Reconstructing the Deep Population History of Central and South America.

We report genome-wide ancient DNA from 49 individuals forming four parallel time transects in Belize, Brazil, the Central Andes, and the Southern Cone, each dating to at least ∼9,000 years ago. The common ancestral population radiated rapidly from just one of the two early branches that contributed to Native Americans today. We document two previously unappreciated streams of gene flow between North and South America. One affected the Central Andes by ∼4,200 years ago, while the other explains an affinity between the oldest North American genome associated with the Clovis culture and the oldest Central and South Americans from Chile, Brazil, and Belize. However, this was not the primary source for later South Americans, as the other ancient individuals derive from lineages without specific affinity to the Clovis-associated genome, suggesting a population replacement that began at least 9,000 years ago and was followed by substantial population continuity in multiple regions.

The taxonomy of Sahelanthropus tchadensis from a craniometric perspective.

Sahelanthropus tchadensis has raised much debate since its initial discovery in Chad in 2001, given its controversial classification as the earliest representative of the hominin lineage. This debate extends beyond the phylogenetic position of the species, and includes several aspects of its habitual behavior, especially in what regards its locomotion. The combination of ancestral and derived traits observed in the fossils associated with the species has been used to defend different hypotheses related to its relationship to hominins. Here, the cranial morphology of Sahelanthropus tchadensis was assessed through 16 linear craniometric measurements, and compared to great apes and hominins through Principal Component Analysis based on size and shape and shape information alone. The results show that S. tchadensis share stronger morphological affinities with hominins than with apes for both the analysis that include size information and the one that evaluates shape alone. Since TM 266-01-060-1 shows a strong morphological affinity with the remaining hominins represented in the analysis, our results support the initial interpretations that S. tchadensis represents an early specimen of our lineage or a stem basal lineage more closely related to hominins than to Panini.

Ledi-Geraru strikes again: Morphological affinities of the LD 350-1 mandible with early Homo.

The origins of the genus Homo have been a focus of much debate in the paleoanthropological literature due to its importance in understanding the evolutionary trajectories that led to the appearance of archaic humans and our species. On the level of taxonomic classification, the controversies surrounding the origins of Homo are the result of lack of clear classification criteria that separate our genus from australopiths, given the general similarities observed between fossils ascribed to late australopiths and early Homo. The challenge in finding clear autapomorphies for Homo has even led to debates about the classification of Homo habilis and Homo rudolfensis as part of our genus. These debates are further complicated by the scarcity of fossils in the timeframe of appearance of our genus, making any fossils dated to between 3.0 and 2.5 Ma of particular relevance in the context of this discussion. The Ledi-Geraru mandible is one such fossils, which has called the attention of researchers due to its combination of primitive traits seen in Australopithecus and derived traits observed in later Homo. Despite being fragmented and poorly preserved, it is one of the key fossil specimens available from the period mentioned above.

The accuracy of age estimation using transition analysis in the Hamann-Todd collection.

OBJECTIVES: Reconstructing demography of past populations using skeletal data is challenging when analyzing adults because the process of biological aging does not always reflect the individual's chronological age. A proposed solution to address the limitations of traditional age estimation methods is transition analysis (TA), a multifactorial method of age estimation. However, despite its methodological refinement, TA has varying degrees of accuracy when applied to different known-age skeletal samples. This study assesses TA's accuracy by comparing age estimates to known age at death in the Hamann-Todd Collection. MATERIALS AND METHODS: We contrasted the maximum likelihood age estimates generated by the ADBOU program to the known ages of 221 individuals. The absolute error was calculated for the entire sample, and compared between sex and ancestry. RESULTS: The mean absolute error in the sample is 11.6 (SD = 10.3) years, with white individuals' errors (14.1 years) being significantly higher than black individuals' (9.1 years; p < 0.001). No significant differences were found between sexes (p = 0.621). A weak to moderate positive correlation was found between known age and absolute error for white males (R = 0.607; p < 0.001), white females (R = 0.509; p < 0.001), and black males (R = 0.371; p = 0.006). The accuracy of TA age estimates varied when each anatomical region was analyzed independently, but the combination of all three anatomical regions yielded the most accurate age estimates. DISCUSSION: These findings further support that TA accuracy depends on the prior distribution used and, in the Hamann-Todd Collection, the accuracy for white individuals is more influenced by this limitation than when black individuals are analyzed.

