Collagen sequence analysis of the extinct giant ground sloths lestodon and megatherium

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Abstract

For over 200 years, fossils of bizarre extinct creatures have been described from the Americas that have ranged from giant ground sloths to the vea South American ungulates, groups of mammals that evolved in relative isolation on South America. Ground sloths belong to the South American xenarthrans, a group with modern although morphologically and ecologically very different representatives (anteaters, armadillos and sloths), which has been proposed to be one of the four main eutherian clades. Recently, proteomics analyses of bone collagen have recently been used to yield a molecular phylogeny for a range of mammals including the unusual 'Malagasy aardvark' shown to be most closely related to the afrotherian tenrecs, and the south American ungulates supporting their morphological association with condylarths. However, proteomics results generate partial sequence information that could impact upon the phylogenetic placement that has not been appropriately tested. For comparison, this paper examines the phylogenetic potential of proteomicsbased sequencing through the analysis of collagen extracted from two extinct giant ground sloths, Lestodon and Megatherium. The ground sloths were placed as sister taxa to extant sloths, but with a closer relationship between Lestodon and the extant sloths than the basal Megatherium. These results highlight that proteomics methods could yield plausible phylogenies that share similarities with other methods, but have the potential to be more useful in fossils beyond the limits of ancient DNA survival.

Figures

  • Fig 1. MALDI-ToFmass spectra of collagen extracted from Lestodon andMegatherium digested with trypsin. *Note the clearly observable difference in deamidation as a marker for protein ageing due to the presence of a glutamine residue in this peptide.
  • Table 1. Number of amino acid variations detected through LC-basedmethods compared with number of most intense 100 peaks shared in MALDI fingerprints (numbers in brackets indicate observations confirmed in both fossil replicates for each species).
  • Table 2. Proteomics information relating to the quality of the Mascot search results, including the False Decoy Rate (FDR), highest scoring false positive peptide (HFPS), the total protein score for sloth collagen, the number of peptidematches used for this score, the number of unique sequences and the percentage coverage.
  • Fig 2. Maximum Likelihood analysis of the concatenated COL1A1 and COL1A2 sequences of eutherian mammals including the proposed consensus sequences of the two extinct ground sloths Lestodon andMegatherium.
  • Fig 3. Phylogenetic analyses of COL1A2 sequences of eutherianmammals including the extinct South American native ungulates and two extinct ground sloths Lestodon andMegatherium in comparison to extant slothsBradypus andCholoepus showing (A) Maximum Likelihood analysis of consensus peptide matches observed in the PMF, (B) Maximum Likelihood of peptidematches observed in the PMF from either specimen, (C) Maximum Likelihood of the alpha 2 (I) sequences only, using the EnsemblCholoepus sequence and (D) Bayes analysis of consensus peptide matches observed in the PMF.

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Buckley, M., Farina, R. A., Lawless, C., Tambusso, P. S., Varela, L., Carlini, A. A., … Martinez, J. G. (2015). Collagen sequence analysis of the extinct giant ground sloths lestodon and megatherium. PLoS ONE, 10(11). https://doi.org/10.1371/journal.pone.0139611

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