Imputed genomes and haplotype-based analyses of the Picts of early medieval Scotland reveal fine-scale relatedness between Iron Age, early medieval and the modern people of the UK.

There are longstanding questions about the origins and ancestry of the Picts of early medieval Scotland (ca. 300-900 CE), prompted in part by exotic medieval origin myths, their enigmatic symbols and inscriptions, and the meagre textual evidence. The Picts, first mentioned in the late 3rd century CE resisted the Romans and went on to form a powerful kingdom that ruled over a large territory in northern Britain. In the 9th and 10th centuries Gaelic language, culture and identity became dominant, transforming the Pictish realm into Alba, the precursor to the medieval kingdom of Scotland. To date, no comprehensive analysis of Pictish genomes has been published, and questions about their biological relationships to other cultural groups living in Britain remain unanswered. Here we present two high-quality Pictish genomes (2.4 and 16.5X coverage) from central and northern Scotland dated from the 5th-7th century which we impute and co-analyse with >8,300 previously published ancient and modern genomes. Using allele frequency and haplotype-based approaches, we can firmly place the genomes within the Iron Age gene pool in Britain and demonstrate regional biological affinity. We also demonstrate the presence of population structure within Pictish groups, with Orcadian Picts being genetically distinct from their mainland contemporaries. When investigating Identity-By-Descent (IBD) with present-day genomes, we observe broad affinities between the mainland Pictish genomes and the present-day people living in western Scotland, Wales, Northern Ireland and Northumbria, but less with the rest of England, the Orkney islands and eastern Scotland-where the political centres of Pictland were located. The pre-Viking Age Orcadian Picts evidence a high degree of IBD sharing across modern Scotland, Wales, Northern Ireland, and the Orkney islands, demonstrating substantial genetic continuity in Orkney for the last ~2,000 years. Analysis of mitochondrial DNA diversity at the Pictish cemetery of Lundin Links (n = 7) reveals absence of direct common female ancestors, with implications for broader social organisation. Overall, our study provides novel insights into the genetic affinities and population structure of the Picts and direct relationships between ancient and present-day groups of the UK.

Sex-biased sampling may influence Homo naledi tooth size variation.

A frequent source of debate in paleoanthropology concerns the taxonomic unity of fossil assemblages, with many hominin samples exhibiting elevated levels of variation that can be interpreted as indicating the presence of multiple species. By contrast, the large assemblage of hominin fossils from the Rising Star cave system, assigned to Homo naledi, exhibits a remarkably low degree of variation for most skeletal elements. Many factors can contribute to low sample variation, including genetic drift, strong natural selection, biased sex ratios, and sampling of closely related individuals. In this study, we tested for potential sex-biased sampling in the Rising Star dental sample. We compared coefficients of variation for the H. naledi teeth to those for eight extant hominoid samples. We used a resampling procedure that generated samples from the extant taxa that matched the sample size of the fossil sample for each possible Rising Star dental sex ratio. We found that variation at four H. naledi tooth positions-I2, M1, P4, M1-is so low that the possibility that one sex is represented by few or no individuals in the sample cannot be excluded. Additional evidence is needed to corroborate this inference, such as ancient DNA or enamel proteome data, and our study design does not address other potential factors that would account for low sample variation. Nevertheless, our results highlight the importance of considering the taphonomic history of a hominin assemblage and suggest that sex-biased sampling is a plausible explanation for the low level of phenotypic variation found in some aspects of the current H. naledi assemblage.

Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans.

Despite broad agreement that the Americas were initially populated via Beringia, the land bridge that connected far northeast Asia with northwestern North America during the Pleistocene epoch, when and how the peopling of the Americas occurred remains unresolved. Analyses of human remains from Late Pleistocene Alaska are important to resolving the timing and dispersal of these populations. The remains of two infants were recovered at Upward Sun River (USR), and have been dated to around 11.5 thousand years ago (ka). Here, by sequencing the USR1 genome to an average coverage of approximately 17 times, we show that USR1 is most closely related to Native Americans, but falls basal to all previously sequenced contemporary and ancient Native Americans. As such, USR1 represents a distinct Ancient Beringian population. Using demographic modelling, we infer that the Ancient Beringian population and ancestors of other Native Americans descended from a single founding population that initially split from East Asians around 36 ± 1.5 ka, with gene flow persisting until around 25 ± 1.1 ka. Gene flow from ancient north Eurasians into all Native Americans took place 25-20 ka, with Ancient Beringians branching off around 22-18.1 ka. Our findings support a long-term genetic structure in ancestral Native Americans, consistent with the Beringian 'standstill model'. We show that the basal northern and southern Native American branches, to which all other Native Americans belong, diverged around 17.5-14.6 ka, and that this probably occurred south of the North American ice sheets. We also show that after 11.5 ka, some of the northern Native American populations received gene flow from a Siberian population most closely related to Koryaks, but not Palaeo-Eskimos, Inuits or Kets, and that Native American gene flow into Inuits was through northern and not southern Native American groups. Our findings further suggest that the far-northern North American presence of northern Native Americans is from a back migration that replaced or absorbed the initial founding population of Ancient Beringians.

