Genetic legacy of Jomon hunter-gatherers linked to increased BMI in modern Japanese

Posted on: 14 November 2024

The research – just published in leading international journal Nature Communications – also found broad support for the “tripartite ancestry model”.

This effectively means variations in modern day Japanese genetic patterns can be explained by the historical influence of ancient Jomon hunter-gatherers and two continental groups from Northeast and East Asia that collectively left their genetic imprint on the people of today.

The research analysed genetic data from Biobank Japan (including over 170,000 individuals), along with ancient Japanese and Eurasian genomes, as well as those from East Asian individuals from the UK Biobank. In total, the analyses used genetic data of ancient and modern genomes that involved over 250,000 participants.

BMI links

The researchers tested associations of Jomon ancestry with 80 different complex traits (from height to BMI) by making robust adjustments for genetic and geographic subpopulations.

They found that the Jomon genetic signature, which on average accounts for 12.5% of a person’s genetic make-up, was associated with an increased BMI. And that held true when they expanded their analyses to include East Asian individuals in the UK Biobank – underlining the robustness of this trait that echoes from a largely forgotten time. 

Shigeki Nakagome, Assistant Professor in Trinity College Dublin’s School of Medicine is a senior author of the research. He said: “Overall, these results suggest that the genetic legacy of the ancient hunter-gatherer Jomon significantly influences BMI across populations today, regardless of geographic differences, and it may consequently contribute to an increased risk of obesity. 

“It is a really important discovery that ancient hunter-gatherer ancestry is likely to play a key role in the health of modern day populations. The link to an increased BMI could also help to explain some of the disparities in obesity prevalence among Asian populations residing in Western countries. 

“By emphasising the importance of incorporating Jomon ancestry as a factor in BMI, this analysis essentially provides a proof-of-concept for research that bridges our human past with current health challenges.” 

The tripartite model

A long-standing model of Japanese origins is a dual-ancestral structure  comprising the Jomon, who were hunter-gatherer-fishers who inhabited the archipelago as far back as 16,500 years ago, and immigrant farmers from Northeast Asia. This was recently refined by the tripartite model, which also incorporates East Asian ancestry linked to the state formation phase, the Kofun period, which began around 1,700 years ago.

And the new research found strong support for that tripartite model.

Prof. Nakagome added: “Our analysis, which presents the first in-depth characterisation of the tripartite structure across the entire Japanese archipelago, widely and consistently fits better than the dual structure hypothesis. It also unveils substantial variation in the proportion of Jomon ancestry, mirroring the genetic ancestry continuum observed in present-day populations. 

“The field of ancient genomics is rapidly evolving, and future research that encompasses a diverse range of ancient humans across various time periods and geographic locations will provide a more comprehensive understanding of the extent to which the human past has shaped genomic and phenotypic variation in contemporary populations. I am sure there is much left to discover, both in Japanese populations, and in others across the globe.”

This research was partially supported by the Wellcome Trust ISSF Award and the Japan Society for the Promotion of Science. 

The published journal article can be read on the Nature Communications website. 

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