The Genomic Diversity of theEliurusgenus in northern Madagascar with a Putative New Species

Abstract

AbstractMadagascar exhibits extraordinarily high level of species richness and endemism, while being severely threatened by habitat loss and fragmentation (HL&F). In front of such threat to biodiversity, conservation effort can be directed, for instance, in the documentation of species that are still unknown to science, or in investigating how species respond to HL&F. The tufted-tail rats genus (Eliurusspp.) is the most speciose genus of endemic rodents in Madagascar, with 13 described species, which occupy two major habitat types: dry or humid forests. The large species diversity and association to specific habitat types make theEliurusgenus a suitable model for investigating species adaptation to new environments, as well as response to HL&F (dryvshumid). In the present study, we investigatedEliurusspp. genomic diversity across northern Madagascar, a region covered by both dry and humid fragmented forests. From the mitochondrial DNA (mtDNA) and nuclear genomic (RAD-seq) data of 124Eliurusindividuals sampled in poorly studied forests of northern Madagascar, we identified an undescribedEliurustaxon (Eliurus sp. nova). We tested the hypothesis of a newEliurusspecies using several approaches: i) DNA barcoding; ii) phylogenetic inferences; iii) species delimitation tests based on the Multi-Species Coalescent (MSC) model, iv) genealogical discordance index (gdi); v) thead-hoctest of isolation-by-distance withinversusbetween sister-taxa, vi) comparisons of %GC content patterns and vii) morphological analyses. All analyses support the recognition of the undescribed lineage as a distinct species. In addition, we show thatEliurus myoxinus, a species known from the dry forests of western Madagascar, is, surprisingly, found mostly in humid forests in northern Madagascar. In conclusion, we discuss the implications of such findings in the context ofEliurusspecies evolution and diversification, and use the distribution of northernEliurusspecies as a proxy for reconstructing past changes in forest cover and vegetation type in northern Madagascar.