Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

Ancient DNA (aDNA) sequencing has enabled reconstruction of speciation, migration, and admixture events for extinct taxa¹. Outside the permafrost, however, irreversible aDNA post-mortem degradation² has so far limited aDNA recovery to the past ~0.5 million years (Ma)³. Contrarily, tandem mass spectrometry (MS) allowed sequencing ~1.5 million year (Ma) old collagen type I (COL1)⁴ and suggested the presence of protein residues in Cretaceous fossil remains⁵, although with limited phylogenetic use⁶. In the absence of molecular evidence, the speciation of several Early and Middle Pleistocene extinct species remain contentious. In this study, we address the phylogenetic relationships of the Eurasian Pleistocene Rhinocerotidae^7–9 using a ~1.77 Ma old dental enamel proteome of a Stephanorhinus specimen from the Dmanisi archaeological site in Georgia (South Caucasus)¹⁰. Molecular phylogenetic analyses place the Dmanisi Stephanorhinus as a sister group to the woolly (Coelodonta antiquitatis) and Merck’s rhinoceros (S. kirchbergensis) clade. We show that Coelodonta evolved from an early Stephanorhinus lineage and that the latter includes at least two distinct evolutionary lines. As such, the genus Stephanorhinus is currently paraphyletic and its systematic revision is therefore needed. We demonstrate that Early Pleistocene dental enamel proteome sequencing overcomes the limits of ancient collagen- and aDNA-based phylogenetic inference. It also provides additional information about the sex and taxonomic assignment of the specimens analysed. Dental enamel, the hardest tissue in vertebrates¹¹, is highly abundant in the fossil record. Our findings reveal that palaeoproteomic investigation of this material can push biomolecular investigation further back into the Early Pleistocene.

Mammoth ivory was the most suitable osseous raw material for the production of Late Pleistocene big game projectile points

Late Pleistocene societies throughout the northern hemisphere used mammoth and mastodon ivory not only for art and adornment, but also for tools, in particular projectile points. A comparative analysis of the mechanical properties of tusk dentine from woolly mammoth (Mammuthus primigenius) and African elephant (Loxodonta africana) reveals similar longitudinal stiffness values that are comparable to those of cervid antler compacta. The longitudinal bending strength and work of fracture of proboscidean ivory are very high owing to its substantial collagen content and specific microstructure. In permafrost, these properties can be fully retained for thousands of years. Owing to the unique combination of stiffness, toughness and size, ivory was obviously the most suitable osseous raw material for massive projectile points used in big game hunting.

Typing single polymorphic nucleotides in mitochondrial DNA as a way to access Middle Pleistocene DNA

In this study, we have used a technique designed to target short fragments containing informative mitochondrial substitutions to extend the temporal limits of DNA recovery and study the molecular phylogeny of Ursus deningeri. We present a cladistic analysis using DNA recovered from 400 kyr old U. deningeri remains, which demonstrates U. deningeri's relation to Ursus spelaeus. This study extends the limits of recovery from skeletal remains by almost 300 kyr. Plant material from permafrost environments has yielded DNA of this age in earlier studies, and our data suggest that DNA in teeth from cave environments may be equally well preserved.

Staying out in the cold: glacial refugia and mitochondrial DNA phylogeography in ancient European brown bears

Models for the development of species distribution in Europe typically invoke restriction in three temperate Mediterranean refugia during glaciations, from where recolonization of central and northern Europe occurred. The brown bear, Ursus arctos, is one of the taxa from which this model is derived. Sequence data generated from brown bear fossils show a complex phylogeographical history for western European populations. Long-term isolation in separate refugia is not required to explain our data when considering the palaeontological distribution of brown bears. We propose continuous gene flow across southern Europe, from which brown bear populations expanded after the last glaciation.