Ethics of DNA research on human remains: five globally applicable guidelines.

We are a group of archaeologists, anthropologists, curators and geneticists representing diverse global communities and 31 countries. All of us met in a virtual workshop dedicated to ethics in ancient DNA research held in November 2020. There was widespread agreement that globally applicable ethical guidelines are needed, but that recent recommendations grounded in discussion about research on human remains from North America are not always generalizable worldwide. Here we propose the following globally applicable guidelines, taking into consideration diverse contexts. These hold that: (1) researchers must ensure that all regulations were followed in the places where they work and from which the human remains derived; (2) researchers must prepare a detailed plan prior to beginning any study; (3) researchers must minimize damage to human remains; (4) researchers must ensure that data are made available following publication to allow critical re-examination of scientific findings; and (5) researchers must engage with other stakeholders from the beginning of a study and ensure respect and sensitivity to stakeholder perspectives. We commit to adhering to these guidelines and expect they will promote a high ethical standard in DNA research on human remains going forward.

Long-term trends in human body size track regional variation in subsistence transitions and growth acceleration linked to dairying.

Evidence for a reduction in stature between Mesolithic foragers and Neolithic farmers has been interpreted as reflective of declines in health, however, our current understanding of this trend fails to account for the complexity of cultural and dietary transitions or the possible causes of phenotypic change. The agricultural transition was extended in primary centers of domestication and abrupt in regions characterized by demic diffusion. In regions such as Northern Europe where foreign domesticates were difficult to establish, there is strong evidence for natural selection for lactase persistence in relation to dairying. We employ broad-scale analyses of diachronic variation in stature and body mass in the Levant, Europe, the Nile Valley, South Asia, and China, to test three hypotheses about the timing of subsistence shifts and human body size, that: 1) the adoption of agriculture led to a decrease in stature, 2) there were different trajectories in regions of in situ domestication or cultural diffusion of agriculture; and 3) increases in stature and body mass are observed in regions with evidence for selection for lactase persistence. Our results demonstrate that 1) decreases in stature preceded the origins of agriculture in some regions; 2) the Levant and China, regions of in situ domestication of species and an extended period of mixed foraging and agricultural subsistence, had stable stature and body mass over time; and 3) stature and body mass increases in Central and Northern Europe coincide with the timing of selective sweeps for lactase persistence, providing support for the "Lactase Growth Hypothesis."

Stature estimation equations for South Asian skeletons based on DXA scans of contemporary adults.

OBJECTIVES: Stature estimation from the skeleton is a classic anthropological problem, and recent years have seen the proliferation of population-specific regression equations. Many rely on the anatomical reconstruction of stature from archaeological skeletons to derive regression equations based on long bone lengths, but this requires a collection with very good preservation. In some regions, for example, South Asia, typical environmental conditions preclude the sufficient preservation of skeletal remains. Large-scale epidemiological studies that include medical imaging of the skeleton by techniques such as dual-energy X-ray absorptiometry (DXA) offer new potential datasets for developing such equations. MATERIALS AND METHODS: We derived estimation equations based on known height and bone lengths measured from DXA scans from the Andhra Pradesh Children and Parents Study (Hyderabad, India). Given debates on the most appropriate regression model to use, multiple methods were compared, and the performance of the equations was tested on a published skeletal dataset of individuals with known stature. RESULTS: The equations have standard errors of estimates and prediction errors similar to those derived using anatomical reconstruction or from cadaveric datasets. As measured by the number of significant differences between true and estimated stature, and the prediction errors, the new equations perform as well as, and generally better than, published equations commonly used on South Asian skeletons or based on Indian cadaveric datasets. CONCLUSIONS: This study demonstrates the utility of DXA scans as a data source for developing stature estimation equations and offer a new set of equations for use with South Asian datasets.

A comparative study of robusticity indices of long bones among hunter-gatherers and early agro-pastoral groups of India.

