Author Correction: The dental proteome of Homo antecessor.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The dental proteome of Homo antecessor.

The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated1-5. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge6-8. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain)9,10 and Homo erectus from Dmanisi (Georgia)1, two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor-that is, similar to that of modern humans-may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.

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.

An ancient cranium from Dmanisi: Evidence for interpersonal violence, disease, and possible predation by carnivores on Early Pleistocene Homo.

Five well-preserved individuals from Dmanisi represent a paleodeme attributed to early Homo. Here we provide a case study of the D2280 adult cranium, which presents four oval-shaped lesions on the frontal, left parietal, and occipital bones. Several conditions are considered as possibly contributing to this pathology, including trauma, cysts, metastatic cancer, and infectious disease. One large but shallow depression on the left parietal bone has slightly elevated boundaries. Imaging reveals inner and outer tables that are reciprocally concave, so that the diploë is diminished or completely absent. This lesion is very likely a result of traumatic injury. Two additional depressions on the left side frontal and occipital bones may also be attributed to blunt force trauma. Such injuries stem from a variety of causes, but interpersonal violence may well be implicated. Based on the location and structure of a fourth lesion on the right-side frontal bone, we advance a possible diagnosis of treponemal disease. Lesions on the cranium and specifically on the frontal bone are common in treponemal disease. The condition develops as a periostitis, which eventually results in the destruction of the osteoperiosteal border of the cranial outer table and rarely involves the inner table. Additional perforations on the occipital bone are interpreted as perimortem damage resulting from predation by carnivores or scavenging by birds. If our reading of this cranial evidence can be confirmed, then D2280 documents one of the earliest instances of blunt force trauma in the Homo lineage. Dmanisi may also reveal the presence of treponemal disease in a population dated ca. 1.77 Ma ago. These findings bear on the social behavior of ancient humans and also the impact of infectious diseases on their survival.

Life and death at Dmanisi, Georgia: Taphonomic signals from the fossil mammals.

There are many hypotheses regarding influences on the early hominin biogeographic spread into Eurasia; among them is increased meat-eating. Dmanisi in Georgia is one of the rare Early Pleistocene sites in Eurasia, and here we present primary information and analysis of the medium and large mammal taphonomy, contributing information about site formation and the hominins' interaction with the fauna. Nearly 85% of the specimens come from the B1 stratum. Relative abundances of mammal families demonstrate some bias toward carnivores, especially Canis borjgali, and diverse Felidae species. Bones display little weathering. Post-depositional surface modifications and matrix obscure many bone surfaces, but carnivore tooth marking is the most common bone surface modification from the nutritive taphonomic phase. Tooth pits are large, in the size range of those made by modern Crocuta crocuta and Panthera leo. Breakage variables indicate most breaks occurred while the bones were still fresh, many by carnivore consumption. Fairly even limb bone representation of herbivores suggests carcasses were introduced to the site nearly whole. Hominin tool marks are present in low frequencies, but they suggest a variety of behaviors. These marks are found on Equus, Palaeotragus, Bison, large cervids, Pseudodama, Canis, and Mammuthus. Some were made by filleting proximal limb segments, and so are likely indicative of early access to carcasses, while other marks suggest scavenging. The Homo taphonomic variables resemble the rest of the taphonomic signatures from the site with little weathering, a slightly higher percentage of their bones are whole, but only a few have probable carnivore damage. The assemblage characteristics are compared to modern actualistic and experimental assemblages, and it is concluded that Dmanisi presents a palimpsest of hyena denning, felid activity, hominin meat-eating and likely natural deaths.

A comparative study of the Early Pleistocene carnivore guild from Dmanisi (Georgia).