Descriptive catalog of Homo naledi dental remains from the 2013 to 2015 excavations of the Dinaledi Chamber, site U.W. 101, within the Rising Star cave system, South Africa.

More than 150 hominin teeth, dated to ∼330-241 thousand years ago, were recovered during the 2013-2015 excavations of the Dinaledi Chamber of the Rising Star cave system, South Africa. These fossils comprise the first large single-site sample of hominin teeth from the Middle Pleistocene of Africa. Though scattered remains attributable to Homo sapiens, or their possible lineal ancestors, are known from older and younger sites across the continent, the distinctive morphological feature set of the Dinaledi teeth supports the recognition of a novel hominin species, Homo naledi. This material provides evidence of African Homo lineage diversity that lasts until at least the Middle Pleistocene. Here, a catalog, anatomical descriptions, and details of preservation and taphonomic alteration are provided for the Dinaledi teeth. Where possible, provisional associations among teeth are also proposed. To facilitate future research, we also provide access to a catalog of surface files of the Rising Star jaws and teeth.

Dental caries in wild primates: Interproximal cavities on anterior teeth.

Dental caries has been reported in a variety of primates, although it is still considered rare in wild populations. In this study, 11 catarrhine primate taxa (n = 339 individuals; 7946 teeth) were studied for the presence of caries. A differential diagnosis of lesions in interproximal regions of anterior teeth was undertaken, since they had been previously described as both carious and non-carious in origin. Each permanent tooth was examined macroscopically, with severity and position of lesions recorded. Two specimens were examined further, using micro-CT scans to assess demineralization. Differential diagnosis confirmed the cariogenic nature of interproximal cavities on anterior teeth (ICATs). Overall results show 3.3% of all teeth (i.e., anterior and posterior teeth combined) were carious (n = 262), with prevalence varying among species from 0% to >7% of teeth affected. Those with the highest prevalence of ICATs include Pan troglodytes verus (9.8% of anterior teeth), Gorilla gorilla gorilla (2.6%), Cercopithecus denti (22.4%), Presbytis femoralis (19.5%), and Cercopithecus mitis (18.3%). ICATs make up 87.9% of carious lesions on anterior teeth. These results likely reflect dietary and food processing differences among species, but also between the sexes (e.g., 9.3% of all female P. troglodytes verus teeth were carious vs. 1.8% in males). Processing cariogenic fruits and seeds with the anterior dentition (e.g., wadging) likely contributes to ICAT formation. Further research is needed in living primate populations to ascertain behavioral/dietary influences on caries occurrence. Given the presence of ICATs in frugivorous primates, their diagnosis in archaeological and paleontological specimens may shed light on diet and food processing behaviors in fossil primates.

The transition from hunting-gathering to agriculture in Nubia: dental evidence for and against selection, population continuity and discontinuity.

Some researchers posit population continuity between Late Palaeolithic hunter-gatherers of the late Pleistocene and Holocene agriculturalists from Lower (northern) Nubia, in northeast Africa. Substantial craniodental differences in these time-successive groups are suggested to result from in situ evolution. Specifically, these populations are considered a model example for subsistence-related selection worldwide in the transition to agriculture. Others question continuity, with findings indicating that the largely homogeneous Holocene populations differ significantly from late Pleistocene Lower Nubians. If the latter are representative of the local populace, post-Pleistocene discontinuity is implied. So who was ancestral to the Holocene agriculturalists? Dental morphological analyses of 18 samples (1075 individuals), including one dated to the 12th millennium BCE from Al Khiday, near the Upper Nubian border, may provide an answer. It is the first Late Palaeolithic sample (n = 55) recovered within the region in approximately 50 years. Using the Arizona State University Dental Anthropology System to record traits and multivariate statistics to estimate biological affinities, Al Khiday is comparable to several Holocene samples, yet also highly divergent from contemporaneous Lower Nubians. Thus, population continuity is indicated after all, but with late Pleistocene Upper-rather than Lower Nubians as originally suggested-assuming dental traits are adequate proxies for ancient DNA.

Relative tooth size, Bayesian inference, and Homo naledi.

