Novel nuclear and mitochondrial genetic markers have been developed and characterized in varied species and populations, facilitated by rapid advances in comparative genomics and the increasing availability of sequence data. The results have contributed to our understanding of the evolutionary history of carnivore and felid species and to the population dynamics and molecular ecology of Iberian lynx, Canada lynx, clouded leopard, tiger, leopard, cheetah, and Florida panther. A radiation-hybrid genetic map of the alpaca is providing additional tools for comparative genomic studies in mammals, especially among ungulate species. Concordant phylogenetic and phylogeogrpahic studies of feline immunodeficiency virus (FIV) transmission among free-ranging cat populations allows a glimpse of the process of emerging infections in species well suited for discovery of these events. Insights gained from these studies reveal evolved mechanisms for immune and natural defenses against fatal infections and neoplastic diseases.