The carnivore guild of the Early Pleistocene site of Dmanisi is among the most diverse of the Early Pleistocene of the entire Old World. It includes 14 carnivoran taxa: Homotherium latidens, Megantereon whitei, Panthera onca georgica, Acinonyx pardinensis, Lynx issiodorensis; Pachycrocuta brevirostris; Canis (Xenocyon) lycaonoides, Canis borjgali, Vulpes alopecoides; Ursus etruscus; Lutra sp., Martes sp., Meles sp., and Pannonictis sp. The analysis of this rich carnivore guild was carried out under different methodological approaches to compare the assemblage with other chronological coeval European, Asian, and African sites from a paleobiological perspective. To achieve the goal, we used a permutational hierarchical method called boostrapping cluster analysis based on taxonomic absence/presence matrices (at both generic and specific level) and on ecological matrices (considering dietary preferences/hunting strategies of each carnivoran) and carried out Mantels tests assessing magnitude of time, space, ecology, and taxonomy as source of difference between guilds. Our results suggest a close similarity among the Dmanisi carnivore assemblage and other guilds recorded from European late Villafranchian sites such as Pirro Nord, Venta Micena, and Apollonia 1 and, in a lesser extent, to European Epivillafranchian sites as Vallonnet, Untermassfeld, or the Vallparadís Section. Early to Middle Pleistocene Asian carnivore assemblages display several similarities with the Dmanisi guild mainly in the record and diversity of felid and the canid ecomorphotypes. Eastern African sites such as Olduvai and Omo, as well as South African sites, display a lower similarity with the studied sample, basically for the most diverse hyenid taphocoenoses. To sum up, the present study suggests a close similarity between the Dmanisi carnivore guild and other European Late Early Pleistocene assemblages without close parallels with African or Asian assemblages.

Zoogeographic significance of Dmanisi large mammal assemblage.

We undertake a comparative mammalian zoogeographic analysis with the aim of revealing the extent to which the Dmanisi Early Pleistocene large mammal assemblage resembles, at the genus level, African, Arabian, and Eurasian localities of similar age. The inclusion of Old World Pliocene and Pleistocene mammalian faunas provides us with insights into the provincial origins of specific mammalian taxa and permits us to assess the relative affiliation of the Dmanisi mammalian faunas to other faunas in the Old World. Our analysis also allows us to consider hypotheses about the timing and direction of zoogeographic connections between western Eurasia and Africa during the Early Pleistocene. We utilize multiple zoogeographic analytical tools as a cross-comparison of Dmanisi with 42 other Eurasian and African mammalian-bearing localities between 2.7 and 0.7 Ma. Overall, we find that Dmanisi compares most closely with a subgroup of Greek, Italian, and Spanish localities that are slightly younger than Dmanisi itself. This could suggest a progressive dispersal from East to West of the large mammal communities during the late Early Pleistocene and the first occurrence at Dmanisi, and then later in Western Europe, of some taxa such as Stephanorhinus ex gr. etruscus-hundsheimensis, Equus altidens, Bison georgicus, Soergelia minor, Megantereon whitei, Canis borjgali, Canis (Xenocyon) lycaonoides. Dmanisi's habitats included drier areas, probably of open wooded savannah and grassland and by mountainous to semiarid rocky terrain. There is evidence that Dmanisi records short intervals of increased aridity in the middle part of the succession contemporaneous with the occurrence of Homo.

Early Pleistocene stratigraphy, sedimentary environments, and formation contexts at Dmanisi in the Georgian Caucasus.

The Early Pleistocene site of Dmanisi is now well known for its large number of fossils of early Homo erectus as well as associated artifacts and faunal remains, recovered mainly in pipe-related geologic features. Testing in the M5 unit 100 m to the west of the main excavations revealed a thick stratigraphy with no evidence of pipes or gullies, indicating that the geologic record at Dmanisi included spatially distinct sedimentary environments that needed further investigation. Here we report the results of a geoarchaeological program to collect data bearing on contexts and formation processes over a large area of the promontory. That work has defined over 40,000 m2 of in situ deposits with artifacts and faunas. Stratum A ashes bury the uppermost Mashavera Basalt, which we have dated to 1.8 Ma in the M5 block. The Stratum A deposits contain stratified occupations that accumulated quickly and offer good potential for recovery of in situ materials. Stratum B1 deposits above the A/B unconformity include all of the pipe and gully facies at Dmanisi, reflecting a brief but very intense phase of geomorphic change. Those deposits contain the majority of faunas and all of the hominin fossils. B1 slope facies offer excellent formation contexts away from the piped area, and all B1 deposits are sealed by Stratum B2 over the whole promontory. Strata B2 to B5 register a return to slope facies, with no further evidence of pipes or gullies. Those deposits also present excellent contexts for recovery of in situ occupations. Overall, Dmanisi's geologic history preserves an exceptional record of the activities and environmental context of occupations during the first colonization of Eurasia.

The Dmanisi Equus: Systematics, biogeography, and paleoecology.

