Virtual reconstruction and geometric morphometric analysis of the Kocabas hominin fossil from Turkey: Implications for taxonomy and evolutionary significance.

The Kocabas specimen comes from a travertine quarry near the homonymous village in the Denizli basin (Turkey). The specimen comprises three main fragments: portions of the right and left parietal and left and right parts of the frontal bone. The fossil was assumed to belong to the Homo erectus s.l. hypodigm by some authors, whereas others see similarities with Middle Pleistocene fossils (Broken Hill 1/Kabwe, Bodo, or Ceprano). Here, we present the first attempt to make a complete reconstruction of the missing medial portion of the frontal bone and a comprehensive geometric morphometric analysis of this bone. We restored the calotte by aligning and mirroring the three preserved fragments. Afterward, we restored the missing portion by applying the thin-plate spline interpolation algorithm of target fossils onto the reconstructed Kocabas specimen. For the geometric morphometric analyses, we collected 80 landmarks on the frontal bone (11 osteometric points, 14 bilateral curve semilandmarks, and 41 surface semilandmarks). The comparative sample includes 21 fossils from different chronological periods and geographical areas and 30 adult modern humans from different populations. Shape analyses highlighted the presence in Kocabas of features usually related to Middle Pleistocene Homo, such as a developed supraorbital torus associated with a relatively short frontal squama and reduced post-toral sulcus. Cluster analysis and linear discriminant analysis classification procedure suggest Kocabas being part of the same taxonomic unit of Eurasian and African Middle Pleistocene Homo. In light of our results, we consider that attributing the Kocabas hominin to H. erectus s.l. may be unwarranted. Results of our analyses are compatible with different evolutionary scenarios, but a more precise chronological framework is needed for a thorough discussion of the evolutionary significance of this specimen. Future work should clarify its geological age, given uncertainties regarding its stratigraphic provenance.

Exploring directional and fluctuating asymmetry in the human palate during growth.

OBJECTIVES: Palate morphology is constantly changing throughout an individual's lifespan, yet its asymmetry during growth is still little understood. In this research, we focus on the study of palate morphology by using 3D geometric morphometric approaches to observe changes at different stages of life, and to quantify the impact of directional and fluctuating asymmetry on different areas at different growth stages. MATERIALS AND METHODS: The sample consists of 183 individuals (1-72 years) from two identified human skeletal collections of 19th and early 20th Century Italian contexts. A 3D-template of 41 (semi)landmarks was applied on digital palate models to observe morphological variation during growth. RESULTS: Asymmetrical components of the morphological structure appears multidirectional on the entire palate surface in individuals <2 years old and become oriented (opposite bilateral direction) between 2 and 6 years of age. Specifically, directional asymmetry differentially impacts palate morphology at different stages of growth. Both the anterior and posterior palate are affected by mild alterations in the first year of life, while between 2 and 6 years asymmetry is segregated in the anterior area, and moderate asymmetry affects the entire palatal surface up to 12 years of age. Our results show that stability of the masticatory system seems to be reached around 13-35 years first by females and then males. From 36 years on both sexes show similar asymmetry on the anterior area. Regarding fluctuating asymmetry, inter-individual variability is mostly visible up to 12 years of age, after which only directional trends can be clearly observed at a group level. DISCUSSION: Morphological structure appears instable during the first year of life and acquires an opposite asymmetric bilateral direction between 2 and 6 years of age. This condition has been also documented in adults; when paired with vertical alteration, anterior/posterior asymmetry seems to characterize palate morphology, which is probably due to mechanical factors during the lifespan. Fluctuating asymmetry is predominant in the first period of life due to a plausible relationship with the strength of morphological instability of the masticatory system. Directional asymmetry, on the other hand, shows that the patterning of group-level morphological change might be explained as a functional response to differential inputs (physiological forces, nutritive and non-nutritive habits, para-masticatory activity as well as the development of speech) in different growth stages. This research has implications with respect to medical and evolutionary fields. In medicine, palate morphology should be considered when planning orthodontic and surgical procedures as it could affect the outcome. As far as an evolutionary perspective is concerned the dominance of directional asymmetries in the masticatory system could provide information on dietary and cultural habits as well as pathological conditions in our ancestors.

Ancient genomes reveal a high diversity of Mycobacterium leprae in medieval Europe.

