Barcoding the dead: ancient protein sequencing resolves litoptern and notoungulate superordinal affinities

MACPHEE, R. ; WELKER, F; THOMAS, J; BRACE, S.; CAPPELLINI, E.; TURVEY, S.; BARNES, I; REGUERO, M.; GELFO J. N.; KRAMARZ, A.

Berlin

Congreso; 74th ANNUAL MEETING OF the SOCIETY OF VERTEBRATE PALEONTOLOGY; 2014

Society of Vertebrate Paleontology

Recent speculations concerning the affinities of South American native ungulates (SANUs) assert that at least some members of this ?paraphyletic group are not laurasiatheres but are instead either sister to Afrotheria or part of a distinct clade that includes afrotheres. Testing of this controversial hypothesis is desirable, optimally with data independent of phenotypic interpretation. Such a test might come from molecular data using short DNA sequences as barcodes (cf. Barcode of Life), but all efforts to acquire such information from SANU fossils have so far failed. There is an alternative: backbones of proteins such as collagen (latter comprising >90% of all bone proteins) are an order of magnitude more stable than DNA and therefore more likely to survive taphonomically. We screened 34 Pleistocene bone samples of Toxodon (Notoungulata) and Macrauchenia (Litopterna) for collagen and DNA. Autochthonous DNA was not recovered, but collagen yield was often excellent. Using soft-ionization tandem mass spectrometry we obtained >90% sequence coverage of COL1α1 and COL1α2 sequences (1057 and 1040 residues, respectively) on the 4 best samples (2 per taxon), yielding 21,428 matching spectra. Aligned fossil sequences were mapped onto a mammalian phylogeny based on collagen gene transcripts from available genomes and MS/MS collagen data obtained for this study or from the literature. Our collagen tree is in overall good agreement with recent genomic and phenomic phylogenies of Placentalia. Importantly, however, it exhibits a basal split between conventional Afrotheria and all other placentals in the sample, with SANU taxa invariably placing inside Euungulata (Laurasiatheria) as follows: (((Toxodon, Macrauchenia)(Perissodactyla))(Cetartiodactyla))). Summary: Representative notoungulate and litoptern taxa fall next to crown Perissodactyla, deep within Laurasiatheria and at the opposite end of the cladogram from Afrotheria. This is consistent with the longstanding view that at least some SANU lineages may have originated from northern archaic ungulates ("condylarths"). To further test SANU affinities and their possible monophyly (as so-called "meridiungulates"), analyses of representative Astrapotheria, Xenungulata, and Pyrotheria would be needed. With improvements in instrumentation and analytical procedures, proteomics may produce a revolution in systematics like that achieved by DNA genomics, but with the possibility of working on much deeper timescales. Partly supported by SYNTAX award "Barcode of Death" & NSF OPP 1142052.