Population history of Brazilian south and southeast shellmound builders inferred through dental morphology.

OBJECTIVE: The Southeast and South Coast of Brazil was inhabited during most of the Holocene by shellmound builders. Although there are cultural differences in the archaeological record between regions, it is still debatable how these differences may relate to different population histories. Here, we contribute to this discussion by exploring dental morphological affinities between several regional series. MATERIALS AND METHODS: Dental morphology of 385 individuals from 14 archaeological sites was analyzed using the Arizona State University Dental Anthropology System. Fifteen traits were used to explore morphological affinities among series through Euclidean distance, Mean Measure of Divergence, and Principal Component Analysis. Mantel matrix correlation and partial correlation tests were used to examine the association between biological, geographic, and chronological distances. RESULTS: Morphological affinities show that ceramic and nonceramic South Coast groups cluster and differ from most Southeast series. In contrast, Southeast coastal and riverine groups display high morphological variance, showing less biological coherence among them. These biological distances between regions are partially explained by geography, but not by chronology. CONCLUSIONS: The results support that these coastal populations were low-mobility groups. Although interactions between individuals of different regions likely existed, gene flow occurred mostly among individuals from local or adjacent areas. The introduction of ceramic in the South Coast is not associated with changes in dental morphology patterns, suggesting its adoption is not exclusively associated with the arrival of different biological groups. Southeast coastal and riverine groups show high phenotypic diversity, suggesting a different history of human occupation and cultural development than observed in the South Coast.

Lagoa Santa's contribution to the origins and life of early Americans.

The region of Lagoa Santa, Central-Eastern Brazil, provides an exceptional archeological record about Late Pleistocene/Early Holocene occupation of the Americas. Since the first interventions made by the Danish naturalist Peter Lund in the 19th century, hundreds of human skeletons have been exhumed in the region. These skeletons are complemented by a rich botanic, faunal, technological, and geomorphological archeological record. We explore here the contributions of Lagoa Santa material to the origins and lifestyle of early Americans, providing an historic background. Cranial morphology of Lagoa Santa skeletons allowed the proposition of a model of two biological components for the occupation of the Americas, in which early Americans are morphologically similar to people of African and Australo-Melanesian origin. Furthermore, the archeological record in the region has revealed an intense use of plant resources, a restricted spatial distribution, and the symbolic elaboration of local hunter-gatherers, unveiling a distinct lifestyle compared to early North American populations.

Brief communication: A re-evaluation of the health index of southern Brazilian shellmound populations.

OBJECTIVES: The southern Brazilian shellmounds provide archaeological evidence of prolonged human activity in the coast from approximately 6000 to 1000 BP. Shellmound building populations exploited the rich coastal estuarine zones, and the human remains recovered from them are important sources of information on health and overall lifestyle of these mid-Holocene groups. Therefore, they were included in the Western Hemisphere Global History of Health project. The shellmounds contribute the highest Health Index in the Western Hemisphere, but these conclusions are based on collections that exclude postcranial remains. Here, we reconstruct the Health Index for one specific shellmound using both cranial and postcranial remains to determine whether the initial studies might misrepresent the relative health of the Brazilian shellmound builders. MATERIALS AND METHODS: The Health Index was calculated for a sample of 18 complete skeletons recovered from the shellmound Porto do Rio Vermelho 02 (Santa Catarina Island, Brazil). The Heath Index was calculated with and without postcranial markers and the results are compared with the Western Hemisphere Global History of Health data. RESULTS: The Health Index for Porto do Rio Vermelho 02 is lower than the reported average for American series in the Western Hemisphere Global History of Health Project and considerably lower than the original index reported for Brazilian shellmounds. This discrepancy is due to an increased prevalence of infectious disease and low stature. CONCLUSIONS: Although the Health Index remains a useful comparison statistic, re-evaluation of fragmentary skeletal remains demonstrates the need for caution when applying it to incomplete skeletal series.