OBJECTIVES: Size-corrected tooth crown measurements were used to estimate phenetic affinities among Homo naledi (~335-236 ka) and 11 other Plio-Pleistocene and recent species. To assess further their efficacy, and identify dental evolutionary trends, the data were then quantitatively coded for phylogenetic analyses. Results from both methods contribute additional characterization of H. naledi relative to other hominins. MATERIALS AND METHODS: After division by their geometric mean, scaled mesiodistal and buccolingual dimensions were used in tooth size apportionment analysis to compare H. naledi with Australopithecus africanus, A. afarensis, Paranthropus robustus, P. boisei, H. habilis, H. ergaster, H. erectus, H. heidelbergensis, H. neanderthalensis, H. sapiens, and Pan troglodytes. These data produce equivalently scaled samples unaffected by interspecific size differences. The data were then gap-weighted for Bayesian inference. RESULTS: Congruence in interspecific relationships is evident between methods, and with many inferred from earlier systematic studies. However, the present results place H. naledi as a sister taxon to H. habilis, based on a symplesiomorphic pattern of relative tooth size. In the preferred Bayesian phylogram, H. naledi is nested within a clade comprising all Homo species, but it shares some characteristics with australopiths and, particularly, early Homo. DISCUSSION: Phylogenetic analyses of relative tooth size yield information about evolutionary dental trends not previously reported in H. naledi and the other hominins. Moreover, with an appropriate model these data recovered plausible evolutionary relationships. Together, the findings support recent study suggesting H. naledi originated long before the geological date of the Dinaledi Chamber, from which the specimens under study were recovered.

Do dental nonmetric traits actually work as proxies for neutral genomic data? Some answers from continental- and global-level analyses.

OBJECTIVES: Crown and root traits, like those in the Arizona State University Dental Anthropology System (ASUDAS), are seemingly useful as genetic proxies. However, recent studies report mixed results concerning their heritability, and ability to assess variation to the level of genomic data. The aim is to test further if such traits can approximate genetic relatedness, among continental and global samples. MATERIALS AND METHODS: First, for 12 African populations, Mantel correlations were calculated between mean measure of divergence (MMD) distances from up to 36 ASUDAS traits, and FST distances from >350,000 single nucleotide polymorphisms (SNPs) among matched dental and genetic samples. Second, among 32 global samples, MMD and FST distances were again compared. Correlations were also calculated between them and inter-sample geographic distances to further evaluate correspondence. RESULTS: A close ASUDAS/SNP association, based on MMD and F ST correlations, is evident, with r m -values between .72 globally and .84 in Africa. The same is true concerning their association with geographic distances, from .68 for a 36-trait African MMD to .77 for F ST globally; one exception is F ST and African geographic distances, r m = 0.49. Partial MMD/F ST correlations controlling for geographic distances are strong for Africa (.78) and moderate globally (.4). DISCUSSION: Relative to prior studies, MMD/F ST correlations imply greater dental and genetic correspondence; for studies allowing direct comparison, the present correlations are markedly stronger. The implication is that ASUDAS traits are reliable proxies for genetic data-a positive conclusion, meaning they can be used with or instead of genomic markers when the latter are unavailable.

Tooth transposition prevalence and type among sub-Saharan Africans.

OBJECTIVES: Although rare, tooth transposition-an exchange in location of two teeth-is a frequent topic of study. Clinical and, to a much lesser extent, dental anthropological research have focused predominantly on prevalence (0.03%-0.74% in several world populations) and case studies, albeit on a restricted spatiotemporal scale. Many regions have received little attention, including sub-Saharan Africa, while premodern data are few. Here, the aim is to supplement both fields of dental research by reviewing previous publications, and newly reporting transposition rates, types, and co-occurring abnormalities in time-successive samples across the subcontinent. METHODS: Dental data in 51 sub-Saharan samples (>2500 individuals) dating >10 000 BC to 20th century were recorded. Of these, 36 are of modern and 15 premodern age, comprising males and females ≥12-years of age. Transposition presence, quadrant, and type were tabulated, cases described, and prevalence presented. In the latter case, Poisson 95% confidence intervals were calculated to better discern true population rates at various geographic levels. RESULTS: Overall, six of 1886 modern individuals (0.32%) and one of premodern age evidence Mx.C.P1, an exchange of the maxillary canine and first premolar. Various associated dental abnormalities are also evident, including retained deciduous teeth, reduced permanent crowns, and agenesis. CONCLUSIONS: This study provides additional insight into the geographic distribution, features, and time depth of transposition, along with hints supporting a genetic etiology and, potentially, some indications of diachronic change from an initial Mx.C.P1 to several types more recently based on premodern evidence. It is of clinical concern today, but is not just a modern anomaly.

