Early Pleistocene enamel proteome sequences from Dmanisi resolve Stephanorhinus phylogeny

Abstract

54 55 Ancient DNA (aDNA) sequencing has enabled unprecedented reconstruction of speciation, 56 migration, and admixture events for extinct taxa1. Outside the permafrost, however, irreversible 57 aDNA post-mortem degradation2 has so far limited aDNA recovery within the ~0.5 million years (Ma) 58 time range3. Tandem mass spectrometry (MS)-based collagen type I (COL1) sequencing provides 59 direct access to older biomolecular information4, though with limited phylogenetic use. In the 60 absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct 61 species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian 62 Pleistocene Rhinocerotidae5-7 using ~1.77 million years (Ma) old dental enamel proteome sequences 63 of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)8. 64 Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly 65 (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that 66 Coelodonta evolved from an early Stephanorhinus lineage and that this genus includes at least two 67 distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its 68 systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel 69 proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic 70 inference, and also provides additional information about the sex and taxonomic assignment of the 71 specimens analysed. Dental enamel, the hardest tissue in vertebrates, is highly abundant in the fossil 72 record. Our findings reveal that palaeoproteomic investigation of this material can push 73 biomolecular investigation further back into the Early Pleistocene. 74 75 3 bioRxiv preprint doi: https://doi.org/10.1101/407692; this version posted September 10, 2018. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license. 76 MAIN TEXT 77 78 Phylogenetic placement of extinct species increasingly relies on aDNA sequencing. …