Retelling the Jomon story

It’s long been assumed the Jomon people, who had inhabited the Japanese archipelago since around 16,000 years ago, had multiple lineages resulting from different migration routes. But, new genetic evidence, including mitochondrial DNA from 13 newly sequenced Jomon skeletons, suggests that an initial migration of a single lineage later split, giving rise to regional diversity. This research puts greater emphasis on environmental and cultural factors being the possible drivers for the East and West of prehistoric Japan, respectively. 

Most of what we know about the Jomon people of ancient Japan comes from pottery and other well-preserved materials. The more subtle history of the Jomon, such as details of the population and their movements, has been largely inferred from archaeological indicators, such as the number and distribution of archaeological sites. However, despite large amounts of genetic data from Jomon remains being available, a comprehensive demographic history covering the entire Japanese archipelago has not been fully examined. Many studies have been conducted using DNA from the present-day Japanese population, but there are many confounding issues with those kinds of studies. 

Researchers sought a more direct reconstruction of Jomon demographic history, in part to answer long-standing questions about the initial migration of the Jomon ancestry to the Japanese archipelago. It’s known from prior studies looking at maternal mitochondrial DNA that there were two main lineages, loosely eastern and western. But, it’s unclear whether the split came before or after that initial migration. Recently, many genetic sequences of the whole mitochondrial DNA from Jomon individuals have become available. As a result, Professor Hiroki Oota from the University of Tokyo’s Department of Biological Studies and his team are finally able to see whether these data could allow direct investigation into the population history of the Jomon people.  

“We used mitochondrial DNA (mtDNA) extracted from the bones of the Jomon people to examine how their population changed over time. By using what are called Bayesian skyline plots, graphs that use DNA mutations and statistical modeling to estimate how a population’s size changed through time, we found that the Jomon population increased significantly between about 13,000 and 8,000 years ago, especially in eastern Japan,” said graduate student Koki Yoshida of the Oota lab. “We also showed that the genetic differences observed between eastern and western Jomon people do not necessarily indicate that people with different ancestors migrated to Japan via multiple routes. Instead, these differences can be explained by chance changes that occurred as people with the same ancestors spread and lay separately within the Japanese archipelago.” 

The significance of this is that it offers a new perspective on Jomon history and suggests that regionally constrained evolutionary and cultural processes may have also played an important role, rather than just the movement of people. 

“During the Jomon period, the climate and natural environments of eastern and western Japan were different. In eastern Japan, forests provided abundant plant and animal resources. In contrast, western Japan was less productive in terms of food availability,” said Yoshida. “Additionally, eastern Jomon are known to have used marine animals such as salmon and trout from an early stage. These differences in climate and food resources may have created conditions in which eastern Jomon people could live more stably and support larger demographic expansion, in line with what we see in the records.” 

The demographic history of the Jomon people revealed in this study agrees with archaeological evidence in some respects, but not in others. An important challenge for future research is to understand and explain these gaps between genetic and other findings. To address this, the team plans to integrate perspectives not only from archaeology but also from paleoenvironmental studies, which examine past climates and environments, as well as ecological approaches that explore relationships between people and nature. 

### 
 

Journal: Koki Yoshida, Yoshiki Wakiyama, Yuka Nakamura, Guido Valverde, Akio Tanino, Daisuke Waku, Takafumi Katsumura, Motoyuki Ogawa, Tomohito Nagaoka, Kazuaki Hirata, Kae Koganebuchi, Yusuke Watanabe, Jun Ohashi, Minoru Yoneda, Ryuzaburo Takahashi, Hiroki Oota, “Demographic history of the Jomon people: insights from whole-mitogenome analysis”, Anthropological Science, DOI: 10.1537/ase.251024. 

https://www.jstage.jst.go.jp/article/ase/advpub/0/advpub_251024/_article  

 
Funding: This study was mainly supported by JSPS KAKENHI Grant-in-Aid for Scientific Research 18H03590 and 22H00020 to R.T. This study was also supported by JSPS KAKENHI Grant-in-Aid for Scientific Research 23H04838, 23KJ0654, 21H04779, 21H00337, 21H05362, 21K19289, 19H04526. 

Useful links: 

Graduate School of Science 

https://www.s.u-tokyo.ac.jp/en/  
 

Department of Biological Sciences 

https://www.bs.s.u-tokyo.ac.jp/english/  

 
Research Contact: 

Professor Hiroki Oota 

Department of Biological Sciences, The University of Tokyo, 

7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, JAPAN 
hiroki_oota@bs.s.u-tokyo.ac.jp  

 
Press contact: 
Mr. Rohan Mehra 
Strategic Communications Group, The University of Tokyo, 
7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan 
press-releases.adm@gs.mail.u-tokyo.ac.jp 
 

About The University of Tokyo: 

The University of Tokyo is Japan's leading university and one of the world's top research universities. The vast research output of some 6,000 researchers is published in the world's top journals across the arts and sciences. Our vibrant student body of around 15,000 undergraduate and 15,000 graduate students includes over 5,000 international students. Find out more at www.u-tokyo.ac.jp/en/ or follow us on X (formerly Twitter) at @UTokyo_News_en.