The Equus datum has been established as a geochronologic 'instantaneous' migratory event of a North American Equus species into Eurasia at the beginning of the Pleistocene (2.58 Ma). A remarkable radiation of Equus followed across Eurasia and Africa. Dmanisi includes excellent remains of Equus, well calibrated between 1.85 and 1.76 Ma. Our morphologic and morphometric analyses of the augmented Dmanisi Equus sample support the co-occurrence of Equus stenonis and Equus altidens in the sequence. Dmanisi E. stenonis is found to be morphologically similar to the European E. stenonis populations and represents the best well-dated easternmost occurrence of this species in Eurasia. The Dmanisi E. altidens represents the oldest well-calibrated occurrence of this species in Western Eurasia. Our analyses demonstrate that E. altidens extended its range westward from west Asia to Greece, Germany, Italy, Spain, and possibly France. Our results do not support distinguishing multiple subspecies of E. altidens, including E. altidens altidens, E. altidens granatensis and E. stenonis mygdoniensis. The Dmanisi cranial and postcranial samples exhibit morphologies close both to extant hemiones and zebras. Equus altidens is believed to have been well adapted to newly emergent arid environments in western Eurasia during the late Early and early Middle Pleistocene. The first occurrence of E. altidens at Dmanisi marks an important turnover in the horse communities of the late Early Pleistocene, with a dispersion of this species from West Asia to West Europe ca. 1.8 Ma.

Paleoecology, biochronology, and paleobiogeography of Eurasian Rhinocerotidae during the Early Pleistocene: The contribution of the fossil material from Dmanisi (Georgia, Southern Caucasus).

Rhinocerotidae represents a common element in the Eurasian Pleistocene faunas. Origin, dispersal route, and biochronology of several species are still poorly understood due to gaps in the fossil record, in particular from central Eurasia. A remarkable collection of rhinoceros remains was recovered from the Early Pleistocene site of Dmanisi (Georgia). This collection is unique for the Early Pleistocene Rhinocerotidae records due to its abundance in remains, its age (ca 1.8 Ma) and geographic position (between Eastern and Western Eurasia). Two crania, which display some different morphological traits, are assigned to two different morphotypes and investigated by means of geometric morphometrics using landmarks and semilandmarks. Shapes in lateral and dorsal views of different Rhinocerotini species are compared with the studied crania to infer paleoecological information. The shape in the lateral view reflects ecological niche, in particular feeding type from browsing to grazing, and it also represent taxonomic discrimination. Morphotypes 1 and 2 from Dmanisi fall in two different clusters, corresponding to two different species, notably in lateral view. The results suggest a niche partitioning during the Early Pleistocene of Dmanisi between a browse-dominated and a grass-dominated mixed feeders, or possibly the presence of two ecomorphotypes of the same species. A comprehensive update of the Early Pleistocene occurrences of Eurasian Rhinocerotidae is reported in the discussion on the paleoecology of the extinct Northern Eurasian rhinocerotines.

Spatial patterning of the archaeological and paleontological assemblage at Dmanisi, Georgia: An analysis of site formation and carnivore-hominin interaction in Block 2.

This study addresses the roles of biotic agents in site formation in the B1 strata of Block 2 at Dmanisi, Georgia, using theoretical and analogous frameworks for the interpretation of spatial behaviors of carnivores and hominins. For this study, stone material, faunal remains, and coprolites are analyzed to determine if any spatially distinct behaviors can be identified, located, and attributed to either hominins or carnivores. Faunal, stone, and coprolite assemblages are compared with each other, and lithic, taxonomic, and taphonomic subassemblages are compared with the overall distribution of their parent material. The spatial and taphonomic signatures suggest that hominin activity was only a small part of the contributing factors to site formation, whereas carnivores played a major role in the accumulation of bone.

Early Neolithic wine of Georgia in the South Caucasus.

Chemical analyses of ancient organic compounds absorbed into the pottery fabrics from sites in Georgia in the South Caucasus region, dating to the early Neolithic period (ca. 6,000-5,000 BC), provide the earliest biomolecular archaeological evidence for grape wine and viniculture from the Near East, at ca. 6,000-5,800 BC. The chemical findings are corroborated by climatic and environmental reconstruction, together with archaeobotanical evidence, including grape pollen, starch, and epidermal remains associated with a jar of similar type and date. The very large-capacity jars, some of the earliest pottery made in the Near East, probably served as combination fermentation, aging, and serving vessels. They are the most numerous pottery type at many sites comprising the so-called "Shulaveri-Shomutepe Culture" of the Neolithic period, which extends into western Azerbaijan and northern Armenia. The discovery of early sixth millennium BC grape wine in this region is crucial to the later history of wine in Europe and the rest of the world.

