rASUDAS: A New Web-Based Application for Estimating Ancestry from Tooth Morphology

The use of crown and root morphology to estimate population relationships has a long history in dental anthropology. Over the past two decades, methods employing dental morphology within forensic anthropology have been formalized with the incorporation of statistical models. This paper presents a new web-based application (rASUDAS) that estimates the ancestry of unknown individuals based on their suite of tooth crown and root traits. The application utilizes 21 independent traits that were scored following the Arizona State University Dental Anthropology System (ASUDAS). The reference sample represents approximately 30,000 individuals from seven biogeographic regions. A naive Bayes classifier algorithm was created in the R open source programming language to assign posterior probabilities for individual group assignment. To test the application, 150 individuals were selected from the C. G. Turner II database with the proviso that an individual had to be scored for a minimum of 12 of the 21 traits. In a seven-group analysis, the model correctly assigned individuals to groups 51.8% of the time. In a four-group analysis, classification accuracy improved to 66.7%. With three groups, accuracy was at 72.7%. It is still necessary to validate the program using forensic cases and to augment the reference sample with modern skeletal data. However, results from the beta version of rASUDAS are presented as proof of concept on the potential of dental morphology in ancestry estimation in forensic contexts

News and views: Response to 'Non-metric dental traits and hominin phylogeny' by Carter et al., with additional information on the Arizona State University Dental Anthropology System and phylogenetic 'place' of Australopithecus sediba

Here we respond to Carter and colleagues’ (2013) remarks concerning our Science article (Irish et al., 2013). The goals for that article were to: 1) further characterize Australopithecus sediba by describing 22 Arizona State University Dental Anthropology System (ASUDAS) traits, 2) compare the traits in A. sediba with those previously recorded in other hominin samples, and 3) present initial phylogenetic analyses using these data. Given the subset of traits, out of 125 possible (below), and small A. sediba sample, our conclusion was that the results “further define [the species’] position relative to other genera,” but that “the phylogenetic place of A. sediba has not been settled” (Irish et al., 2013: 1233062–12330624). These goals were met, as a basis for more comprehensive study. Below we summarize and reply to the eight objections of Carter et al. (2013), while: 1) demonstrating that there is a strong theoretical basis for using the ASUDAS in phylogenetic analyses, 2) presenting results (which corroborate previous cladistic analyses) that are congruent using different methodological approaches, and 3) introducing new results using a second outgroup, Pan troglodytes, that fully uphold our original analysis

Neuronal network disintegration: common pathways linking neurodegenerative diseases

Neurodegeneration refers to a heterogeneous group of brain disorders that progressively evolve. It has been increasingly appreciated that many neurodegenerative conditions overlap at multiple levels and therefore traditional clinicopathological correlation approaches to better classify a disease have met with limited success. Neuronal network disintegration is fundamental to neurodegeneration, and concepts based around such a concept may better explain the overlap between their clinical and pathological phenotypes. In this Review, promoters of overlap in neurodegeneration incorporating behavioural, cognitive, metabolic, motor, and extrapyramidal presentations will be critically appraised. In addition, evidence that may support the existence of large-scale networks that might be contributing to phenotypic differentiation will be considered across a neurodegenerative spectrum. Disintegration of neuronal networks through different pathological processes, such as prion-like spread, may provide a better paradigm of disease and thereby facilitate the identification of novel therapies for neurodegeneration

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 genu

A sub-continent of caries: prevalence and severity in early Holocene through recent Africans

The most recognizable pathological condition of the human oral cavity is, arguably, dental caries. Beyond a direct impact on oral health, caries presence (or absence) provides important data for bioarchaeologists—to help reconstruct the diet of past populations and individuals. This study explores such data in 44 samples (n=2,119 individuals, 33,444 teeth) dating between 10,000 BP and recent times across the African sub-continent. It is, to date, the most extensive investigation of its kind in this part of the world, entailing descriptions and quantitative comparisons of caries by period, environment, sub-sistence strategy and sex. Mann-Whitney U tests and factorial ANOVA results provide expected and some unexpected findings, including: 1) a diachronic increase in caries prevalence across the sub-continent, likely related to diet change from widespread population movement; 2) savanna peoples exhibit more caries than those from other environmental regions; 3) subsistence strategy plays a major role in caries occurrence; and 4) males and females do not evidence significant differences in caries frequencies, but variation does exist in several regional groups. These findings reveal that global trends described by previous researchers often apply, though not always—so it is prudent to consider regions independently

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

Who were they really? model-free and model-bound dental nonmetric analyses to affirm documented population affiliations of seven South African "Bantu" samples.

OBJECTIVES: For bioarchaeological biodistance analyses it is common to "assume" that skeletal samples are representative of the populations to which they are attributed. Here, alternatively, samples with "known" attribution in the Raymond A. Dart Collection are assessed regarding their suitability for use in such analyses. Prior curation issues may call their ascribed identities into question. MATERIALS AND METHODS: These 20th century samples ostensibly derive from South African Ndebele, Sotho, Swazi, Tswana, Venda, Xosa, and Zulu populations. First, the mean measure of divergence (MMD) is used to obtain among-sample dental phenetic distances for comparison with documented population relationships. Second, the Mantel test evaluates fit of the isolation-by-distance model between MMD and geographic distances, i.e., among the historic homelands. Third, R-matrices and minimum and estimated Fst from MMD distances give an indication of genetic micro-differentiation. RESULTS: Output from these model-free and model-bound analyses suggest that five and perhaps six samples are representative of their attributed populations-presenting differences along population lines and evidence of more ancient ancestry. DISCUSSION: Other than the Swazi and perhaps Nedebele, the among-sample variation: 1) mirrors documented population history, 2) reveals a moderately positive correlation between phenetic and geographic distances, and 3) although evidencing much homogeneity, provides measures of genetic distance in support of the phenetic distances. Therefore, with the two noted exceptions-perhaps from collection issues, swamping of past genetic structure, or both, most samples appear suitable for bioarchaeological analyses. On this basis, results are offered to supplement published findings concerning the biological relationships of these peoples. Am J Phys Anthropol, 2015. © 2015 Wiley Periodicals, Inc

