Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.

The sequencing of ancient DNA has enabled the reconstruction of speciation, migration and admixture events for extinct taxa1. However, the irreversible post-mortem degradation2 of ancient DNA has so far limited its recovery-outside permafrost areas-to specimens that are not older than approximately 0.5 million years (Myr)3. By contrast, tandem mass spectrometry has enabled the sequencing of approximately 1.5-Myr-old collagen type I4, and suggested the presence of protein residues in fossils of the Cretaceous period5-although with limited phylogenetic use6. In the absence of molecular evidence, the speciation of several extinct species of the Early and Middle Pleistocene epoch remains contentious. Here we address the phylogenetic relationships of the Eurasian Rhinocerotidae of the Pleistocene epoch7-9, using the proteome of dental enamel from a Stephanorhinus tooth that is approximately 1.77-Myr old, recovered from the archaeological site of Dmanisi (South Caucasus, Georgia)10. Molecular phylogenetic analyses place this Stephanorhinus as a sister group to the clade formed by the woolly rhinoceros (Coelodonta antiquitatis) and Merck's rhinoceros (Stephanorhinus kirchbergensis). We show that Coelodonta evolved from an early Stephanorhinus lineage, and that this latter genus includes at least two distinct evolutionary lines. The genus Stephanorhinus is therefore currently paraphyletic, and its systematic revision is needed. We demonstrate that sequencing the proteome of Early Pleistocene dental enamel overcomes the limitations of phylogenetic inference based on ancient collagen or DNA. Our approach also provides additional information about the sex and taxonomic assignment of other specimens from Dmanisi. Our findings reveal that proteomic investigation of ancient dental enamel-which is the hardest tissue in vertebrates11, and is highly abundant in the fossil record-can push the reconstruction of molecular evolution further back into the Early Pleistocene epoch, beyond the currently known limits of ancient DNA preservation.

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.

Resorptive depressions on a horn core of Late Pleistocene (MIS 3) Bison priscus (Bovidae, Mammalia) from northeastern Germany.

This report describes an isolated right horn core of a fossil steppe bison (Bison priscus) recovered from Late Pleistocene deposits near Langsdorf in the federal state of Mecklenburg-Vorpommern (Germany). AMS radiocarbon dating provided an age of 45353±2894cal yr BP for the specimen. The horn core, which by morphological criteria belonged to a female, has two depressions in its basal portion that differ in size, shape, and depth. While depressions are known from horn cores of domestic cattle, sheep, and goats, this is the first case reported from a wild bovid. Formation of the depressions on the steppe bison's horn core likely was caused by localized bone resorption during periods of increased demand for mineral elements that could not be met by dietary uptake. Such situations may have occurred in relation to pregnancy and/or lactation. Pronounced bone resorption as a means to mobilize skeletally stored mineral elements was observed in other mammals, too. Since horn cores are recovered frequently among skeletal remains of fossil bison, a systematic inspection of fossil collections for similar horn core depressions is encouraged.

Healed fracture of the tibia in a bison (Bison menneri) from the late Early Pleistocene site of Untermassfeld (Thuringia, Germany).

We present the case of a healed tibial fracture in a fossil bison (Bison menneri) from the late Early Pleistocene site of Untermassfeld. The tibia belonged to a large bull and was found as part of an articulated unit, including the lateral malleolus and the elements of the tarsus. A comminuted fracture had occurred in the midshaft region, with considerable overriding of the two main fragments. The fracture healed with shortening and angulation of the bone, and the misaligned fragments are firmly united by a thick bridging callus that exhibits a coarse surface structure. This indicates that the initial phases of fracture healing had been completed, but that the process had not appreciably progressed to the remodelling phase when the animal died. The trauma to the left hind leg and the shortening of the extremity certainly caused an impairment of locomotion. After surviving the initial phases of fracture healing, the bison may have fallen victim to one of the large predators present in the Untermassfeld fauna or it drowned in one of the high flood events that occurred in the valley of the Early Pleistocene Werra River and led to the accumulation of skeletal remains at the Untermassfeld site.

Ancient DNA analyses exclude humans as the driving force behind late Pleistocene musk ox (Ovibos moschatus) population dynamics.

The causes of the late Pleistocene megafaunal extinctions are poorly understood. Different lines of evidence point to climate change, the arrival of humans, or a combination of these events as the trigger. Although many species went extinct, others, such as caribou and bison, survived to the present. The musk ox has an intermediate story: relatively abundant during the Pleistocene, it is now restricted to Greenland and the Arctic Archipelago. In this study, we use ancient DNA sequences, temporally unbiased summary statistics, and Bayesian analytical techniques to infer musk ox population dynamics throughout the late Pleistocene and Holocene. Our results reveal that musk ox genetic diversity was much higher during the Pleistocene than at present, and has undergone several expansions and contractions over the past 60,000 years. Northeast Siberia was of key importance, as it was the geographic origin of all samples studied and held a large diverse population until local extinction at approximately 45,000 radiocarbon years before present ((14)C YBP). Subsequently, musk ox genetic diversity reincreased at ca. 30,000 (14)C YBP, recontracted at ca. 18,000 (14)C YBP, and finally recovered in the middle Holocene. The arrival of humans into relevant areas of the musk ox range did not affect their mitochondrial diversity, and both musk ox and humans expanded into Greenland concomitantly. Thus, their population dynamics are better explained by a nonanthropogenic cause (for example, environmental change), a hypothesis supported by historic observations on the sensitivity of the species to both climatic warming and fluctuations.

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.

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.