Résumé
Mylodon darwinii is the extinct giant ground sloth named after Charles
Darwin, who first discovered its remains in South America. We have
successfully obtained a high-quality mitochondrial genome at 99-fold
coverage using an Illumina shotgun sequencing of a 12,880 year-old bone
fragment from Mylodon Cave in Chile. Low level of DNA damage showed that
this sample was 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 with 22% of the assembled
metagenomic contigs assigned to Xenarthra. Additionally, we enriched over
15 kilobases of sequence data from seven nuclear exons, using target
sequence capture designed against a wide xenarthran dataset. Phylogenetic
and dating analyses of the mitogenomic dataset including all extant
species of xenarthrans and the assembled nuclear supermatrix unambiguously
place Mylodon darwinii as the sister-group of modern two-fingered sloths
from which it diverged around 22 million years ago. These congruent
results from both the mitochondrial and nuclear data support the diphyly
of the two modern sloths lineages, 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.