Abstract
Mylodon darwinii is the extinct giant ground sloth named after Charles Darwin, who first collected 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 subfossil, probably 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 kb 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 sloth 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.
Highlights
Darwin’s extinct ground sloth (Mylodon darwinii) was named by Richard Owen in honour of Charles Darwin who discovered its early remains in South America during the voyage of the Beagle [1]
Numerous subfossils of M. darwinii have been found across the South American southern cone [3], including the famous Mylodon Cave (Cueva del Milodon, Ultima Esperanza, Chile)
Slater et al [15] have reported a partial and composite M. darwinii mitogenome reconstructed by mixing reads obtained by DNA target sequence capture from a bone and a paleofeces both sampled at Mylodon Cave
Summary
Darwin’s extinct ground sloth (Mylodon darwinii) was named by Richard Owen in honour of Charles Darwin who discovered its early remains in South America during the voyage of the Beagle [1]. Slater et al [15] have reported a partial and composite M. darwinii mitogenome reconstructed by mixing reads obtained by DNA target sequence capture from a bone and a paleofeces both sampled at Mylodon Cave. Twenty-two of the modern xenarthran libraries previously prepared by Gibb et al [21], were enriched with the designed bait set in order to capture target sequences representing the seven loci of interest for a representative diversity of Xenarthra (electronic supplementary material, table S1). Osteoderm sample of the same age (up to 25% and 20%) and the Calyptophractus museum specimen (up to 4% and 3%), whereas modern xenarthran tissue samples exhibit values below 1% These values argue in favour of the endogenous origin of the Mylodon shotgun reads and set our bone sample among some of the best ancient samples analysed so far [44].
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