Disentangling human geographic history in India with genetic genealogies

Objectives

The objective of this research is to disentangle the geographic history of humans in India using genetic genealogies.

Study design

We will first combine the provided vcf with publicly-available vcfs (of worldwide contemporary and ancient genomes) to infer the genetic genealogies of the samples. We will do this with two different open-source programs, Relate (Speidel et al. 2019) and tsinfer (Kelleher et al. 2019). We will then use the genealogies to infer the spatial locations of the genetic ancestors of each sample back in time, from their sampling time to the time of the most recent common ancestor in each genealogy. We will do this with two different open-source programs developed by our group, spacetrees (Osmond & Coop 2024) and sparg (Deraje, Kitchens, et al. 2025).

Analysis plan

The inferred locations of the genetic ancestors will allow us to visualize an estimate of the geographic history of humans in and around India. This may help support or refute exisiting hypotheses of migration and admixture, and suggest new ones. The spatial population genetics of India is complex, with several waves of migration both within the country and from outside. For instance, it is well known that North Indians have larger proportion of ancestry from West Eurasians compared to South Indians, while the latter harbour ancestry from ancient indigenous South Indians (which are related to the hunter gatherers from the Andamon Islands). More recent studies have found significant amounts of archaic hominin ancestry (from Neandrathals and Denisovans), larger than observed in most other worldwide populations. Estimating the timing and location of these admixtures (and many more) is still an area of ongoing research. We think our analysis will provide new insight into these questions.

Collaboration

This project will be led by a PhD student in my group, Puneeth Deraje (University of Toronto). We plan to collaborate with Professor Stephen Wright (University of Toronto), who specializes in empirical population genomics.

The geographic movements of our genetic ancestors, from one generation to the next, leave patterns in our genomes. We can therefore use these patterns to infer something about the spatial history of our genetic ancestors. We have developed two new methods for estimating the location of shared genetic ancestors from a set of sampled genomes. We propose to use these methods on a large sample of human genomes from India to help disentangle the complex geographic history of humans in this area. We think our results will provide new visuals of and insight into the spatial history of modern-day Indians.