|
Ancient Epidemics in Bats
Viruses are a major driver of adaptation in mammals, accounting for up to 30% of protein-coding adaptation (Enard et al. 2016). Using Myotis bats as a model system, we are using genomic signatures of adaptation at Virus Interacting Proteins to understand ancient epidemics - their viral causes, frequency, strength, and evolutionary impacts, as well as the most important mechanisms of adaptation, whether that is protein-coding changes, changes in gene expression, or other factors.
Myotis is a highly diverse genus of insectivorous bats, with 10 species in the western United States alone. It is an ideal system in which to study specific differences in selective pressures because these species are closely related, but have important differences in habitat preferences, as well as more subtle differences in diet and behavior. In collaboration with Dr. Peter Sudmant and Dr. Juan Vasquez, we have generated reference genomes for eight of these species, as well as cell lines and a data set of more than 140 individual short read genomes to 30x coverage. We are in the process of fully annotating these genomes, followed by phylogenomic comparative analyses of adaptation in protein-coding genes and structural variation, introgression and hybridization, and convergence across these species, focusing on disease adaptation and longevity. We are also conducting population genomic analyses of adaptation within these species, using my machine learning sweep detection method Flex-sweep and Bayesian statistical models to link disease adaptation to habitat factors such as temperature and humidity. |
|