Paleogenomics of the Mesolithic Ganges Plain: Deep Population Continuity at Damdama and Sarai Nahar Rai

The central Ganges Plain contains some of the earliest human skeletal series discovered in North India, excavated from terminal Pleistocene and early Holocene lacustrine deposits (Sharma, 1973). Archaeological sites located in Uttar Pradesh's Pratapgarh district—notably Sarai Nahar Rai and Damdama—yielded dozens of human burials during systematic field investigations led by Allahabad University (Sharma, 1973; Pal, 1985).

For decades, physical anthropologists analyzed these remains through osteometry, dental morphology, and paleopathology (Kennedy et al., 1986; Lukacs and Pal, 1993). Recent advances in paleogenomics have made it possible to sequence ancient DNA directly from these Mesolithic skeletons (Rai et al., 2025). The resulting genomic profiles clarify the genetic relationship between early Holocene hunter-gatherers and present-day South Asian populations.

Genomic Structure of the Mesolithic Ganges Basin

Genomic modeling of ancient South Asian populations relies on isolating deep ancestral components (Reich et al., 2009). Modern South Asians derive their ancestry primarily from three main ancestral sources: an indigenous hunter-gatherer lineage termed Ancient Ancestral South Indian (AASI), an Iranian agriculturalist-related lineage, and a Steppe pastoralist-related lineage (Narasimhan et al., 2019).

Ancient DNA extracted from Mesolithic burials at Damdama and Sarai Nahar Rai provides a direct genomic baseline for the unadmixed AASI lineage (Rai et al., 2025). Unlike later Bronze Age individuals from the Indus Valley Basin, who possessed significant Iranian agriculturalist-related ancestry (Shinde et al., 2019), the Mesolithic Ganges individuals show maximum affinity to the unmixed AASI proxy (Narasimhan et al., 2019).

Principal Component Analysis (PCA) places these Mesolithic Ganges genomes at the extreme baseline of South Asian genetic diversity (Narasimhan et al., 2019). Their profile demonstrates deep population continuity: the AASI genetic contribution remains widespread across modern South Asian groups, present in varying proportions across regional and social demographic groups (Moorjani et al., 2013).

Bioarchaeology and Subsistence Stratigraphy

The genetic continuity observed at Damdama and Sarai Nahar Rai complements earlier bioarchaeological studies of the region's mortuary and faunal assemblages (Kennedy et al., 1986; Lukacs and Pal, 2003).

Excavations at Damdama recovered 41 human graves containing both single and multiple burials (Pal, 1985). Morphometric evaluations by physical anthropologist Kenneth Kennedy noted pronounced cranial capacity, robust muscle attachment sites (entheses), and tall stature among the skeletons (Kennedy et al., 1986). Analysis of distal limb segments indicates thermoregulatory adaptations to a warm, humid post-glacial climate (Lukacs and Pal, 2003).

Faunal stratigraphy at Damdama demonstrates a broad-spectrum foraging economy. Excavated layers contain abundant remains of wild ungulates, including Axis axis (chital), Cervus duvauceli (swamp deer), and Bos gaurus (gaur), alongside aquatic resources like fish bones and freshwater mollusk shells (Misra et al., 1996). Microwear analysis of geometric microliths—primarily lunates and blades crafted from chert and chalcedony—indicates their use as composite projectile tips and plant-processing tools (Pal, 1985).

Dental pathology studies by John Lukacs show low rates of carious lesions among the Damdama skeletons, alongside high rates of dental wear (attrition) (Lukacs and Pal, 1993). This pattern reflects a diet reliant on hunted meat and wild forage rather than cultivated carbohydrates, confirming an early Holocene hunter-gatherer adaptation prior to the local adoption of plant cultivation (Lukacs and Pal, 1993; Lukacs and Misra, 1997).

⚖ Scholarly debate

The demographic history of South Asia and the mechanics of genetic turnover between the Mesolithic period and the Iron Age remain topics of active scientific discussion.

One perspective, supported by paleogenomic models from David Reich and Vagheesh Narasimhan, holds that major demographic additions occurred in post-Mesolithic periods (Reich et al., 2009; Narasimhan et al., 2019). Under this model, agricultural expansion from the Iranian plateau introduced West Eurasian-related ancestry into northwestern South Asia, mixing with local AASI groups to form the Indus Valley Civilization (IVC) population (Shinde et al., 2019). Subsequently, during the Middle to Late Bronze Age, gene flow from Steppe pastoralist populations moved into North India, combining with IVC-related groups to form Ancestral North Indian (ANI) lineages, while IVC groups moving southward mixed further with AASI hunter-gatherers to form Ancestral South Indian (ASI) lineages (Narasimhan et al., 2019).

An alternative model, argued by archaeological researchers including Vasant Shinde, places greater emphasis on long-term local continuity (Shinde et al., 2019). Evidence shows that the single high-coverage genome recovered from Rakhigarhi contained no detectable Steppe-related ancestry, which some scholars interpret as evidence for indigenous agricultural development and cultural evolution without large-scale population replacements in the third millennium BCE (Shinde et al., 2019).

Archaeobotanical evidence from Gangetic sites like Lahuradewa further complicates the timing of early agricultural transitions, as early wild rice exploitation preceded fully domesticated cereal farming in the region (Tewari et al., 2008).

The high-coverage genomic data from Damdama and Sarai Nahar Rai anchors the AASI end-member of South Asian genetic history (Narasimhan et al., 2019). By confirming that early Holocene Ganges foragers carried the unadmixed AASI signature, paleogenomics demonstrates that despite later demographic additions, the genetic foundation established during the Mesolithic period remains structurally preserved in modern South Asian populations (Moorjani et al., 2013; Narasimhan et al., 2019).