Studying ancient DNA allows us to retrace the evolutionary history of human pathogens, such as Mycobacterium leprae, the main causative agent of leprosy. Leprosy is one of the oldest recorded and most stigmatizing diseases in human history. The disease was prevalent in Europe until the 16th century and is still endemic in many countries with over 200,000 new cases reported annually. Previous worldwide studies on modern and European medieval M. leprae genomes revealed that they cluster into several distinct branches of which two were present in medieval Northwestern Europe. In this study, we analyzed 10 new medieval M. leprae genomes including the so far oldest M. leprae genome from one of the earliest known cases of leprosy in the United Kingdom-a skeleton from the Great Chesterford cemetery with a calibrated age of 415-545 C.E. This dataset provides a genetic time transect of M. leprae diversity in Europe over the past 1500 years. We find M. leprae strains from four distinct branches to be present in the Early Medieval Period, and strains from three different branches were detected within a single cemetery from the High Medieval Period. Altogether these findings suggest a higher genetic diversity of M. leprae strains in medieval Europe at various time points than previously assumed. The resulting more complex picture of the past phylogeography of leprosy in Europe impacts current phylogeographical models of M. leprae dissemination. It suggests alternative models for the past spread of leprosy such as a wide spread prevalence of strains from different branches in Eurasia already in Antiquity or maybe even an origin in Western Eurasia. Furthermore, these results highlight how studying ancient M. leprae strains improves understanding the history of leprosy worldwide.

A geometric morphometric approach to the study of sexual dimorphism in the modern human frontal bone.

OBJECTIVES: We analyzed the main anatomical traits found in the human frontal bone by using a geometric morphometric approach. The objectives of this study are to explore how the frontal bone morphology varies between the sexes and to detect which part of the frontal bone are sexually dimorphic. MATERIALS AND METHODS: The sample is composed of 161 skulls of European and North American individuals of known sex. For each cranium, we collected 3D landmarks and semilandmarks on the frontal bone, to examine the entire morphology and separate modules (frontal squama, supraorbital ridges, glabellar region, temporal lines, and mid-sagittal profile). We used Procrustes ANOVAs and LDAs (linear discriminant analyses) to evaluate the relation between frontal bone morphology and sexual dimorphism and to calculate precision and accuracy in the classification of sex. RESULTS: All the frontal bone traits are influenced by sexual dimorphism, though each in a different manner. Variation in shape and size differs between the sexes, and this study confirmed that the supraorbital ridges and glabella are the most important regions for sex determination, although there is no covariation between them. The variable size does not contribute significantly to the discrimination between sexes. Thanks to a geometric morphometric analysis, it was found that the size variable is not an important element for the determination of sex in the frontal bone. CONCLUSION: The usage of geometric morphometrics in analyzing the frontal bone has led to new knowledge on the morphological variations due to sexual dimorphism. The proposed protocol permits to quantify morphological covariation between modules, to calculate the shape variations related to sexual dimorphism including or omitting the variable size.

Root caries on a Paranthropus robustus third molar from Drimolen.

OBJECTIVES: Dental caries is often perceived as a modern human disease. However, their presence is documented in many early human groups, various nonhuman primates and, increasingly, our hominin ancestors and relatives. In this study, we describe an antemortem lesion on the root of a Paranthropus robustus third molar from Drimolen, South Africa, which likely represents another example of caries in fossil hominins. MATERIALS AND METHODS: The molar, DNH 40, is dated to 2.0-1.5 Ma and displays a lesion on the mesial root surface, extending from the cementoenamel junction 3 mm down toward the apex. The position and severity of the lesion was macroscopically recorded and micro-CT scanned to determine the extent of dentine involvement. RESULTS: A differential diagnosis indicates root caries, as the lesion is indistinguishable from clinical examples. Although necrotic in appearance, external tertiary dentine is evident on a micro CT scan. Gingival recession and/or continuous eruption of the tooth as a result of extensive occlusal wear would have occurred to facilitate caries formation. Therefore, the lesion is likely linked to relative old age of this individual. DISCUSSION: This new example increases the total number of carious lesions described in P. robustus teeth to 10, on occlusal, interproximal, and now, root surfaces. Beyond the consumption of caries-causing food, caries formation would have also required the presence of requisite intraoral cariogenic bacteria in this individual and the species. Of interest, the presence of tertiary dentine on the outward surface suggests the DNH 40 lesion may have been arrested, that is, no longer active, perhaps relating to a change in diet or oral microbiome just prior to the individual's death.

Ages-at-death distribution of the early Pleistocene hominin fossil assemblage from Drimolen (South Africa).

