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.
Mitochondrial dataset
Concatenation of mitochondrial genes for 35 xenarthran taxa
Mylo_mitos_seqCat.nex
Mitochondrial RAxML tree
Maximum likelihood tree for 35 xenarthran mitogenomes inferred with RAxML under a partitioned model as estimated by PartitionFinder
Mylo_mitos_RAxML_part.tre
Mitochondrial PartitionFinder best scheme for RAxML
PartitionFinder best scheme for running RAxML on the mitochondrial dataset
Mylo_mitos_PartitionFinder_RAxML.txt
Mitochondrial MrBayes consensus tree
Bayesian consensus tree for 35 xenarthran mitogenomes inferred with MrBayes under a partitioned model as estimated by PartitionFinder
Mylo_mitos_MrBayes_part.tre
Mitochondrial PartitionFinder best scheme for MrBayes
PartitionFinder best scheme for running MrBayes on the mitochondrial dataset
Mylo_mitos_PartitionFinder_MrBayes.txt
Mitochondrial PhyloBayes consensus tree
Bayesian consensus tree for 35 xenarthran mitogenomes inferred with PhyloBayes under the CAT-GTR+G4 mixture model. This phylogram corresponds to Figure 2a.
Mylo_mitos_PhyloBayes_cat.tre
Mitochondrial PhyloBayes chronogram
Bayesian chronogram for 35 xenarthran mitogenomes inferred with PhyloBayes under the CAT-GTR+G4 mixture model and a autocorrelated lognormal relaxed molecular clock. The file in nexus format can be opened in FigTree and corresponds to Figure 3a.
Mylo_mitos_PhyloBayes_chrono.tree
Nuclear dataset
Concatenation of 7 nuclear exons for 28 xenarthran taxa
Mylo_7exons_seqCat.nex
Nuclear RAxML tree
Maximum likelihood tree for 7 nuclear exons inferred with RAxML under a partitioned model as estimated by PartitionFinder
Mylo_7exons_RAxML_part.tre
Nuclear PartitionFinder best scheme for RAxML
PartitionFinder best scheme for running RAxML on the nuclear dataset
Mylo_7exons_PartitionFinder_RAxML.txt
Nuclear MrBayes consensus tree
Bayesian consensus tree for 7 nuclear exons inferred with MrBayes under a partitioned model as estimated by PartitionFinder
Mylo_7exons_MrBayes_part.tre
Nuclear PartitionFinder best scheme for MrBayes
PartitionFinder best scheme for running MrBayes on the nuclear dataset
Mylo_7exons_PartitionFinder_MrBayes.txt
Nuclear PhyloBayes consensus tree
Bayesian consensus tree for 7 nuclear exons inferred with PhyloBayes under the CAT-GTR+G4 mixture model. This phylogram corresponds to Figure 2b.
Mylo_7exons_PhyloBayes_cat.tre
Nuclear PhyloBayes chronogram
Bayesian chronogram for 7 nuclear exons inferred with PhyloBayes under the CAT-GTR+G4 mixture model and a autocorrelated lognormal relaxed molecular clock. The file in nexus format can be opened in FigTree and corresponds to Figure 3b.
Mylo_7exons_PhyloBayes_chrono.tree
Mylo_7exons_Final_bait_set
Final set of 4,381 baits of 80nt length used to capture the seven nuclear exons