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Palaeoproteomics resolves sloth relationships

Abstract

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.

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Data availability

Mass spectrometry proteomics data have been deposited with the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD012859. Collagen sequences are available on the Uniprot website (https://www.uniprot.org/); the complete list can be found in Supplementary Table 5. Phylogenetic datasets have been deposited at DataDryad (https://doi.org/10.5061/dryad.7dd64gs).

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Change history

  • 14 June 2019

    An old version of the Supplementary Information was originally uploaded. This has now been replaced with the correct version.

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Acknowledgements

We thank the curatorial staffs of the following museums and private collections for permission to sample specimens in their care: AMNH-M, American Museum of Natural History (Mammalogy), New York, USA; AMNH-P, American Museum of Natural History (Paleontology), New York, USA; CIV, Iota Quatro faunal collection, courtesy of Lazaro Vinola; El Trebol faunal collection, Bariloche, Argentina; FR, Forest Reserve (Trinidad) faunal collection currently housed in Department of Mammalogy, AMNH, New York, USA; IANIGLA-PV, Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales, CCT-CONICET-Mendoza, Mendoza, Argentina; MACN-PV, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’ (Sección Paleovertebrados), Buenos Aires, Argentina; MAPBAR, Museo de la Asociación Paleontológica Bariloche (APB), prov. Río Negro, Argentina; MMP, Museo Municipal de Ciencias Naturales ‘Lorenzo Scaglia’ Mar del Plata, prov. Buenos Aires, Argentina; MNHN SAO, Muséum national d’Histoire naturelle, Paris, France; MPS, Museo Paleontológico ‘Fray Manuel de Torres’, San Pedro, prov. Buenos Aires, Argentina; MUSM, Museo de Historia Natural de la Universidad Nacional Mayor de San Marcos, Lima, Peru; NYSM VP, New York State Museum (Vertebrate Paleontology), Albany, USA; RM, Cuban faunal collection currently housed in Department of Mammalogy, AMNH, New York, USA; UF, University of Florida, Natural History Museum of Florida (Vertebrate Paleontology), Gainesville, USA; UMAG ah, Instituto de La Patagonia, Universidad de Magallanes, Punta Arenas, Chile; USNM, United States National Museum of Natural History (Paleobiology), Washington DC, USA. Samples of specimens housed in Argentinian collections were sampled before 2009. S.P. would like to thank B. Demarchi for useful discussion and support. The authors thank the National Science Foundation for grants (No. OPP 0636639 to R.D.E.M. and No. DEB 1547414 to R.D.E.M., M.C. and K.P.).

Author information

R.D.E.M., M.C. and S.P. conceived the project. S.P. undertook AAR, proteomic analysis and concatenated collagen sequences, with laboratory and technical assistance from R.F., J.V.O., K.M., M.M., M.C., K.P. and B.T.C. G.J.S. conducted phylogenetic analyses. F.P. and A.M.F. supplied palaeontological information. A.K., M.T., F.S., M.L., A.H., R.F., J.B., J.L.L., F.M.M., R.S.G., M.R., A.G., C.d.M. and J.S. supplied fossil samples, locality information, dating, species identifications and commentary on the manuscript. R.D.E.M., S.P. and G.J.S. wrote the manuscript, with input from all authors.

Competing interests

The authors declare no competing interests.

Correspondence to Ross D. E. MacPhee.

Supplementary information

  1. Supplementary Information

    Supplementary analyses, Supplementary References, Supplementary Figs. 1–6 and legends for Supplementary Tables 1–5

  2. Reporting Summary

  3. Supplementary Table 1

    Information on all samples investigated for this study

  4. Supplementary Table 2

    Radiocarbon dates for specimens successfully screened for MS/MS

  5. Supplementary Table 3

    Marginal Likelihoods estimated for three clock models for proteomic data alone and proteomic + genomic data using the path sampling algorithm in BEAST 2.5.1

  6. Supplementary Table 4

    Detected amino acid differences between Megatherium sequence reported in ref. 15 (denoted by B) and the sequence concatenated in this study (TS)

  7. Supplementary Table 5

    Accession numbers of collagen sequences used in this study

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Fig. 1: Phylogenetic relationships among major folivoran taxa based on morphological evidence, with existence of unallocated taxa acknowledged.
Fig. 2: Geographical locations of sequenced samples.
Fig. 3: Fifty percent majority rule consensus tree from Bayesian analysis of the proteomic data without temporal information, as performed in MrBayes.
Fig. 4: Time-scaled maximum clade credibility tree from BEAST analysis of 24 extant and extinct xenarthran collagen sequences plus published mitochondrial genomes.