protein_data_MrBayesNexus file containing collagen alignments for extinct and extant xenarthrans. Also includes MrBayes block with specifications for running Bayesian topology searchcombined_data_MrBayesalignment in nexus format containing collagen protein sequences and mitochondrial genomes as available for living and extinct xenarthrans. Also includes MrBayes block.protein_mtDNA_morphology_sloths_MRBnexus file containing protein and mtDNA data plus the morphological character dataset from Varela et al., 2019.BEAST_protein_Xenarthraxml file to run BEAST under fossilized birth death process with xenarthran proteomic dataBEAST_combined_data_bradypus_constraintxml file to run beast with combined proteomic and mitochondrial genome data. Note that this file enforces a monophyly constraint on Bradypus, which can be removed by commenting out the associated lines of the xmlprotein_only_xenarthra_beastmaximum clade crediibility chronogram from analysis of xenarthran proteomic datacombined_protein_mtDNA_xenarthra_bradypus_constraint_beastmaximum clade credibility chronogram from beast analysis of xenarthran proteomic and mitochondrial genome data.

The living tree sloths Choloepus and Bradypus are the only remaining members of Folivora, a major xenarthran radiation that occupied a wide range of habitats in many parts of the western hemisphere during the Cenozoic, including both continents and the West Indies. Ancient DNA evidence has played only a minor role in folivoran systematics, as most sloths lived in places not conducive to genomic preservation. Here we utilize collagen sequence information, both separately and in combination with published mitochondrial DNA evidence, to assess the relationships of tree sloths and their extinct relatives. Results from phylogenetic analysis of these datasets differ substantially from morphology-based concepts: Choloepus groups with Mylodontidae, not Megalonychidae; Bradypus and Megalonyx pair together as megatherioids, while monophyletic Antillean sloths may be sister to all other folivorans. Divergence estimates are consistent with fossil evidence for mid-Cenozoic presence of sloths in the West Indies and an early Miocene radiation in South America.