Variation among the Dmanisi hominins: Multiple taxa or one species?

OBJECTIVES: There is continuing controversy over the number of taxa documented by the Dmanisi hominins. Variation may reflect age and sex differences within a single population. Alternatively, two (or more) distinct species may be present. Our null hypothesis states that just one population is represented at the site. MATERIALS AND METHODS: We assess the likely sources of variation in endocranial capacity, craniofacial and mandibular morphology, and the expression of characters related to aging and sex dimorphism. We use the coefficient of variation and a modified version of Levene's test for equal variances to compare trait variation at Dmanisi with that in fossil hominins and modern Homo sapiens from Africa. RESULTS: Skull 5 presents a low, massive vault, and a muzzle-like lower face. Other individuals have larger brains and more globular vaults. Despite such variation, the five crania share numerous features. All of the mandibles possess marginal tubercles, mandibular tori, and a distinctive patterning of mental foramina. Relative variation at Dmanisi is comparable to that in selected reference groups. Further growth anticipated in Skull 3, age-related remodeling affecting the D2600 mandible, pathology, and sex dimorphism can account for much of the interindividual variation observed. The preponderance of evidence supports our null hypothesis. DISCUSSION: Sources of the variation within ancient Homo assemblages remain poorly understood. Skull 5 is a very robust male, with a brain smaller than that of both a juvenile (Skull 3) and a probable female (Skull 2). Skull 1 has the largest brain, but cranial superstructures do not clearly mark this individual as male or female. It is likely that the Dmanisi hominins represent a single paleospecies of Homo displaying a pattern of sex dimorphism not seen in living hominids.

Skull 5 from Dmanisi: Descriptive anatomy, comparative studies, and evolutionary significance.

A fifth hominin skull (cranium D4500 and mandible D2600) from Dmanisi is massively constructed, with a large face and a very small brain. Traits documented for the first time in a basal member of the Homo clade include the uniquely low ratio of endocranial volume to basicranial width, reduced vertex height, angular vault profile, smooth nasal sill coupled with a long and sloping maxillary clivus, elongated palate, and tall mandibular corpus. The convex clivus and receding symphysis of skull 5 produce a muzzle-like form similar to that of Australopithecus afarensis. While the Dmanisi cranium is very robust, differing from OH 13, OH 24, and KNM-ER 1813, it resembles Homo habilis specimens in the "squared off" outline of its maxilla in facial view, maxillary sulcus, rounded and receding zygomatic arch, and flexed zygomaticoalveolar pillar. These characters distinguish early Homo from species of Australopithecus and Paranthropus. Skull 5 is unlike Homo rudolfensis cranium KNM-ER 1470. Although it appears generally primitive, skull 5 possesses a bar-like supraorbital torus, elongated temporal squama, occipital transverse torus, and petrotympanic traits considered to be derived for Homo erectus. As a group, the Dmanisi crania and mandibles display substantial anatomical and metric variation. A key question is whether the fossils document age-related growth and sex dimorphism within a single population, or whether two (or more) distinct taxa may be present at the site. We use the coefficient of variation to compare Dmanisi with Paranthropus boisei, H. erectus, and recent Homo sapiens, finding few signals that the Dmanisi sample is excessively variable in comparison to these reference taxa. Using cranial measurements and principal components analysis, we explore the proposal that the Dmanisi skulls can be grouped within a regionally diverse hypodigm for H. erectus. Our results provide only weak support for this hypothesis. Finally, we consider all available morphological and paleobiological evidence in an attempt to clarify the phyletic relationship of Dmanisi to Homo species evolving >2.0 to 1.0 Ma.

Comparative analysis of dentognathic pathologies in the Dmanisi mandibles.