A probable genetic origin for pitting enamel hypoplasia on the molars of Paranthropus robustus.

We report the frequencies of linear enamel hypoplasia (LEH) and, specifically, pitting enamel hypoplasia (PEH) defects in the teeth of Paranthropus robustus, for comparison with four other South African hominin species and three extant nonhuman primate species. Unlike LEH, the lesser known PEH is characterized by multiple circular depression defects across a tooth crown and is often difficult to interpret in terms of developmental timing and etiology. Teeth in all samples were examined macroscopically with type, position and number of defects recorded. Frequencies of teeth with LEH vary among hominin species, but the differences in PEH are considerable. That is, P. robustus has much higher rates of pitting defects, with 47% of deciduous teeth and 14% of permanent teeth affected, relative to 6.7% and 4.3%, respectively, for all other hominin teeth combined; none of the extant primate samples evidences comparable rates. The defects on P. robustus molars are unlike those in other species, with entire crowns often covered in small circular depressions. The PEH is most consistent with modern human examples of amelogenesis imperfecta. Additionally, the defects are: 1) not found on anterior teeth, 2) uniform in shape and size, and 3) similar in appearance/severity on all molars. Therefore, this form of PEH may have been a side effect of selection on another trait that shares the same coding gene(s), i.e., these defects have a genetic origin. We discuss a possible scenario that may explain how this form of PEH evolved to become so common in the Paranthropus genus.

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.

The functional significance of dental and mandibular reduction in Homo: A catarrhine perspective.

The reduction in dental size and mandibular robusticity is regarded as a major trend in human evolution, traditionally considered the result of the peculiar extra-oral food processing skills of Homo. The use of stone tools and fire would have allowed our ancestors to chew softer food in smaller bite size, thus relaxing the selective pressures to keep a large dentition and a robust lower jaw. This perspective assumes that differences in dental size and mandibular robusticity in hominins represent functional dissimilarities. This study uses a catarrhine comparative approach to test this fundamental assumption of the hypotheses on dental and mandibular reduction in Homo. A sample of extant catarrhines and fossil hominins was used to test for correlations between dental size, mandibular robusticity, and dietary proxies, the latter include diet quality, diet heterogeneity, feeding time, and microwear variables. The effects of phylogeny and body size were considered. Findings support the association between technological developments in Homo and reduction in incisor size and mandibular corpus robusticity, though not for premolar, molar size, and symphyseal robusticity. These results challenge the functional interpretation of postcanine reduction and symphyseal changes in the genus Homo.

Ancient teeth, phenetic affinities, and African hominins: Another look at where Homo naledi fits in.

A new species of Homo, Homo naledi, was described in 2015 based on the hominin skeletal remains from the Dinaledi Chamber of the Rising Star cave system, South Africa. Subsequent craniodental comparative analyses, both phenetic and cladistic, served to support its taxonomic distinctiveness. Here we provide a new quantitative analysis, where up to 78 nonmetric crown and root traits of the permanent dentition were compared among samples of H. naledi (including remains from the recently discovered Lesedi Chamber) and eight other species from Africa: Australopithecus afarensis, Australopithecus africanus, Paranthropus boisei, Paranthropus robustus, Homo habilis, Homo erectus, Middle Pleistocene Homo sp., and Pleistocene and Holocene Homo sapiens. By using the mean measure of divergence distance statistic, phenetic affinities were calculated among samples to evaluate interspecific relatedness. The objective was to compare the results with those previously obtained, to assess further the taxonomic validity of the Rising Star hominin species. In accordance with earlier findings, H. naledi appears most similar dentally to the other African Homo samples. However, the former species is characterized by its retention and full expression of features relating to the main cusps, as well as the root numbers, with a near absence of accessory traits-including many that, based on various cladistic studies, are plesiomorphic in both extinct and extant African hominins. As such, the present findings provide additional support for the taxonomic validity of H. naledi as a distinct species of Homo.

Amelogenesis imperfecta in the dentition of a wild chimpanzee.

This report describes a case of amelogenesis imperfecta in the dentition of a female chimpanzee. Amelogenesis imperfecta is a group of rare genetic conditions that create severe enamel defects, which, although well researched in humans, has not yet been investigated in wild non-human primates.

Neuromandibular integration in humans and chimpanzees: Implications for dental and mandibular reduction in Homo.

