Ecological genomics of Myotis bats and their ectoparasites in the Baja California peninsula

In this thesis I investigated diversity, population structure and species boundaries in Myotis bats and their ectoparasite community structure, from the Baja California peninsula and continental sites in Mexico. Using mitochondrial cytb haplotypes and ddRAD derived SNP markers, traces of introgression were found in four sympatric Myotis species, particularly over the mid and north peninsula, and one continental site. Recent hybrids were detected among Myotis yumanensis and M. californicus individuals from mid and north peninsula. Population structure for M. californicus was detected, but also potential migrants, suggesting some long-distance dispersal. Cluster analysis suggested M. californicus to be split in two groups. M. yumanensis showed weak nuclear population structure, but strong mitochondrial differentiation, suggesting long-distance male dispersal and female philopatry. Admixture analyses with ddRAD SNP data showed that bats with ancestry similar to M. velifer clustered along with the putatively Baja endemic M. peninsularis. However, mitochondrial haplotypes and nuclear FST results indicated M. peninsularis population as demographically isolated from continental M. velifer. I also identified two potential new cryptic Myotis lineages with strongly divergent mitochondrial haplotypes: a population showing morphological features not matching currently recorded species, designated M. sv, and specimens from Baja that were morphologically assigned to M. volans. Bat ectoparasite phylogenetic analysis revealed multiple novel lineages of bat bugs, flies and ticks, five new records of known bat flies and one tick species previously unrecorded for the peninsula. Host-specific and generalist ectoparasites were found, as well as locally restricted and widely dispersed species, with the latter potentially reflecting bat dispersal across the peninsula. The main driver of ectoparasite diversity and community structure was host diversity and composition, with a strong pattern of phylogenetic association at the host family level. This research discovered novel cryptic diversity of bats and ectoparasites in north-western Mexico, showing porous species boundaries and potential incipient species. Both bat and ectoparasite research are highly relevant to disease ecology as potential vectors of zoonotic diseases.