Danilo V. Bernardo

Exomic variants of an elderly cohort of Brazilians in the ABraOM database

Brazilians are highly admixed with ancestry from Europe, Africa, America, and Asia and yet still underrepresented in genomic databanks. We hereby present a collection of exomic variants from 609 elderly Brazilians in a census‐based cohort (SABE609) with comprehensive phenotyping. Variants were deposited in ABraOM (Online Archive of Brazilian Mutations), a Web‐based public database. Population representative phenotype and genotype repositories are essential for variant interpretation through allele frequency filtering; since elderly individuals are less likely to harbor pathogenic mutations for early‐ and adult‐onset diseases, such variant databases are of great interest. Among the over 2.3 million variants from the present cohort, 1,282,008 were high‐confidence calls. Importantly, 207,621 variants were absent from major public databases. We found 9,791 potential loss‐of‐function variants with about 300 mutations per individual. Pathogenic variants on clinically relevant genes (ACMG) were observed in 1.15% of the individuals and were correlated with clinical phenotype. We conducted incidence estimation for prevalent recessive disorders based upon heterozygous frequency and concluded that it relies on appropriate pathogenicity assertion. These observations illustrate the relevance of collecting demographic data from diverse, poorly characterized populations. Census‐based datasets of aged individuals with comprehensive phenotyping are an invaluable resource toward the improved understanding of variant pathogenicity.

The Oldest Case of Decapitation in the New World (Lapa do Santo, East-Central Brazil)

We present here evidence for an early Holocene case of decapitation in the New World (Burial 26), found in the rock shelter of Lapa do Santo in 2007. Lapa do Santo is an archaeological site located in the Lagoa Santa karst in east-central Brazil with evidence of human occupation dating as far back as 11.7–12.7 cal kyBP (95.4% interval). An ultra-filtered AMS age determination on a fragment of the sphenoid provided an age range of 9.1–9.4 cal kyBP (95.4% interval) for Burial 26. The interment was composed of an articulated cranium, mandible and first six cervical vertebrae. Cut marks with a v-shaped profile were observed in the mandible and sixth cervical vertebra. The right hand was amputated and laid over the left side of the face with distal phalanges pointing to the chin and the left hand was amputated and laid over the right side of the face with distal phalanges pointing to the forehead. Strontium analysis comparing Burial 26’s isotopic signature to other specimens from Lapa do Santo suggests this was a local member of the group. Therefore, we suggest a ritualized decapitation instead of trophy-taking, testifying for the sophistication of mortuary rituals among hunter-gatherers in the Americas during the early Archaic period. In the apparent absence of wealth goods or elaborated architecture, Lapa do Santo’s inhabitants seemed to use the human body to express their cosmological principles regarding death.

Rock Art at the Pleistocene/Holocene Boundary in Eastern South America

Background Most investigations regarding the First Americans have primarily focused on four themes: when the New World was settled by humans; where they came from; how many migrations or colonization pulses from elsewhere were involved in the process; and what kinds of subsistence patterns and material culture they developed during the first millennia of colonization. Little is known, however, about the symbolic world of the first humans who settled the New World, because artistic manifestations either as rock-art, ornaments, and portable art objects dated to the Pleistocene/Holocene transition are exceedingly rare in the Americas. Methodology/Principal Findings Here we report a pecked anthropomorphic figure engraved in the bedrock of Lapa do Santo, an archaeological site located in Central Brazil. The horizontal projection of the radiocarbon ages obtained at the north profile suggests a minimum age of 9,370±40 BP, (cal BP 10,700 to 10,500) for the petroglyph that is further supported by optically stimulated luminescence (OSL) dates from sediment in the same stratigraphic unit, located between two ages from 11.7±0.8 ka BP to 9.9±0.7 ka BP. Conclusions These data allow us to suggest that the anthropomorphic figure is the oldest reliably dated figurative petroglyph ever found in the New World, indicating that cultural variability during the Pleistocene/Holocene boundary in South America was not restricted to stone tools and subsistence, but also encompassed the symbolic dimension.

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.

A casa e a roça: socioeconomia, demografia e agricultura em populações quilombolas do Vale do Ribeira, São Paulo, Brasil

This study aims to characterize the socioeconomic and demographic profile of nine Quilombola populations in the Ribeira Valley, State of Sao Paulo, and to identify the main factors responsible for the recent changes in their subsistence system. Since the first assemblages of runway and abandoned slaves in the 18th. century, the relations established by these populations with nearby towns and regional market have gone through periods of expansion and retraction, adapting and adjusting to new socioeconomic and political changes. In the last five decades, the impact of external factors on the local subsistence patterns appears to have had a significant increase. Our results show that restrictions imposed by environmental laws, conflict over land, the construction of a major road in the region, the growing insertion into a market economy, and the intervention of governmental and non-governmental development agencies are the main factors behind the changes observed in the subsistence system and, consequently, in the socioeconomic organization of these populations.

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.

Origem e dispersão dos Tupiguarani: o que diz a morfologia craniana?

