On Comparative Genomic Approaches: Evolutionary Investigations Within Mammalia and Crocodilia

This dissertation presents two major comparative genomic studies that reveal novel insights into transposable element (TE) evolution in mammals and phylogenetic relationships in crocodylians. The first study represents the largest manual curation of TEs undertaken in eukaryotes, analyzing 248 placental mammal genomes from the Zoonomia Consortium. Our analyses revealed dramatic variation in TE content across mammals (27.6% to 74.5% of genome size) and identified ecological drivers of genome evolution. Most significantly, we discovered that carnivorous mammals accumulate significantly more DNA transposons than herbivorous species. Additionally, we found that mammalian genomes typically accumulate one TE type at a time, indicating sophisticated host defense mechanisms that create structured, non-random patterns of TE evolution. The second study generated the largest molecular dataset applied to crocodylian systematics, using 13,332 single-copy orthologous genes from 12 Crocodylus species and outgroup taxa. Our analyses provide additional context to the longstanding phylogenetic uncertainties of neotropic Crocodylus by revealing extensive gene tree discordance indicating complex evolutionary histories. Systematic introgression detection using HyDe and PhyloNet identified widespread ancient hybridization across crocodylian lineages, requiring four reticulation events to optimally explain genomic patterns. Investigation of positive selection in predominantly freshwater Crocodylus yielded unexpected results, identifying six genes involved in DNA repair, immune function, and cellular maintenance rather than classic osmoregulatory pathways, suggesting that freshwater adaptation involves indirect mechanisms addressing multifaceted environmental stresses. This dissertation demonstrates that ecological factors actively shape genome evolution through mechanisms like horizontal transfer, that reticulate evolution through hybridization is more pervasive than previously recognized, and that environmental adaptation involves unexpected molecular pathways. All genomic resources and analytical pipelines have been made publicly available, supporting open science principles and enabling future research with practical applications for understanding TE-associated diseases, informing conservation strategies for threatened species, and advancing our fundamental understanding of how genomes evolve in response to environmental pressures.