High-depth African genomes inform human migration and health.

The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals-comprising 50 ethnolinguistic groups, including previously unsampled populations-to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon-but in other genes, variants denoted as 'likely pathogenic' in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health.

An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers.

Human culture, biology, and health were shaped dramatically by the onset of agriculture ∼12,000 y B.P. This shift is hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a decline in physiological health as inferred from skeletal remains. Here, we consider osteological and ancient DNA data from the same prehistoric individuals to study human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared "predicted" genetic contributions to height from paleogenomic data and "achieved" adult osteological height estimated from long bone measurements for 167 individuals across Europe spanning the Upper Paleolithic to Iron Age (∼38,000 to 2,400 B.P.). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of −3.82 cm relative to individuals from the Upper Paleolithic and Mesolithic (P = 0.040) and −2.21 cm shorter relative to post-Neolithic individuals (P = 0.068), with osteological vs. expected stature steadily increasing across the Copper (+1.95 cm relative to the Neolithic), Bronze (+2.70 cm), and Iron (+3.27 cm) Ages. These results were attenuated when we additionally accounted for genome-wide genetic ancestry variation: for example, with Neolithic individuals −2.82 cm shorter than expected on average relative to pre-Neolithic individuals (P = 0.120). We also incorporated observations of paleopathological indicators of nonspecific stress that can persist from childhood to adulthood in skeletal remains into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory.

Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus.

Recent genomic data have revealed multiple interactions between Neanderthals and modern humans, but there is currently little genetic evidence regarding Neanderthal behaviour, diet, or disease. Here we describe the shotgun-sequencing of ancient DNA from five specimens of Neanderthal calcified dental plaque (calculus) and the characterization of regional differences in Neanderthal ecology. At Spy cave, Belgium, Neanderthal diet was heavily meat based and included woolly rhinoceros and wild sheep (mouflon), characteristic of a steppe environment. In contrast, no meat was detected in the diet of Neanderthals from El Sidrón cave, Spain, and dietary components of mushrooms, pine nuts, and moss reflected forest gathering. Differences in diet were also linked to an overall shift in the oral bacterial community (microbiota) and suggested that meat consumption contributed to substantial variation within Neanderthal microbiota. Evidence for self-medication was detected in an El Sidrón Neanderthal with a dental abscess and a chronic gastrointestinal pathogen (Enterocytozoon bieneusi). Metagenomic data from this individual also contained a nearly complete genome of the archaeal commensal Methanobrevibacter oralis (10.2× depth of coverage)-the oldest draft microbial genome generated to date, at around 48,000 years old. DNA preserved within dental calculus represents a notable source of information about the behaviour and health of ancient hominin specimens, as well as a unique system that is useful for the study of long-term microbial evolution.

Ancient human microbiomes.

Very recently, we discovered a vast new microbial self: the human microbiome. Our native microbiota interface with our biology and culture to influence our health, behavior, and quality of life, and yet we know very little about their origin, evolution, or ecology. With the advent of industrialization, globalization, and modern sanitation, it is intuitive that we have changed our relationship with microbes, but we have little information about the ancestral state of our microbiome, and we therefore lack a foundation for characterizing this change. High-throughput sequencing has opened up new opportunities in the field of paleomicrobiology, allowing us to investigate the evolution of the complex microbial ecologies that inhabit our bodies. By focusing on recent coprolite and dental calculus research, we explore how emerging research on ancient human microbiomes is changing the way we think about ancient disease and how archaeological studies can contribute to a medical understanding of health and nutrition today.

Contribution of the intestinal microbiota to human health: from birth to 100 years of age.

Our intestinal tract is colonized since birth by multiple microbial species that show a characteristic succession in time. Notably the establishment of the microbiota in early life is important as it appears to impact later health. While apparently stable in healthy adults, the intestinal microbiota is changing significantly during aging. After 100 years of symbiosis marked changes have been observed that may relate to an increased level of intestinal inflammation. There is considerable interest in the microbiota in health and disease as it may provide functional biomarkers, the possibility to differentiate subjects, and avenues for interventions. This chapter reviews the present state of the art on the research to investigate the contribution of the intestinal microbiota to human health. Specific attention will be given to the healthy microbiota and aberrations due to disturbances such as celiac disease, irritable bowel syndrome, inflammatory bowel disease, obesity and diabetes, and non-alcoholic fatty liver disease.

Birth is but our death begun: a bioarchaeological assessment of skeletal emaciation in immature human skeletons in the context of environmental, social, and subsistence transition.