OBJECTIVES: Diaphyseal robusticity and cross-sectional shapes of the bone tissues are influenced by mechanical loading history. It changes according to work demand on the body. It is the objective of this study to identify the shifts in the modes of subsistence, activities and mobility patterns through the comparison of the shape and strength of bone diaphyses among the Mesolithic, Chalcolithic and Harappan populations of India. MATERIALS AND METHODS: For the analysis, 7 sites including 2 from Mesolithic (8000-4000 bc), 2 from Chalcolithic (2000-700 bc) and 3 from Harappan (3500-1800 bc) contexts are considered. The ratio obtained from the maximum length of the bones to their girth (at 50% or 35% from the distal end) and that from anterior-posterior and medio-lateral diameters were calculated (following Martin and Saller codes, 1957) to understand certain functional adaptations and stress markers on preserved long bones. Independent-sample T-tests and ANOVA were applied to detect mean differences of statistical significance within and between cultures. RESULTS: The robusticity indices obtained from the humeri increase from the hunting-gathering phase (M/F; 19.39/18.45) to the Chalcolithic phase (M/F; 21.99/19.39) showing a slight drop in the Harappan phase (M/F; 18.58/18.37). The right humeri of Mesolithic females show a directional asymmetry of length (4.08%-5.13%) while that in males reach up to 26.09% indicating right-dominant lateralization. In the Harappan phase, females show a greater value for the right ranging from 0.31% to 3.07%. The femoral robusticity of females increases from 11.42 in hunting-gathering societies to 13.28 in Harappan times while mid-shaft of the Mesolithic population clearly shows greater loading along the anterior-posterior (A-P) plane as the index in most cases exceeds 100. There are significant differences among males and females within each group in terms of the indices but significant differences could be discerned between the Mesolithic, Chalcolithic and Harappan populations in case of tibiae, radii and ulnae only. CONCLUSION: The occupation patterns certainly changed as humans became a food-producer from a hunter-gatherer. Occupations involving the extensive flexion and extension of upper limbs in the Chalcolithic period increase particularly in the Harappan phase. Sedentism gave rise to roundness of the femur and reduced the magnitude of lateralization. While equal level of mobility can be traced in case of both the sexes before the advent of agriculture, this distinction increases between the males and females in the agro-pastoral phases.

Maternal ancestry of first Parsi settlers of India using ancient mitogenome.

The rich cultural and genetic diversity of South Asia emerged from multiple migrations and cultural assimilation of multiple waves of migrants. The Parsi community of North-western India were one of those who migrated from West Eurasia in the aftermath of 7th century CE and assimilated into the local cultural framework. Earlier genetic studies further strengthened this notion with the finding that they harbour both Middle Eastern and South Asian genetic components. Although these studies covered both autosomal and uniparental markers, still maternal ancestry was not covered in depth and with good resolution of mitochondrial markers. Hence in our current study, we have first time generated a complete mitogenome of 19 ancient samples of the first Parsi settlers excavated from the archaeological site of Sanjan and performed detailed phylogenetic analysis to infer their maternal genetic affinity. In our analysis, we found that the Parsi mitogenome with mtDNA haplogroup M3a1 + 204 shares clade with both Middle Eastern and South Asian modern individuals in both the Maximum Likelihood tree and Bayesian phylogenetic tree. This haplogroup was also prevalent among the medieval Swat valley population of present-day Northern Pakistan and was also observed in two Roopkund A individuals. In the phylogenetic network this sample share haplotype with both South Asian and Middle Eastern samples. So conclusively, the first Parsi settlers' maternal ancestry encompasses both South Asian and Middle Eastern genetic composition.

Ancient origins of low lean mass among South Asians and implications for modern type 2 diabetes susceptibility.

Living South Asians have low lean tissue mass relative to height, which contributes to their elevated type 2 diabetes susceptibility, particularly when accompanied by obesity. While ongoing lifestyle transitions account for rising obesity, the origins of low lean mass remain unclear. We analysed proxies for lean mass and stature among South Asian skeletons spanning the last 11,000 years (n = 197) to investigate the origins of South Asian low lean mass. Compared with a worldwide sample (n = 2,003), South Asian skeletons indicate low lean mass. Stature-adjusted lean mass increased significantly over time in South Asia, but to a very minor extent (0.04 z-score units per 1,000 years, adjusted R2 = 0.01). In contrast stature decreased sharply when agriculture was adopted. Our results indicate that low lean mass has characterised South Asians since at least the early Holocene and may represent long-term climatic adaptation or neutral variation. This phenotype is therefore unlikely to change extensively in the short term, so other strategies to address increasing non-communicable disease rates must be pursued.

