Conservation genomic analysis reveals ancient introgression and declining levels of genetic diversity in Madagascar's hibernating dwarf lemurs

Madagascar9s biodiversity is notoriously threatened by deforestation and climate change. Many of these organisms are rare, cryptic, and severely threatened, making population-level sampling unrealistic. Such is the case with Madagascar9s dwarf lemurs (genus Cheirogaleus), the only obligate hibernator within the primates. We here apply comparative genomic approaches to generate the first genome-wide estimates of genetic diversity within species of Cheirogaleus. We generate a reference genome for the fat-tailed dwarf lemur, Cheirogaleus medius, and use this resource to facilitate analyses of high-coverage (~30x) genomes for wild-caught individuals representing four dwarf lemur species: Cheirogaleus sp. cf. medius, C. major, C. crossleyi and C. sibreei. This study therefore represents the largest contribution to date of novel genomic resources for Madagascar9s lemurs. We show that phylogenetic relationships among the four lineages of Cheirogaleus demonstrate broad-scale concordance across the genome, and yet we detect a number of discordant genomic regions. Using the size distribution of introgressed regions, we estimate that admixture, and subsequent introgression, occurred between species an average of 4.1 Mya. Introgressed regions contain genes associated with hibernation, though most significantly, show over-represented gene ontology categories relating to transcription. Finally, we estimate levels of heterozygosity and find particularly low levels in an individual sampled from an isolated population of C. medius that we refer to as C. sp. cf. medius. Our study highlights the power of comparative genomic analysis for identifying species and populations of conservation concern, as well as for illuminating possible mechanisms of adaptive phenotypic evolution - in this case, hibernation.