Wearing the marks of violence: Unusual trauma patterning at Coyo Oriental, Northern Chile.

OBJECTIVES: In this article, we present analyses of traumatic injury data from the Middle Period Coyo Oriental cemetery in northern Chile. We test a series of hypotheses about the role of sex, foreign contact, ritual access, and temporal shifts, in the patterning of cranial trauma in this cemetery. METHODS: Two hundred and twenty-seven crania from Coyo Oriental were analyzed using standard bioarcheological methods to determine sex and age as well as the presence of cranial fractures. We also documented the presence of Tiwanaku goods, objects tied to warfare or hunting, camelid offerings, snuff paraphernalia, and items related to mining. RESULTS: We recorded 98 cranial fractures in the sample with 94.9% (93/98) on the anterior of the cranium. No significant differences are observed in the prevalence of trauma by sex, type of grave, or date. However, Coyo Oriental's trauma prevalence is two to three times higher than other Middle Period sites. CONCLUSION: The prevalence and location of these injuries suggest that conflict at Coyo Oriental, while of the same nature, was at a scale different to that seen elsewhere in the oases. We posit here that the development of social hierarchy, population growth, expansive social networks, and foreign contact that characterized the Middle Period may have resulted in a need for social control among the emergent elites of the region.

Investigating cranial morphological variation of early human skeletal remains from Chile: A 3D geometric morphometric approach.

OBJECTIVES: Archaeological and genetic research has demonstrated that the Pacific Coast was a key route in the early colonization of South America. Research examining South American skeletons >8000 cal BP has revealed differences in cranial morphology between early and late Holocene populations, which may reflect distinct migration events and/or populations. However, genetic, cultural, and some skeletal data contradict this model. Given these discrepancies, this study examines ∼9000 years of prehistory to test the hypothesis that Early skeletons have a distinct cranial morphology from later skeletons. MATERIALS AND METHODS: Using 3D digital models, craniofacial landmarks, and geometric morphometric analyses, we compared Early Holocene crania (n = 4) to later Chilean samples (n = 90) frequently absent in continental assessments of craniofacial variation. PCA, Mahalanobis distances, posterior and typicality probabilities were used to examine variation. RESULTS: Two of the earliest skeletons from northern Chile show clear affinities to individuals from later sites in the same region. However, the hypothesis cannot be rejected as one Early individual from northern Chile and one individual from inland Patagonia did not always show clear affinities to coastal populations. DISCUSSION: Biological affinities among northern populations and other regions of Chile align with genetic and archaeological data, supporting cultural and biological continuity along the Pacific Coast. In Patagonia, archaeological data are in accordance with skeletal differences between the Early inland steppe individual and coastal populations. This study incorporates 3D methods and skeletal datasets not widely used in assessments of biological affinity, thus contributing to a critical body of research examining the ancient population history of western South America.

Comparisons of statistical techniques to assess age-related skeletal markers in bioarchaeology.

OBJECTIVES: Many authors argue that inconsistencies between studies of skeletal markers are based on different data collection protocols, especially when comparing age-related markers such as osteoarthritis. Less attention is given to the choice of statistical techniques that are used to test the hypotheses associated with the data. This paper addresses how different statistical techniques compare the prevalence of age-related skeletal indicators, specifically osteoarthritis. MATERIALS AND METHODS: Osteoarthritis prevalence was scored in eight postcranial joints in 243 adult individuals from seven prehistoric archaeological sites in Central California, and data was compared between three time periods [Early (4800-2800 BP), Middle (2800-1200 BP), and Late (1200-250 BP)] using commonly used statistical tests: chi-square, Fisher's exact, and odds ratios. In addition, we analyzed the data with tests that are able to take into consideration the effect of age on osteoarthritis prevalence: ANCOVA and Factorial ANOVA. Finally, bootstraps were applied to the data to investigate how fluctuating frequencies, sample size, and age-at-death distributions affected the interpretations resulting from each test. RESULTS: The results demonstrate that the tests that consider age as a covariate (ANCOVA and Factorial ANOVA) are more efficient in rejecting the null hypothesis when smaller magnitudes of difference are observed between samples, irrespective of sample size, even though osteoarthritis prevalence fails to meet assumptions of normal distribution and homoscedasticity. DISCUSSION: ANCOVAs or Factorial ANOVAs that incorporate age as a covariate should be considered more often in studies that test different prevalences of age-related osteological markers among past populations.