Estimating body mass and composition from proximal femur dimensions using dual energy x-ray absorptiometry.

Body mass prediction from the skeleton most commonly employs femoral head diameter (FHD). However, theoretical predictions and empirical data suggest the relationship between mass and FHD is strongest in young adults, that bone dimensions reflect lean mass better than body or fat mass and that other femoral measurements may be superior. Here, we generate prediction equations for body mass and its components using femoral head, neck and proximal shaft diameters and body composition data derived from dual-energy x-ray absorptiometry (DXA) scans of young adults (n = 155, 77 females and 78 males, mean age 22.7 ± 1.3 years) from the Andhra Pradesh Children and Parents Study, Hyderabad, India. Sex-specific regression of log-transformed data on femoral measurements predicted lean mass with smaller standard errors of estimate (SEEs) than body mass (12-14% and 16-17% respectively), while none of the femoral measurements were significant predictors of fat mass. Subtrochanteric mediolateral shaft diameter gave lower SEEs for lean mass in both sexes and for body mass in males than FHD, while FHD was a better predictor of body mass in women. Our results provide further evidence that lean mass is more closely related to proximal femur dimensions than body or fat mass and that proximal shaft diameter is a better predictor than FHD of lean but not always body mass. The mechanisms underlying these relationships have implications for selecting the most appropriate measurement and reference sample for estimating body or lean mass, which also depend on the question under investigation.

Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India.

Situated at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake, and find that they cluster into three distinct groups. A group of 23 individuals have ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simultaneously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups.

"Like sugar in milk": reconstructing the genetic history of the Parsi population.

BACKGROUND: The Parsis are one of the smallest religious communities in the world. To understand the population structure and demographic history of this group in detail, we analyzed Indian and Pakistani Parsi populations using high-resolution genetic variation data on autosomal and uniparental loci (Y-chromosomal and mitochondrial DNA). Additionally, we also assayed mitochondrial DNA polymorphisms among ancient Parsi DNA samples excavated from Sanjan, in present day Gujarat, the place of their original settlement in India. RESULTS: Among present-day populations, the Parsis are genetically closest to Iranian and the Caucasus populations rather than their South Asian neighbors. They also share the highest number of haplotypes with present-day Iranians and we estimate that the admixture of the Parsis with Indian populations occurred ~1,200 years ago. Enriched homozygosity in the Parsi reflects their recent isolation and inbreeding. We also observed 48% South-Asian-specific mitochondrial lineages among the ancient samples, which might have resulted from the assimilation of local females during the initial settlement. Finally, we show that Parsis are genetically closer to Neolithic Iranians than to modern Iranians, who have witnessed a more recent wave of admixture from the Near East. CONCLUSIONS: Our results are consistent with the historically-recorded migration of the Parsi populations to South Asia in the 7th century and in agreement with their assimilation into the Indian sub-continent's population and cultural milieu "like sugar in milk". Moreover, in a wider context our results support a major demographic transition in West Asia due to the Islamic conquest.

Evidence for Patterns of Selective Urban Migration in the Greater Indus Valley (2600-1900 BC): A Lead and Strontium Isotope Mortuary Analysis.

Just as modern nation-states struggle to manage the cultural and economic impacts of migration, ancient civilizations dealt with similar external pressures and set policies to regulate people's movements. In one of the earliest urban societies, the Indus Civilization, mechanisms linking city populations to hinterland groups remain enigmatic in the absence of written documents. However, isotopic data from human tooth enamel associated with Harappa Phase (2600-1900 BC) cemetery burials at Harappa (Pakistan) and Farmana (India) provide individual biogeochemical life histories of migration. Strontium and lead isotope ratios allow us to reinterpret the Indus tradition of cemetery inhumation as part of a specific and highly regulated institution of migration. Intra-individual isotopic shifts are consistent with immigration from resource-rich hinterlands during childhood. Furthermore, mortuary populations formed over hundreds of years and composed almost entirely of first-generation immigrants suggest that inhumation was the final step in a process linking certain urban Indus communities to diverse hinterland groups. Additional multi disciplinary analyses are warranted to confirm inferred patterns of Indus mobility, but the available isotopic data suggest that efforts to classify and regulate human movement in the ancient Indus region likely helped structure socioeconomic integration across an ethnically diverse landscape.