Changes in the Genome: Polyploidy, Hybridization, and Genome Size Evolution Explored Through Selaginella and Vascular Plants

Abstract

The evolutionary processes responsible for generating and maintaining the remarkable diversity of life on earth are mutation, selection, drift, recombination, and gene flow. The relative magnitude of these processes, and their tempo, can be inferred from studying genomes or samples of the genome from individuals or multiple individuals. My dissertation focuses on three types of change in vascular plant genomes, with a focus on lycophytes in the genus Selaginella (Selaginellaceae). In Appendix A I characterize the extremely small genome sizes of Selaginella, and compare their observed disparity in genome size to other vascular plant clades. In Appendix B I examine the temporal activity of long terminal repeat retrotransposons (LTR-RTs) in vascular plants. I illustrate that across vascular plants LTR-RT activity largely explains the observed diversity in genome size. In Appendix C and D I focus on abrupt changes in the genome via polyploidy and hybridization. In Appendix C I demonstrate the importance of climatic niche divergence in polyploid plant species. In Appendix D I investigate the evidence of hybrid speciation in hybrids formed between Selaginella arizonica and S. eremophila in the Sonoran Desert. Using transcriptome sequencing and complementary morphological and ploidal inference, I suggest that both homoploid hybrid and allopolyploid species were formed from the same parents S. arizonica and S. eremophila. This system is the first known example of two types of stabilized hybrid derivatives from the same parents in natural populations.