Morphological variation among late holocene Mexicans: Implications for discussions about the human occupation of the Americas.

OBJECTIVES: Cranial morphology has previously been used to estimate phylogenetic relationships among populations, and has been an important tool in the reconstruction of ancient human dispersals across the planet. In the Americas, previous morphological studies support a scenario of people entering the Americas and dispersing from North America into South America through Meso America, making the Mexican territory the natural funnel through which biological diversity entered South America. MATERIALS AND METHODS: We explore the cranial morphological affinities of three late Holocene Mexican series, in relation to ancient and modern crania from North and South America, Australo-Melanesia, and East Asia. Morphological affinities were assessed through Mahalanobis Distances, and represented via Multidimensional Scaling and Ward's Linkage Cluster analysis. Minimum FST values were also calculated for each series. RESULTS: Our results show Mexican groups share morphological affinities with the Native American series, but do not cluster together as would be expected. The minimum FST estimates show between-group variation in the Americas is higher than the Asian or Australo-Melanesian populations, and that Mexican series have high between-group variance (FST = 0.124), compared to the geographically larger South America (FST = 0.116) and North America (FST = 0.076). DISCUSSION: These results show that the Mexican series share morphological affinities with the East Asian series, but maintains high levels of between-group variation, similar to South America. This supports the suggestion that the high phenotypic variation seen the Americas is not a result of its size, as it can be found in more constricted areas, such as the Mexican territory.

Testing modern human out-of-Africa dispersal models and implications for modern human origins.

The modern human expansion process out of Africa has important implications for understanding the genetic and phenotypic structure of extant populations. While intensely debated, the primary hypotheses focus on either a single dispersal or multiple dispersals out of the continent. Here, we use the human fossil record from Africa and the Levant, as well as an exceptionally large dataset of Holocene human crania sampled from Asia, to model ancestor-descendant relationships along hypothetical dispersal routes. We test the spatial and temporal predictions of competing out-of-Africa models by assessing the correlation of geographical distances between populations and measures of population differentiation derived from quantitative cranial phenotype data. Our results support a model in which extant Australo-Melanesians are descendants of an initial dispersal out of Africa by early anatomically modern humans, while all other populations are descendants of a later migration wave. Our results have implications for understanding the complexity of modern human origins and diversity.

Technical note: A linear model for predicting δ13 Cprotein.

OBJECTIVE: Development of a model for the prediction of δ(13) Cprotein from δ(13) Ccollagen and Δ(13) Cap-co . Model-generated values could, in turn, serve as "consumer" inputs for multisource mixture modeling of paleodiet. METHODS: Linear regression analysis of previously published controlled diet data facilitated the development of a mathematical model for predicting δ(13) Cprotein (and an experimentally generated error term) from isotopic data routinely generated during the analysis of osseous remains (δ(13) Cco and Δ(13) Cap-co ). RESULTS: Regression analysis resulted in a two-term linear model (δ(13) Cprotein (%) = (0.78 × Î´(13) Cco ) - (0.58× Δ(13) Cap-co ) - 4.7), possessing a high R-value of 0.93 (r(2) = 0.86, P < 0.01), and experimentally generated error terms of ±1.9% for any predicted individual value of δ(13) Cprotein . This model was tested using isotopic data from Formative Period individuals from northern Chile's Atacama Desert. CONCLUSIONS: The model presented here appears to hold significant potential for the prediction of the carbon isotope signature of dietary protein using only such data as is routinely generated in the course of stable isotope analysis of human osseous remains. These predicted values are ideal for use in multisource mixture modeling of dietary protein source contribution.

The cranial morphology of the Botocudo Indians, Brazil.