OBJECTIVES: A prevailing hypothesis in paleoanthropology is that early Pleistocene hominin bones were accumulated in South African caves by carnivores, which used those shelters, and the trees surrounding them, as refuge and feeding sites. We tested this hypothesis at the site of Drimolen, by comparing its hominin age-at-death distribution to that of the nearby and roughly contemporaneous site of Swartkrans. MATERIALS AND METHODS: We employed standard dental aging systems in order to categorize the Drimolen hominin teeth into age classes of 5 years each. We then compared the age-at-death distribution for Drimolen with the published data available for the Swartkrans hominins. RESULTS: Age-at-death distributions indicate that the age category "young adults" is the best represented age category at Swartkrans and the most poorly represented one at Drimolen. Moreover, Drimolen has a preponderance of infant specimens. Both sites have a low frequency of old adult specimens. CONCLUSIONS: Differences observed in frequencies of the age-at-death categories suggest different mechanisms of hominin skeletal accumulation at Drimolen and Swartkrans. Swartkrans' frequency curve reflects mortality in a population subjected to predation and is thus consistent with the carnivore-accumulating hypothesis. In contrast, the Drimolen curve is similar to that of wild populations of living apes. Living primates have been observed exploiting caves as sleeping shelters, for nutritional, security, drinking, and thermoregulatory purposes. We suggest that similar cave use by Pleistocene hominins can explain, in large part, the accumulation of hominin bones at Drimolen. Such a conclusion is another illustration of the growing awareness that a "one-size-fits-all" taphonomic model for South African early Pleistocene hominin sites is probably insufficient.

Tooth fractures in the Krapina Neandertals.

Dental fractures can be produced during life or post-mortem. Ante-mortem chipping may be indicative of different uses of the dentition in masticatory and non-masticatory activities related to variable diets and behaviors. The Krapina collection (Croatia, 130,000 years BP), thanks to the large number of teeth (293 teeth and tooth fragments) within it, offers an excellent sample to investigate dental fractures systematically. Recorded were the distribution, position and severity of the ante-mortem fractures according to standardized methods. High frequencies of teeth with chipping in both Krapina adults and subadults suggest that the permanent and deciduous dentition were heavily subjected to mechanical stress. This is particularly evident when the frequencies of chipping are compared with those in modern humans (Upper Paleolithic and historic samples) that we analysed using the same methods. The distribution of chipping in the Krapina sample (anterior teeth are more affected) and its position (labial) suggest a systematic use of the anterior teeth for non-masticatory tasks.

The dawn of dentistry in the late upper Paleolithic: An early case of pathological intervention at Riparo Fredian.

OBJECTIVES: Early evidence for the treatment of dental pathology is found primarily among food-producing societies associated with high levels of oral pathology. However, some Late Pleistocene hunter-gatherers show extensive oral pathology, suggesting that experimentation with therapeutic dental interventions may have greater antiquity. Here, we report the second earliest probable evidence for dentistry in a Late Upper Paleolithic hunter-gatherer recovered from Riparo Fredian (Tuscany, Italy). MATERIALS AND METHODS: The Fredian 5 human consists of an associated maxillary anterior dentition with antemortem exposure of both upper first incisor (I1 ) pulp chambers. The pulp chambers present probable antemortem modifications that warrant in-depth analyses and direct dating. Scanning electron microscopy, microCT and residue analyses were used to investigate the purported modifications of external and internal surfaces of each I1 . RESULTS: The direct date places Fredian 5 between 13,000 and 12,740 calendar years ago. Both pulp chambers were circumferentially enlarged prior to the death of this individual. Occlusal dentine flaking on the margin of the cavities and striations on their internal aspects suggest anthropic manipulation. Residue analyses revealed a conglomerate of bitumen, vegetal fibers, and probable hairs adherent to the internal walls of the cavities. DISCUSSION: The results are consistent with tool-assisted manipulation to remove necrotic or infected pulp in vivo and the subsequent use of a composite, organic filling. Fredian 5 confirms the practice of dentistry-specifically, a pathology-induced intervention-among Late Pleistocene hunter-gatherers. As such, it appears that fundamental perceptions of biomedical knowledge and practice were in place long before the socioeconomic changes associated with the transition to food production in the Neolithic.

Environmental stress increases variability in the expression of dental cusps.

