Advancements and Challenges in Ancient DNA Research: Bridging the Global North-South Divide.

Ancient DNA (aDNA) research first began in 1984 and ever since has greatly expanded our understanding of evolution and migration. Today, aDNA analysis is used to solve various puzzles about the origin of mankind, migration patterns, and the spread of infectious diseases. The incredible findings ranging from identifying the new branches within the human family to studying the genomes of extinct flora and fauna have caught the world by surprise in recent times. However, a closer look at these published results points out a clear Global North and Global South divide. Therefore, through this research, we aim to emphasize encouraging better collaborative opportunities and technology transfer to support researchers in the Global South. Further, the present research also focuses on expanding the scope of the ongoing conversation in the field of aDNA by reporting relevant literature published around the world and discussing the advancements and challenges in the field.

Lipid residues in pottery from the Indus Civilisation in northwest India.

This paper presents novel insights into the archaeology of food in ancient South Asia by using lipid residue analysis to investigate what kinds of foodstuffs were used in ceramic vessels by populations of the Indus Civilisation in northwest India. It examines how vessels were used in urban and rural Indus settlements during the Mature Harappan period (c.2600/2500-1900 BC), the relationship between vessels and the products within them, and identifies whether changes in vessel use occurred from the Mature Harappan to Late Harappan periods, particularly during climatic instability after 4.2 ka BP (c.2100 BC). Despite low lipid concentrations, which highlight challenges with conducting residue analysis in arid, seasonally-wet and alkaline environments, 71% of the vessels yielded appreciable quantities of lipid. Lipid profiles revealed the use of animal fats in vessels, and contradictory to faunal evidence, a dominance of non-ruminant fats, with limited evidence of dairy processing. The absence of local modern reference fats makes this dataset challenging to interpret, and it is possible that plant products or mixtures of plant and animal products have led to ambiguous fatty acid-specific isotopic values. At the same time, it appears that urban and rural populations processed similar types of products in vessels, with limited evidence for change in vessel use from the urban to the post-urban period. This study is a systematic investigation into pot lipid residues from multiple sites, demonstrating the potential of the method for examining ancient Indus foodways and the need for the development of further research in ancient organic residues in South Asia.

Craniofacial reconstruction of the Indus Valley Civilization individuals found at 4500-year-old Rakhigarhi cemetery.

Despite academic efforts to study the Indus Valley Civilization (IVC), there have as yet been no successful attempts to unveil the IVC people's craniofacial appearance. We investigated the IVC cemetery area of Rakhigarhi site, which was estimated to be of 2273 ± 38 and 2616 ± 73 years BCE. By craniofacial reconstruction (CFR) procedure using computed tomography (CT) data of two Rakhigarhi skulls (A1 BR02 and A2 BR36), we successfully reconstructed the faces of the IVC individuals who were buried about 4500 years ago. This is the first attempt to unveil scientifically accurate representations of IVC people's actual facial morphology.

An Ancient Harappan Genome Lacks Ancestry from Steppe Pastoralists or Iranian Farmers.

We report an ancient genome from the Indus Valley Civilization (IVC). The individual we sequenced fits as a mixture of people related to ancient Iranians (the largest component) and Southeast Asian hunter-gatherers, a unique profile that matches ancient DNA from 11 genetic outliers from sites in Iran and Turkmenistan in cultural communication with the IVC. These individuals had little if any Steppe pastoralist-derived ancestry, showing that it was not ubiquitous in northwest South Asia during the IVC as it is today. The Iranian-related ancestry in the IVC derives from a lineage leading to early Iranian farmers, herders, and hunter-gatherers before their ancestors separated, contradicting the hypothesis that the shared ancestry between early Iranians and South Asians reflects a large-scale spread of western Iranian farmers east. Instead, sampled ancient genomes from the Iranian plateau and IVC descend from different groups of hunter-gatherers who began farming without being connected by substantial movement of people.

A young couple's grave found in the Rakhigarhi cemetery of the Harappan Civilization.

The Harappan Civilization, one of the earliest complex societies in the world, flourished on the Indian subcontinent. Although many additional Harappan settlements and cemeteries have been discovered and investigated, no coupled burials at Harappan cemeteries have been reported to date. In 2013-2016, we excavated the cemetery of the Rakhigarhi site (Haryana), the largest city of the Harappan Civilization. At the site, we found a grave that turned out to be a coupled (joint) burial of the primary type. This report is the first anthropologically confirmed case of coupled burial from a Harappan cemetery.

Genetic resolution of applied biosystems™ precision ID Ancestry panel for seven Asian populations.

Massively parallel sequencing (MPS) offers additional information in cases that lack reference samples for comparison. The HID-Ion AmpliSeq Ancestry Panel is a forensic multiplex platform consisting of 165 autosomal markers designed to provide biogeographic ancestry information. We analyzed seven different population groups from Asia to assess the accuracy and reliability of analysis, using this panel. In this study, we have designated 750 unrelated Asians, from southern China (n = 99), Beijing (n = 100), Japan (n = 101), Korea (n = 100), Vietnam (n = 100), Nepal (n = 100), India (n = 51), and Pakistan (n = 99). The likelihood ratios of 750 Asians were calculated, using the Torrent Server and the HID SNP Genotyper Plugin Version 4.3.2. The results reveal that all Northeast Asians (China, Japan, and Korea), and Vietnamese, were predicted as East Asians with the highest ethnicity likelihood values from reference data. Although the samples from Nepal, India and Pakistan (Southwest Asians), were predominantly predicted as South Asians, there were seven cases of which results revealed as Europeans, with similar likelihood patterns. Population structure analysis indicated that Southwest Asians have a genetic profile that is distinguishable from those of other Asian populations. This panel was validated for potential usefulness in forensic analysis and the findings could be used as a basis for building additional Asian specific reference databases. Nevertheless, additional analyses comprising larger sample sizes will be necessary, especially Southeast Asians, to fully understand the Asian population structure, and to discriminate them with further details.

Archaeological and anthropological studies on the Harappan cemetery of Rakhigarhi, India.

An insufficient number of archaeological surveys has been carried out to date on Harappan Civilization cemeteries. One case in point is the necropolis at Rakhigarhi site (Haryana, India), one of the largest cities of the Harappan Civilization, where most burials within the cemetery remained uninvestigated. Over the course of the past three seasons (2013 to 2016), we therefore conducted excavations in an attempt to remedy this data shortfall. In brief, we found different kinds of graves co-existing within the Rakhigarhi cemetery in varying proportions. Primary interment was most common, followed by the use of secondary, symbolic, and unused (empty) graves. Within the first category, the atypical burials appear to have been elaborately prepared. Prone-positioned internments also attracted our attention. Since those individuals are not likely to have been social deviants, it is necessary to reconsider our pre-conceptions about such prone-position burials in archaeology, at least in the context of the Harappan Civilization. The data presented in this report, albeit insufficient to provide a complete understanding of Harappan Civilization cemeteries, nevertheless does present new and significant information on the mortuary practices and anthropological features at that time. Indeed, the range of different kinds of burials at the Rakhigarhi cemetery do appear indicative of the differences in mortuary rituals seen within Harappan societies, therefore providing a vivid glimpse of how these people respected their dead.

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.