The Botocudo Indians were hunter-gatherer groups that occupied the East-Central regions of Brazil decimated during the colonial period in the country. During the 19th century, craniometric studies suggested that the Botocudo resembled more the Paleoamerican population of Lagoa Santa than typical Native Americans groups. These results suggest that the Botocudo Indians might represent a population that retained the biological characteristics of early groups of the continent, remaining largely isolated from groups that gave origin to the modern Native South American variation. Moreover, recently, some of the Botocudo remains have been shown to have mitochondrial and autosomal DNA lineages currently found in Polynesian populations. Here, we explore the morphological affinities of Botocudo skulls within a worldwide context. Distinct multivariate analyses based on 32 craniometric variables show that 1) the two individuals with Polynesian DNA sequences have morphological characteristics that fall within the Polynesian and Botocudo variation, making their assignation as Native American specimens problematic, and 2) there are high morphological affinities between Botocudo, Early Americans, and the Polynesian series of Easter Island, which support the early observations that the Botocudo can be seen as retaining the Paleoamerican morphology, particularly when the neurocranium is considered. Although these results do not elucidate the origin of the Polynesian DNA lineages among the Botocudo, they support the hypothesis that the Botocudo represent a case of late survival of ancient Paleoamerican populations, retaining the morphological characteristics of ancestral Late Pleistocene populations from Asia.

Intra-population variation in anemia status and its relationship to economic status and self-perceived health in the Mexican Family Life Survey: implications for bioarchaeology.

Recently scholars have advocated for the use of a critical biocultural approach in bioarchaeology, where osteological and dental markers of stress are used to understand the broader biosocial context of past populations. However, the ability to accomplish this task rests on the assumption that ultimate-level environmental stressors and well-being in the past can be reconstructed from the prevalence of pathologies in skeletal collections. Here we test this assumption using anemia prevalence in the Mexican Family Life Survey. Specifically we test three hypotheses: (1) that individuals sharing the same household are more likely to share anemia status; (2) anemia status is a predictor of economic status (a common proxy for broader environmental context); and (3) anemia status is related to self-rated health. Results demonstrate that: anemia status was not commonly shared between household members; there was a significant overlap in economic status between anemic and nonanemic individuals (i.e., anemia poorly predicted economic status) and; while anemia status was associated with self-perceived health, the majority of those who reported poor health were nonanemic while a significant number of those who reported very good health were anemic. We argue that these findings are likely related to variation in individual frailty, which is shaped by biological and cultural risk factors. Therefore, we advocate for greater incorporation of individual frailty into bioarchaeological investigations, and, in effort to overcome some of the difficulties associated with this task, increased use of data from living populations and greater collaboration between bioarchaeologists and human biologists.

Cranial morphological diversity of early, middle, and late Holocene Brazilian groups: implications for human dispersion in Brazil.

The history of human occupation in Brazil dates to at least 14 kyr BP, and the country has the largest record of early human remains from the continent. Despite the importance and richness of Brazilian human skeletal collections, the biological relationships between groups and their implications for knowledge about human dispersion in the country have not been properly explored. Here, we present a comprehensive assessment of the morphological affinities of human groups from East-Central, Coastal, Northeast, and South Brazil from distinct periods and test for the best dispersion scenarios to explain the observed diversity across time. Our results, based on multivariate assessments of shape and goodness of fit tests of dispersion and adaptation models, favor the idea that Brazil experienced at least two large dispersion waves. The first dispersive event brought the morphological pattern that characterize Late Pleistocene groups continent-wide and that persisted among East-Central Brazil groups until recently. Within the area covered by our samples, the second wave was probably restricted to the coast and is associated with a distinct morphological pattern. Inland and coastal populations apparently did not interact significantly during the Holocene, as there is no clear signal of admixture between groups sharing the two morphological patterns. However, these results cannot be extended to the interior part of the country (Amazonia and Central Brazil), given the lack of skeletal samples in these regions.

Systemic versus local patterns of limb joint articular morphology inferred from relative distances from morphological centroid.