Teeth are an important model for developmental studies but, despite an extensive literature on the genetics of dental development, little is known about the environmental influences on dental morphology. Here we test whether and to what extent the environment plays a role in producing morphological variation in human teeth. We selected a sample of modern human skulls and used dental enamel hypoplasia as an environmental stress marker to identify two groups with different stress levels, referred to as SG ("stressed" group) and NSG ("nonstressed" group). We collected data on the occurrence and the relative development of 15 morphological traits on upper molars using a standard methodology (ASU-DAS system) and then we compared the frequencies of the traits in the two groups. Overall, the results suggest that (a) stressors like malnutrition and/or systemic diseases have a significant effect on upper molar morphology; (b) stress generates a developmental response which increases the morphological variability of the SG; and (c) the increase in variability is directional, since individuals belonging to the SG have more developed and extra cusps. These results are consistent with the expectations of the current model of dental development.

The Middle Pleistocene human metatarsal from Sedia del Diavolo (Rome, Italy).

The peopling of Europe during the Middle Pleistocene is a debated topic among paleoanthropologists. Some authors suggest the coexistence of multiple human lineages in this period, while others propose a single evolving lineage from Homo heidelbergensis to Homo neanderthalensis. The recent reassessment of the stratigraphy at the Sedia del Diavolo (SdD) site (Latium, Italy), now dated to the beginning of marine isotope stage (MIS) 8, calls for a revision of the human fossils from the site. In this paper, we present the morphometric, biomechanical and palaeopathological study of the second right metatarsal SdD2, to both re-evaluate its taxonomical affinities and possibly determine the levels of physical activity experienced by the individual during lifetime. Results demonstrate the persistence of archaic features in SdD2 suggesting new insights into the technology and hunting strategies adopted by Homo between MIS 9 and MIS 8.

Variation of the anterior aspect of the femoral head-neck junction in a modern human identified skeletal collection.

The effectiveness of the so-called skeletal markers of activity as functional indicators is widely debated. Among them, certain morphological features of the anterior aspect of the femoral head-neck junction (Poirier's facet, cervical fossa of Allen, etc.) have been considered in relation to some behaviors and specific activities (e.g., squatting, horseback riding, etc.). However, disagreement on terminology and descriptions, the absence of standardized scoring methods and poor knowledge of the variability and distribution of these features make it difficult to interpret their meaning. The aim of this study is to analyze the variability of the anterior aspect of the femoral neck through a new scoring method taking into account three main traits: Poirier's facet, plaque, and cribra (including the Allen's fossa). This method has been applied to a sample of 225 adult individuals of both sexes coming from an identified modern skeletal collection, achieving low intraobserver and interobserver error values. The results highlight some significant trends: plaque, almost always bilateral, appears to be a normal condition of the femur, being present in approximately 90% of the individuals. Cribra is more frequent in females and decreases with age. Poirier's facet shows a very low frequency. This method allows the representation of both the anatomical diversity of the region already described in literature and part of the variability never considered before. Our results suggest caution in considering these features as markers related to specific activities.

The origin and legacy of the Etruscans through a 2000-year archeogenomic time transect.

The origin, development, and legacy of the enigmatic Etruscan civilization from the central region of the Italian peninsula known as Etruria have been debated for centuries. Here we report a genomic time transect of 82 individuals spanning almost two millennia (800 BCE to 1000 CE) across Etruria and southern Italy. During the Iron Age, we detect a component of Indo-European­associated steppe ancestry and the lack of recent Anatolian-related admixture among the putative non­Indo-European­speaking Etruscans. Despite comprising diverse individuals of central European, northern African, and Near Eastern ancestry, the local gene pool is largely maintained across the first millennium BCE. This drastically changes during the Roman Imperial period where we report an abrupt population-wide shift to ~50% admixture with eastern Mediterranean ancestry. Last, we identify northern European components appearing in central Italy during the Early Middle Ages, which thus formed the genetic landscape of present-day Italian populations.

In situ observations on the dentition and oral cavity of the Neanderthal skeleton from Altamura (Italy).

The Neanderthal specimen from Lamalunga Cave, near Altamura (Apulia, Italy), was discovered during a speleological survey in 1993. The specimen is one of the most complete fossil hominins in Europe and its state of preservation is exceptional, although it is stuck in calcareous concretions and the bones are mostly covered by calcite depositions. Nevertheless, it is possible to carry out some observations on craniodental features that have not previously been described. In this work, we present an account of the oral cavity, made possible by the use of a videoscope, which allowed us to reach some hidden parts of the mandible and palate. This is the first detailed overview of the teeth and maxillary bones of the Neanderthal skeleton from Altamura. The dentition is almost complete. However, two teeth (upper right P3 and upper left M1) were lost ante mortem and four teeth (lower right I1 and P3 and lower left I1 and I2) were lost most probably post mortem. Dental wear is marked. The erupted M3s and the inversion of the compensating curve of Wilson in the M1s and M2s but not in the M3s suggest that the individual is fully adult, but not old. Although most of the teeth have their roots exposed for several millimeters, the periodontal bone appears to be in good condition overall, except in correspondence of the two ante-mortem tooth losses. X-rays of the anterior teeth show a periapical lesion, probably linked to the advanced dental wear. We also observed a weak expression of taurodontism in the posterior dentition and the presence of a retromolar space, features consistent with an attribution to the Neanderthal hypodigm; this attribution is also supported by aspects of the cranial morphology, the morphometric analysis of the scapula and preliminary mtDNA data. There is also a well-developed palatine torus, to the best of our knowledge a feature not previously described in Neanderthals.