OBJECTIVES: Although the evolution of the hominin masticatory apparatus has been linked to diet and food processing, the physical connection between neurocranium and lower jaw suggests a role of encephalization in the trend of dental and mandibular reduction. Here, the hypothesis that tooth size and mandibular robusticity are influenced by morphological changes in the neurocranium was tested. MATERIALS AND METHODS: Three-dimensional landmarks, alveolar lengths, and mandibular robusticity data were recorded on a sample of chimpanzee and human skulls. The morphological integration between the neurocranium and the lower jaw was analyzed by means of Singular Warps Analysis. Redundancy Analysis was performed to understand if the pattern of neuromandibular integration affects tooth size and mandibular robusticity. RESULTS: There is significant morphological covariation between neurocranium and lower jaw in both chimpanzees and humans. In humans, changes in the temporal fossa seem to produce alterations of the relative orientation of jaw parts, while the influence of similar neurocranial changes in chimpanzees are more localized. In both species, postcanine alveolar lengths and mandibular robusticity are associated with shape changes of the temporal fossa. CONCLUSIONS: The results of this study support the hypothesis that the neurocranium is able to affect the evolution and development of the lower jaw, although most likely through functional integration of mandible, teeth, and muscles within the masticatory apparatus. This study highlights the relative influence of structural constraints and adaptive factors in the evolution of the human skull.

Two contemporaneous mitogenomes from terminal Pleistocene burials in eastern Beringia.

Pleistocene residential sites with multiple contemporaneous human burials are extremely rare in the Americas. We report mitochondrial genomic variation in the first multiple mitochondrial genomes from a single prehistoric population: two infant burials (USR1 and USR2) from a common interment at the Upward Sun River Site in central Alaska dating to ∼11,500 cal B.P. Using a targeted capture method and next-generation sequencing, we determined that the USR1 infant possessed variants that define mitochondrial lineage C1b, whereas the USR2 genome falls at the root of lineage B2, allowing us to refine younger coalescence age estimates for these two clades. C1b and B2 are rare to absent in modern populations of northern North America. Documentation of these lineages at this location in the Late Pleistocene provides evidence for the extent of mitochondrial diversity in early Beringian populations, which supports the expectations of the Beringian Standstill Model.

Behavioral inferences from the high levels of dental chipping in Homo naledi.

OBJECTIVES: A variety of mechanical processes can result in antemortem dental chipping. In this study, chipping data in the teeth of Homo naledi are compared with those of other pertinent dental samples to give insight into their etiology. MATERIALS AND METHODS: Permanent teeth with complete crowns evidencing occlusal wear were examined macroscopically. The location, number, and severity of fractures were recorded and compared to those found in samples of two other South African fossil hominin species and in samples of nonhuman primates (n = 3) and recent humans (n = 7). RESULTS: With 44% of teeth affected, H. naledi exhibits far higher rates of chipping than the other fossil hominin samples. Specifically, 50% of posterior teeth and 31% of anterior teeth display at least one chip. The maxillary teeth are more affected than the mandibular teeth (45% vs 43%, respectively), 73% of molar chipping occurs on interproximal surfaces, and right teeth are more often affected than left teeth (50% vs 38%). DISCUSSION: Results indicate that the teeth of H. naledi were exposed to acute trauma on a regular basis. Because interproximal areas are more affected than buccal and posterior teeth more than anterior, it is unlikely that nonmasticatory cultural behavior was the cause. A diet containing hard and resistant food, or contaminants such as grit, is more likely. The small chip size, and steep occlusal wear and cupped dentine on some molars are supportive of the latter possibility. This pattern of chipping suggests that H. naledi differed considerably-in terms of diet, environment, and/or specialized masticatory processing-relative to other African fossil hominins.

New insights into Eastern Beringian mortuary behavior: a terminal Pleistocene double infant burial at Upward Sun River.

Here we report on the discovery of two infant burials dating to ∼11,500 calibrated years (cal) B.P. at the Upward Sun River site in central Alaska. The infants were interred in a pit feature with associated organic and lithic grave goods, including the earliest known North American hafted bifaces with decorated antler foreshafts. Skeletal and dental analyses indicate that Individual 1 died shortly after birth and Individual 2 was a late-term fetus, making these the youngest-aged late Pleistocene individuals known for the Americas and the only known prenate, offering, to our knowledge, the first opportunity to explore mortuary treatment of the youngest members of a terminal Pleistocene North American population. This burial was situated ∼40 cm directly below a cremated 3-y-old child previously discovered in association with a central hearth of a residential feature. The burial and cremation are contemporaneous, and differences in body orientation, treatment, and associated grave goods within a single feature and evidence for residential occupation between burial episodes indicate novel mortuary behaviors. The human remains, grave goods, and associated fauna provide rare direct data on organic technology, economy, seasonality of residential occupations, and infant/child mortality of terminal Pleistocene Beringians.