Joint morphogenesis is a complex process known to require the interaction of developmental cascades and mechanical loading, yet many details of this interaction are incompletely understood. While prior work has established populational patterns of joint morphological (co)variance, exploring how these patterns manifest within the individual provides information on the deployment of morphogenic processes as either systemic or local influences on joint shape. To better identify the patterns of variance-generating morphogenic processes, this study investigates the degree to which individual joint shapes deviate from population averages systematically across the body. Using three-dimensional landmark data from 200 adult skeletons, we ranked individuals based on their distances from morphological centroids for eight major joints. Spearman correlations assessed associations between ranks across various articular pairings, testing hypotheses regarding systemic versus localized variance. Results reveal low coordination between deviations observed in conarticular surfaces, functional analogs, and same-bone surfaces; however strong associations exist between antimeres, suggesting the left-right deployment of variance-generating morphogenic patterns is highly consistent. These results support a model of localized rather than systemic processes driving variation in joint shape. While more remains to be elucidated about the specifics of articular surface morphogenesis, these findings advance our understanding of the systems of variance generation at play during development and growth of our definitive joint morphology.

Sex differences in workload in medieval Poland: Patterns of asymmetry and biomechanical adaptation in the upper limb at Giecz.

OBJECTIVES: This study characterizes sexual dimorphism in skeletal markers of upper limb mechanical loading due to lateralization as evidence of division of labor in medieval Giecz, Poland. METHODS: Twenty-six dimensions for paired humeri, clavicles, and radii representing adult males (n = 89) and females (n = 53) were collected from a skeletal sample from the cemetery site Gz4. Percent directional asymmetry (DA) and absolute asymmetry (AA) for each dimension were compared among bones, osteometric subcategories, and sex. Additionally, side bias and sex differences were assessed in degenerative joint disease (DJD) and entheseal changes (ECs). RESULTS: Nearly all measurements revealed significant asymmetry favoring the right side. Asymmetry was most pronounced in midshaft dimensions with few sex differences. There were more correlations among dimensions within elements than between elements, mainly in the midshaft. No laterality in DJD frequencies was noted for either sex, but females demonstrated significantly lower odds of having DJD than males in most joints. Most ECs demonstrated a right-bias and association with DA with no sex-specific patterns except the biceps brachii insertion, where females were ~5 times more likely to be scored "right" than males. DISCUSSION: The general lack of sex differences in asymmetry and ECs suggests similarly demanding workloads for females and males, with the exception of sex-specific functional loading differences in the forearm. Further, DJD data suggest males engaged in more intensive activities involving the upper limb. These results enhance understanding of workload in this important historical period and provide a comparison for asymmetry in past populations.

Nutritional supplementation, tooth crown size, and trait expression in individuals from Tezonteopan, Mexico.

Understanding how epigenetic factors impact dental phenotypes can help refine the use of teeth for elucidating biological relationships among human populations. We explored relationships among crown size, principal cusp spacing, and accessory cusp expression in maxillary dental casts of nutritionally supplemented (n = 34) and non-supplemented (n = 39) individuals from Tezonteopan, Mexico. We hypothesized that the non-supplemented group would exhibit smaller molar crowns and reduced intercusp spacing. Since intercusp spacing is thought to be more sensitive to epigenetic influences than crown size, we predicted that the supplemented and non-supplemented groups would differ more in the former than the latter. Previous work suggests that molar accessory cusp expression may be elevated under conditions of stress. We therefore expected evidence of greater Carabelli and Cusp 5 trait expression in the non-supplemented group. We further hypothesized that anterior teeth would be affected by nutritional stress during development, with the non-supplemented group having smaller anterior tooth crowns and therefore limited space to form the tuberculum dentale. Finally, we tested whether the presence of molar accessory traits followed predictions of the Patterning Cascade Model of tooth morphogenesis in the entire sample. Our results supported the expectation that cusp spacing would differ more than molar crown size between the two groups. Carabelli trait showed little evidence of frequency differences between groups, but some evidence of greater trait scores in the non-supplemented group. The non-supplemented group also showed evidence of greater Cusp 5 frequency and expression. In the central incisors and canines, there was strong evidence for smaller crown sizes and reduced tuberculum dentale frequency in the non-supplemented group. With both groups pooled together, there was strong evidence of closer mesiodistal distances among principal cusps in molars with accessory cusps, a finding that is consistent with the PCM. Overall, our findings suggest that nutritional stress may affect accessory cusp expression.