DOI: 10.5061/dryad.ft3k3
title: Data from: Resolving the phylogenetic position of Darwin’s extinct ground sloth (Mylodon darwinii) using mitogenomic and nuclear exon data

description: 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.
description: Mitochondrial
 datasetConcatenation of
 mitochondrial genes for 35 xenarthran taxaMylo_mitos_seqCat.nexMitochondrial RAxML treeMaximum likelihood tree for 35 xenarthran mitogenomes inferred with RAxML under a partitioned model as estimated by PartitionFinderMylo_mitos_RAxML_part.treMitochondrial PartitionFinder best scheme for RAxMLPartitionFinder best scheme for running RAxML on the mitochondrial datasetMylo_mitos_PartitionFinder_RAxML.txtMitochondrial MrBayes consensus treeBayesian consensus tree for 35 xenarthran mitogenomes inferred with MrBayes under a partitioned model as estimated by PartitionFinderMylo_mitos_MrBayes_part.treMitochondrial PartitionFinder best scheme for MrBayesPartitionFinder best scheme for running MrBayes on the mitochondrial datasetMylo_mitos_PartitionFinder_MrBayes.txtMitochondrial PhyloBayes consensus treeBayesian 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.treMitochondrial PhyloBayes chronogramBayesian 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.treeNuclear datasetConcatenation of 7 nuclear exons for 28 xenarthran taxaMylo_7exons_seqCat.nexNuclear RAxML treeMaximum likelihood tree for 7 nuclear exons inferred with RAxML under a partitioned model as estimated by PartitionFinderMylo_7exons_RAxML_part.treNuclear PartitionFinder best scheme for RAxMLPartitionFinder best scheme for running RAxML on the nuclear datasetMylo_7exons_PartitionFinder_RAxML.txtNuclear MrBayes consensus treeBayesian consensus tree for 7 nuclear exons inferred with MrBayes under a partitioned model as estimated by PartitionFinderMylo_7exons_MrBayes_part.treNuclear PartitionFinder best scheme for MrBayesPartitionFinder best scheme for running MrBayes on the nuclear datasetMylo_7exons_PartitionFinder_MrBayes.txtNuclear PhyloBayes consensus treeBayesian 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.treNuclear PhyloBayes chronogramBayesian 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.treeMylo_7exons_Final_bait_setFinal set of 4,381 baits of 80nt length used to capture the seven nuclear exons