Resumo: A origem e a dispersao dos povos Tupiguarani tem sido intensamente debatidas entre arqueologos e linguistas nas ultimas cinco decadas. Em resumo, pode-se dizer que a ideia de que esses povos, que ocuparam grande parte do territorio brasileiro e parte da Bolivia, do Paraguai, do Uruguai e da Argentina, tiveram sua etnogenese na Amazonia e dali partiram para o leste e para o sul, por volta de 2.500 anos antes do presente, e bastante aceita entre os especialistas, embora uma dispersao no sentido oposto, isto e, do sul para o norte, com origem na bacia do Tiete-Parana, nao seja completamente descartada. Entre os arqueologos que consideram a Amazonia como berco desses povos, alguns acreditam que esse surgimento se deu na Amazonia central. Outros acreditam que a etnogenese Tupiguarani ocorreu no sudoeste da Amazonia, onde hoje se concentra a maior diversidade linguistica do tronco Tupi. Neste trabalho, a morfologia de 19 crânios associados a cerâmica Tupiguarani ou etnograficamente classificados como tais foram comparados a varias series cranianas pre-historicas e etnograficas brasileiras por meio de estatisticas multivariadas. Duas tecnicas multivariadas foram empregadas: Analise de Componentes Principais, aplicada sobre os centroides de cada serie, e Distâncias de Mahalanobis, aplicadas aos dados individuais. Os resultados obtidos sugerem uma origem amazonica para os povos Tupiguarani, sobretudo pela forte associacao encontrada entre crânios Tupi e Guarani do sudeste e do sul brasileiro e dos Tupi do norte do Brasil, com os especimes provenientes da ilha de Marajo incluidos no estudo. Palavras-chave: Analise multivariada. Craniometria. Nativos americanos.

Early Holocene ritual complexity in South America: the archaeological record of Lapa do Santo (east-central Brazil)

Abstract Early Archaic human skeletal remains found in a burial context in Lapa do Santo in east-central Brazil provide a rare glimpse into the lives of hunter-gatherer communities in South America, including their rituals for dealing with the dead. These included the reduction of the body by means of mutilation, defleshing, tooth removal, exposure to fire and possibly cannibalism, followed by the secondary burial of the remains according to strict rules. In a later period, pits were filled with disarticulated bones of a single individual without signs of body manipulation, demonstrating that the region was inhabited by dynamic groups in constant transformation over a period of centuries.

Morfologia craniana dos remanescentes ósseos humanos da Lapa do Santo, Lagoa Santa, Minas Gerais, Brasil: implicações para o povoamento das Américas

The karstic region of Lagoa Santa has been highly important for the discussion about the tempo and mode of the initial human dispersal into the Americas. Lapa do Santo rockshelter, excavated during the past decade, represents to date one of the largest collections of early Holocene human remains recovered from the region. Here we analyze the morphological affinities of Lapa do Santo individuals with other early series from Lagoa Santa and Colombia, contextualizing them within the modern human cranial variation across the planet. Our analyses, performed on a total of 2,059 skulls (1,071 males and 988 females), are based on complementary multivariate approaches, aiming to characterize the within-group variance and the between-group morphological affinities of the 24 series included in the analyses. Our results indicate that Lapa do Santo, and other Lagoa Santa, individuals do not present higher levels of within-group variation than modern human groups, supporting the idea that they represent a single biological population. When compared to worldwide series, the early South American groups, Lapa do Santo included, share high morphological affinities among themselves and with Australo-Melanesian and Easter Island groups. Taken together, these results suggest an increase of biological diversity in the continent during the Holocene, possibly a result of the influx of new extra-continental diversity after its initial settlement.Abstract: The karstic region of Lagoa Santa has been highly important for the discussion about the tempo and mode of the initial human dispersal into the Americas. Lapa do Santo rockshelter, excavated during the past decade, represents to date one of the largest collections of early Holocene human remains recovered from the region. Here we analyze the morphological affinities of Lapa do Santo individuals with other early series from Lagoa Santa and Colombia, contextualizing them within the modern human cranial variation across the planet. Our analyses, performed on a total of 2,059 skulls (1,071 males and 988 females), are based on complementary multivariate approaches, aiming to characterize the within-group variance and the between-group morphological affinities of the 24 series included in the analyses. Our results indicate that Lapa do Santo, and other Lagoa Santa, individuals do not present higher levels of within-group variation than modern human groups, supporting the idea that they represent a single biological population. When compared to worldwide series, the early South American groups, Lapa do Santo included, share high morphological affinities among themselves and with Australo-Melanesian and Easter Island groups. Taken together, these results suggest an increase of biological diversity in the continent during the Holocene, possibly a result of the influx of new extra-continental diversity after its initial settlement.

Origin and dispersion of the Tupiguarani: what does cranial morphology say?

Resumo: A origem e a dispersao dos povos Tupiguarani tem sido intensamente debatidas entre arqueologos e linguistas nas ultimas cinco decadas. Em resumo, pode-se dizer que a ideia de que esses povos, que ocuparam grande parte do territorio brasileiro e parte da Bolivia, do Paraguai, do Uruguai e da Argentina, tiveram sua etnogenese na Amazonia e dali partiram para o leste e para o sul, por volta de 2.500 anos antes do presente, e bastante aceita entre os especialistas, embora uma dispersao no sentido oposto, isto e, do sul para o norte, com origem na bacia do Tiete-Parana, nao seja completamente descartada. Entre os arqueologos que consideram a Amazonia como berco desses povos, alguns acreditam que esse surgimento se deu na Amazonia central. Outros acreditam que a etnogenese Tupiguarani ocorreu no sudoeste da Amazonia, onde hoje se concentra a maior diversidade linguistica do tronco Tupi. Neste trabalho, a morfologia de 19 crânios associados a cerâmica Tupiguarani ou etnograficamente classificados como tais foram comparados a varias series cranianas pre-historicas e etnograficas brasileiras por meio de estatisticas multivariadas. Duas tecnicas multivariadas foram empregadas: Analise de Componentes Principais, aplicada sobre os centroides de cada serie, e Distâncias de Mahalanobis, aplicadas aos dados individuais. Os resultados obtidos sugerem uma origem amazonica para os povos Tupiguarani, sobretudo pela forte associacao encontrada entre crânios Tupi e Guarani do sudeste e do sul brasileiro e dos Tupi do norte do Brasil, com os especimes provenientes da ilha de Marajo incluidos no estudo. Palavras-chave: Analise multivariada. Craniometria. Nativos americanos.