Hyperdontia across sub-Saharan Africa: Prevalence, patterning, and implications

Objective: Hyperdontia data in modern and premodern sub-Saharan Africans are presented by region—West, Central, East, and South, and sex. Beyond describing the anomaly, comparisons are made with other world populations and future work is promoted. These findings may be useful to both dental clinicians and anthropologists. Methods: Hyperdontia presence and patterning were recorded in 51 samples of skeletal dentitions and hardstone casts (n = 1916). Its infrequency prompted regional pooling after grouping by time. Only adults were included to record later forming fourth molars reportedly common in Africans. Quantitative analyses, including 95% confidence intervals, were conducted to characterize spatiotemporally sub-Saharan peoples. Results: Forty-four of 1429 modern individuals (3.08%) exhibit hyperdontia (CI 2.24–4.13%). Regional variation is significant, particularly West-Central vs. East-South, between 6.8% and 1.5%. Four of 487 premodern individuals, 0.82%, have hyperdontia (0.22–2.10%), with minimal regional differences. Males are most affected, as reported by other researchers. Other similarities with non-African research are evident regarding isomere, antimere, and form, with one key exception—a proclivity for the posterior over anterior maxilla. Conclusions: 3.08% is toward the upper end of published world ranges, including an oft-cited 0.1–3.6 + %. However, the regional variation argues against a single prevalence to describe collectively the subcontinental inhabitants. This variation parallels past west to east and south migrations like other biocultural indicators. Thus, beyond a health concern to clinicians or interesting anomaly to anthropologists, hyperdontia may be useful in other studies. There are no equivalent premodern ranges for comparison. Similarity in patterning overall to previous findings suggests a shared, potentially ancient genetic component in expression

Agenesis of the permanent teeth in sub-Saharan Africans: Prevalence, patterns, interpretations

Objective: Dental agenesis data in modern and premodern sub-Saharan Africans are presented by region, West, Central, East, and South, and by sex. Beyond characterizing the anomaly, comparisons are made with other populations and future work is encouraged. The findings should be of use to dental clinicians and anthropologists. Methods: Agenesis of the UI2, LI1, UP2, LP2, UM3, and LM3 was recorded in 52 discrete samples of mainly skeletal dentitions (n = 2162) from across the subcontinent. After dividing into temporal categories, regional pooling was effected for adequate sample sizes across the vast geographic area. Only adults were included to record M3 status. Analyses included 95% confidence intervals and chi-square comparisons by region and sex. Results: Of 1668 modern individuals 2.3% have UI2-LP2 agenesis (CI 1.6–3.1%). Regional and sex differences are non-significant, though females are most affected. For M3s it is 7.0% (5.7–8.4%), with the Central region sample differing significantly from the East and South. Females again have greater prevalence, with the difference in the West significant. UI2-LP2 agenesis affects 0.6% of 494 premodern individuals (0.1–1.8%), while M3 agenesis is 8.5% (6.1–11.5%). None of these differences are significant. Conclusions: Rates are toward the low end of global ranges, including 0.0–12.6% for UI2-LP2 from case reports, and 5.3–56.0% for M3 agenesis. With exceptions, generally insignificant inter-region differences imply that rates reasonably represent sub-Saharan peoples overall. Results will be of interest to anthropologists, but those related to risk factors, patterning, and prevalence may assist clinicians in tailoring treatment, while informing patients how this anomaly differs by population ancestry

Double Teeth and Coexistent Anomalies: Examples From Continental Africa

OBJECTIVES: Whether gemination or fusion, double teeth are rare worldwide, including Africa based on few published data. New cases from the continent are tallied, and anomalies potentially associated with double teeth are identified. These findings should interest a range of dental researchers. METHODS: The presence of double teeth was recorded in 97 modern and premodern North and sub-Saharan African samples (5631 inds.). They and coexistent anomalies are described relative to published examples. Prevalence was estimated as possible, using a Poisson model for 95% confidence intervals (CI). RESULTS: Three maxillary double teeth were identified: a primary left lateral incisor in a Nubian child (1938-1756 BC), permanent left central incisor in an adult Egyptian (3650-3500 BC), and permanent right central incisor in a modern (19th century) adult from Guinea. Each co-occurs, respectively, with a talon cusp, peg lateral incisor and, in the latter individual, second premolar crown variation with rotation, and third molar dens evaginatus. Double tooth prevalence is 0.048% (CI 0.001%-0.270%), with regional variation, in premodern, and 0.000% in modern North Africans. It is 0.000% for premodern and 0.048% for modern sub-Saharan Africans (0.008%-1.714%). CONCLUSIONS: The double incisors are comparable to other global examples, indicative of common developmental processes during odontogenesis. Prevalence is lower than published modern rates, to suggest some exceptionality in Africans as reported earlier for other dental variants. Finally, though circumstantial, double teeth and accompanying anomalies may share an etiology. Continuing research overall, and in Africa specifically, will promote an improved understanding of double teeth formation and expression