OBJECTIVES: Due to the scarcity of the fossil record, in vivo changes in the dentognathic system of early Homo are typically documented at the level of individual fossil specimens, and it remains difficult to draw population-level inferences about dietary habits, diet-related activities and lifestyle from individual patterns of dentognathic alterations. The Plio-Pleistocene hominin sample from Dmanisi (Georgia), dated to 1.77 million years ago, offers a unique opportunity to study in vivo changes in the dentognathic system of individuals belonging to a single paleodeme of early Homo. MATERIALS AND METHODS: We analyze dentognathic pathologies in the Dmanisi sample, and in comparative samples of modern Australian and Greenlander hunter-gatherer populations, applying clinical protocols of dentognathic diagnostics. RESULTS: The Dmanisi hominins exhibit a similarly wide diversity and similar incidence of dentognathic pathologies as the modern human hunter-gatherer population samples investigated here. Dmanisi differs from the modern population samples in several respects: At young age tooth wear is already advanced, and pathologies are more prevalent. At old age, hypercementosis is substantial. CONCLUSIONS: Results indicate that dentognathic pathologies and disease trajectories are largely similar in early Homo and modern humans, but that the disease load was higher in early Homo, probably as an effect of higher overall stress on the dentognathic system. Am J Phys Anthropol 160:229-253, 2016. © 2016 Wiley Periodicals, Inc.

Tooth wear and dentoalveolar remodeling are key factors of morphological variation in the Dmanisi mandibles.

The Plio-Pleistocene hominin sample from Dmanisi (Georgia), dated to 1.77 million years ago, is unique in offering detailed insights into patterns of morphological variation within a paleodeme of early Homo. Cranial and dentoalveolar morphologies exhibit a high degree of diversity, but the causes of variation are still relatively unexplored. Here we show that wear-related dentoalveolar remodeling is one of the principal mechanisms causing mandibular shape variation in fossil Homo and in modern human hunter-gatherer populations. We identify a consistent pattern of mandibular morphological alteration, suggesting that dental wear and compensatory remodeling mechanisms remained fairly constant throughout the evolution of the genus Homo. With increasing occlusal and interproximal tooth wear, the teeth continue to erupt, the posterior dentition tends to drift in a mesial direction, and the front teeth become more upright. The resulting changes in dentognathic size and shape are substantial and need to be taken into account in comparative taxonomic analyses of isolated hominin mandibles. Our data further show that excessive tooth wear eventually leads to a breakdown of the normal remodeling mechanisms, resulting in dentognathic pathologies, tooth loss, and loss of masticatory function. Complete breakdown of dentognathic homeostasis, however, is unlikely to have limited the life span of early Homo because this effect was likely mediated by the preparation of soft foods.

Earliest human occupations at Dmanisi (Georgian Caucasus) dated to 1.85-1.78 Ma.

The early Pleistocene colonization of temperate Eurasia by Homo erectus was not only a significant biogeographic event but also a major evolutionary threshold. Dmanisi's rich collection of hominin fossils, revealing a population that was small-brained with both primitive and derived skeletal traits, has been dated to the earliest Upper Matuyama chron (ca. 1.77 Ma). Here we present archaeological and geologic evidence that push back Dmanisi's first occupations to shortly after 1.85 Ma and document repeated use of the site over the last half of the Olduvai subchron, 1.85-1.78 Ma. These discoveries show that the southern Caucasus was occupied repeatedly before Dmanisi's hominin fossil assemblage accumulated, strengthening the probability that this was part of a core area for the colonization of Eurasia. The secure age for Dmanisi's first occupations reveals that Eurasia was probably occupied before Homo erectus appears in the East African fossil record.

Postcranial evidence from early Homo from Dmanisi, Georgia.

The Plio-Pleistocene site of Dmanisi, Georgia, has yielded a rich fossil and archaeological record documenting an early presence of the genus Homo outside Africa. Although the craniomandibular morphology of early Homo is well known as a result of finds from Dmanisi and African localities, data about its postcranial morphology are still relatively scarce. Here we describe newly excavated postcranial material from Dmanisi comprising a partial skeleton of an adolescent individual, associated with skull D2700/D2735, and the remains from three adult individuals. This material shows that the postcranial anatomy of the Dmanisi hominins has a surprising mosaic of primitive and derived features. The primitive features include a small body size, a low encephalization quotient and absence of humeral torsion; the derived features include modern-human-like body proportions and lower limb morphology indicative of the capability for long-distance travel. Thus, the earliest known hominins to have lived outside of Africa in the temperate zones of Eurasia did not yet display the full set of derived skeletal features.