Phylogenetic Perspectives on Viviparity, Gene-Tree Discordance, and Introgression in Lizards (Squamata)
AuthorLambert, Shea Maddock
AdvisorWiens, John J.
MetadataShow full item record
PublisherThe University of Arizona.
RightsCopyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction, presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
EmbargoRelease after 08/21/2019
AbstractThis dissertation consists of three works of phylogenetic biology. In each case, my collaborators and I contribute to the field by providing novel empirical results germane to each topic and study system, but also in a broader sense by facilitating the use and understanding of modern phylogenetic methods. In appendix A, I investigate the evolution of viviparity in phylogenetic test of the cold-climate hypothesis. This long-standing hypothesis states that the evolution of viviparity is an adaptation that prevents egg and/or juvenile mortality in cold climates. I apply a suite of cutting-edge phylogenetic comparative methods to phylogenetic, climatic, and life history data from the lizard family Phrynosomatidae. The results strongly support the cold-climate hypothesis, and help to explain two counter-intuitive patterns in Phrynosomatidae. In appendix B, I examine discordance in phylogenetic reconstruction in order to answer an unresolved question with significant practical implications for phylogeneticists: can disagreement between concatenated and multi-species coalescent estimates be predicted? Using an empirical example in higher-level scincid lizard relationships, I find that discordance between these methods is related to short, weakly supported branches, and the presence of conflicting gene trees. These results suggest that concatenation may provide a reasonable approximation of theoretically preferable species-tree methods under most circumstances. Moreover, standard methods for incorporating phylogenetic uncertainty may be sufficient to account for disagreements by species-tree method estimates. In appendix C, I demonstrate a novel workflow for the detection of nuclear introgression in an empirical case study of closely related spiny lizard (Sceloporus) species. I first show that mitochondrial data independently suggests a repeated history of introgression between the focal taxa. I then show that an exhaustive application of the DFOIL method to double-digest RADseq data from many individuals is effective at identifying introgression in the nuclear genome. This novel approach also reveals intra-specific geographic variation in in patterns of introgression, without the need to determine population structure. Finally, I find that that batch effects in ddRADseq data may mislead D-statistics (and DFOIL) under certain circumstances.
Degree ProgramGraduate College
Ecology & Evolutionary Biology