The phylogenetic position of Mylodon darwinii

Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first discovered its remains from South America. We have successfully obtained a high-quality mitochondrial genome at 99-fold coverage using an Illumina shotgun sequencing of a 13,000 year-old bone fragment from Mylodon cave in Chile. Low level of DNA damage shows that this sample is exceptionally well preserved for an ancient sub-fossil, likely the result of the dry and cold conditions prevailing within the cave. Accordingly, taxonomic assessment of our shotgun metagenomic data showed a very high percentage of endogenous DNA. Additionally, we collected sequences from seven nuclear exons representing more than 15 kilobases using target sequence capture. Phylogenetic and dating analyses of the mitogenomic dataset including all extant species of xenarthrans and the nuclear supermatrix unambiguously position Mylodon darwinii as the sister-group of modern two-toed sloths from which it diverged around 22 million years ago. These results support the diphyly of the two modern sloths lineage implying the convergent evolution of their unique suspensory behaviour as an adaption to arboreality. Our results offer promising perspectives for whole genome sequencing of this emblematic extinct taxon.