. Rather than making an a priori determination concerning which of these phylogenetic models to apply to our data, I seek to provide a framework for choosing between concatenation and species-tree methods that treat genes as independently evolving lineages. In Chapter 2 I demonstrate that parametric bootstrapping can be used to assess the extent to which genealogical incongruence across loci can be attributed to phylogenetic estimation error, and demonstrate the application of our approach using an empirical dataset from 10 species of the Natricine snake sub-family. Since our data exhibit incongruence across loci that is clearly caused by a mixture of coalescent stochasticity and phyogenetic estimation error, we also develop an approach for choosing among species tree estimation methods that take gene trees as input and those that simultaneously estimate gene trees and species trees. Ideally, existing taxonomy would be consistent with phylogenetic estimates derived from rigorously analyzed data using appropriate methods. In Chapter 3 I present a multi-locus molecular analysis of the relationships among nine genera in the North American snake tribe Thamnophiini in order to test the monophyly of the crayfish snakes (genus Regina) and the earth snakes (genus Virginia). Sequence data from seven genes were analyzed to assess relationships among representatives of the nine genera by performing multi-locus phylogeny and species tree estimations, and we performed constraint-based tests of monophyly of classic taxonomic designations on a gene-by-gene basis. Estimates of species trees demonstrate that both genera are paraphyletic, and this inference is supported by a concatenated tree. This finding was supported using gene tree constraint tests and Bayes factors, where we rejected the monophyly of both the crayfish snakes (genus Regina)