Maternal Genetic Ancestry of Gujarat: A Pleistocene Passage to India

This study aims to present a comprehensive maternal genetic perspective on the population history of coastal northwestern India, especially Gujarat. The region is important due to its paleoanthropological significance, its role in the Indus Valley civilization, and its location within routes of Indo-European and Dravidian speaking populations. Previous studies have often used limited samples, underscoring the need for more extensive mitochondrial DNA analyses.

We sequenced and analyzed complete mitochondrial genomes from 168 individuals in Gujarat. To place these within a broader phylogenetic framework, we included an additional 529 complete mitogenomes representing East-West Eurasian and South Asian lineages. Phylogenetic relationships and chronological expansions were examined, and Bayesian analysis was used to assess changes in maternal effective population size over time.

Our findings show that the majority of (76%) of maternal lineages in Gujarat are from South Asia. East Eurasian and West Eurasian contributions are comparatively low, at 0.6% and 21%, respectively. Looking at the events of the last few millennia, we note that only 19% of West Eurasian lineages appear to have entered the region within the last 5000 years. Most Eurasian haplogroups represent early founding lineages, while 81% of West Eurasian lineages predate the Steppe migration.

The data suggest that western India retains largely indigenous maternal ancestry, with little evidence for major maternal migration or replacement over the last 40,000 years. West Eurasian lineages entered in several small waves rather than a single large influx, challenging the classic Indo-Aryan migration model.