Emergence of human-adapted Salmonella enterica is linked to the Neolithization process.

It has been hypothesized that the Neolithic transition towards an agricultural and pastoralist economy facilitated the emergence of human-adapted pathogens. Here, we recovered eight Salmonella enterica subsp. enterica genomes from human skeletons of transitional foragers, pastoralists and agropastoralists in western Eurasia that were up to 6,500 yr old. Despite the high genetic diversity of S. enterica, all ancient bacterial genomes clustered in a single previously uncharacterized branch that contains S. enterica adapted to multiple mammalian species. All ancient bacterial genomes from prehistoric (agro-)pastoralists fall within a part of this branch that also includes the human-specific S. enterica Paratyphi C, illustrating the evolution of a human pathogen over a period of 5,000 yr. Bacterial genomic comparisons suggest that the earlier ancient strains were not host specific, differed in pathogenic potential and experienced convergent pseudogenization that accompanied their downstream host adaptation. These observations support the concept that the emergence of human-adapted S. enterica is linked to human cultural transformations.

Human deciduous teeth from the Middle Stone Age layers of Sibudu Cave (South Africa).

In the African Pleistocene, the fossil evidence for early Homo sapiens populations is still relatively limited. Here we present two additional specimens (two deciduous teeth) recovered from the Middle Stone Age (MSA) deposits of Sibudu Cave (KwaZulu-Natal, South Africa). We describe their morphology and metrics, using three-dimensional models of the teeth obtained from high-resolution micro-CT images. The first specimen is a Ldm1 (HUM. TO 1) recovered in the BS5 layer dated 77.3±2.7 ka, and associated with stone tools assigned to the "pre-Still Bay" assemblage. The other specimen is a Rdi1 (HUM. TO 2) coming from the Pinkish Grey Sand (PGS) layer, dated 64.7±2.3 ka, and associated with a Howieson's Poort industry. Both teeth are well preserved, with minor post mortem cracks not affecting the overall morphology, and they comprise the intact, worn crown and the remnants of the roots, naturally resorbed. A large carious lesion occupies most of the distal face and part of the occlusal surface in the Ldm1; also a chip of enamel is missing from the disto-buccal corner. For both teeth, we compared mesio-distal (MD) and bucco-lingual (BL) diameters with those of other Late Pleistocene deciduous teeth and extant Homo sapiens. The analysis has shown that the teeth are comparable in size with the other MSA specimens described in the literature.

A migration-driven model for the historical spread of leprosy in medieval Eastern and Central Europe.

Leprosy was rare in Europe during the Roman period, yet its prevalence increased dramatically in medieval times. We examined human remains, with paleopathological lesions indicative of leprosy, dated to the 6th-11th century AD, from Central and Eastern Europe and Byzantine Anatolia. Analysis of ancient DNA and bacterial cell wall lipid biomarkers revealed Mycobacterium leprae in skeletal remains from 6th-8th century Northern Italy, 7th-11th century Hungary, 8th-9th century Austria, the Slavic Greater Moravian Empire of the 9th-10th century and 8th-10th century Byzantine samples from Northern Anatolia. These data were analyzed alongside findings published by others. M. leprae is an obligate human pathogen that has undergone an evolutionary bottleneck followed by clonal expansion. Therefore M. leprae genotypes and sub-genotypes give information about the human populations they have infected and their migration. Although data are limited, genotyping demonstrates that historical M. leprae from Byzantine Anatolia, Eastern and Central Europe resembles modern strains in Asia Minor rather than the recently characterized historical strains from North West Europe. The westward migration of peoples from Central Asia in the first millennium may have introduced different M. leprae strains into medieval Europe and certainly would have facilitated the spread of any existing leprosy. The subsequent decline of M. leprae in Europe may be due to increased host resistance. However, molecular evidence of historical leprosy and tuberculosis co-infections suggests that death from tuberculosis in leprosy patients was also a factor.