The second millennium BC was a period of significant social and environmental changes in prehistoric India. After the disintegration of the Indus civilization, in a phase known as the Early Jorwe (1400-1000 BC), hundreds of agrarian villages flourished in the Deccan region of west-central India. Environmental degradation, combined with unsustainable agricultural practices, contributed to the abandonment of many communities around 1000 BC. Inamgaon was one of a handful of villages to persist into the Late Jorwe phase (1000-700 BC), wherein reliance on dry-plough agricultural production declined. Previous research demonstrated a significant decline in body size (stature and body mass index) through time, which is often used to infer increased levels of biocultural stress in bioarchaeology. This article assesses evidence for growth disruption in the immature human skeletal remains from Inamgaon by correlating measures of whole bone morphology with midshaft femur compact bone geometry and histology. Growth derangement is observable in immature archaeological femora as an alteration in the expected amount and distribution of bone mass and porosity in the midshaft cross-section. Cross-section shape matched expectations for older infants with the acquisition of bipedal locomotion. These results support the hypothesis that small body size was related to disruptions in homeostasis and high levels of biocultural stress in the Late Jorwe at Inamgaon. Further, the combined use of geometric properties and histological details provides a method for teasing apart the complex interactions among activity and "health," demonstrating how biocultural stressors affect the acquisition and quality of bone mass.

[The Fiocruz archives: sources for research on science and health during the military dictatorship (1964-1985)]. / Os arquivos da Fiocruz: fontes para a pesquisa sobre a ciência e a saúde na ditadura militar (1964-1985).

The scope of this paper is to analyze the relationship between the country's political redemocratization process from the 1980s onwards and the issue of identification, preservation and access to the archives of information and security bodies that worked to combat the opponents of the authoritarian regime during the military dictatorship (1964-1985). It addresses the dictatorship's action on university and scientific institutions, to highlight the importance of the archive of the Oswaldo Cruz Foundation, as well as the personal files maintained by scientists and donated to Casa de Oswaldo Cruz. It features archives and collections organized and available for public consultation, which can serve as research sources for historical studies on science and health during the dictatorship.

Analisa a relação entre o processo de redemocratização política do país a partir da década de 1980 e a questão da identificação, preservação e acesso aos arquivos dos órgãos de informação e segurança que durante a ditadura militar (1964-1985) atuaram no combate aos adversários do regime autoritário. Aborda a ação da ditadura sob as instituições universitárias e científicas, de forma a destacar a importância do arquivo institucional da Fundação Oswaldo Cruz, assim como os arquivos pessoais mantidos pelos cientistas e doados à Casa de Oswaldo Cruz. Apresenta os arquivos e coleções organizados e disponíveis à consulta pública, que podem servir como fontes de pesquisa para os estudos históricos sobre a ciência e a saúde na ditadura.

Going local with ancient DNA: A review of human histories from regional perspectives.

Ancient DNA (aDNA) has added a wealth of information about our species' history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.

Integrated Behavioral Health Care: Reflections of the Past.

Humans have long sought to be provided with optimal health care, and the research continues in the twenty-first century. In the spirit of Galen from 19 centuries ago, empowering the patient's physician remains an important approach in health care. There is an emphasis on primary care and integration of behavioral consultation services in primary care. It remains a work in progress with help from the past and realistic hope for the future.

[Violence, health and ailment of bodies in the parish of Vila Rica, eighteenth century]. / Violência, saúde e adoecimento dos corpos na comarca de Vila Rica, século XVIII.

Studies into violence in the eighteenth century tend to address questions related to justice and criminality, but not health. The aim of this study is to understand how, in eighteenth century Minas Gerais, Brazil, bodies were affected by violent acts. The investigation records from the parish of Vila Rica held at the historical archive of the Museu da Inconfidência were investigated. The results showed crimes of different kinds associated with a variety of motives, primarily crimes against the body, with the resulting bodily injuries being caused by sharp or pointed objects/instruments. There were more male victims than female, the head being the principal part of the body affected. Criminal and violent acts, very commonplace in this society, interfered in the health and disease processes of the bodies.

Estudos sobre violência no século XVIII abrangem especialmente questões relacionadas à justiça e à criminalidade, mas não à saúde. A pesquisa objetivou compreender como os corpos nas Minas Gerais setecentistas eram afetados por atos violentos. Foram investigados autos de devassas do termo de Vila Rica pertencentes ao acervo do Arquivo Histórico do Museu da Inconfidência. Os resultados mostraram crimes causados por motivos distintos e de tipologias diferentes, predominando os crimes contra o corpo, com consequentes lesões corporais provocadas predominantemente por objetos/instrumentos perfurocortantes. Os homens foram os mais acometidos, sendo a cabeça a principal região atingida. Atos criminosos e violentos, muito comuns nessa sociedade, interferiam na saúde e no adoecimento dos corpos.