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Ancient DNA Rewrites Japanese History

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An interdisciplinary team of researchers from Japan and Ireland have discovered that modern day populations in Japan have a tripartite genetic origin, rather dual genomic ancestry as previously thought. The study is published in Science Advances.

The history of Japan

Archaeological data suggests that humans have occupied the Japanese archipelago for over 30,000 years. The ancestral roots of the modern Japanese population have been explored through many different hypotheses, the longest being the dual structure model that was proposed by Hanihara.

What is an archipelago?

Japan is an archipelago, meaning it consists of a group of islands that exist in close proximity to a body of water. Hokkaido, Shikoku, Honshu and Kyushi are the four largest islands in the Japanese archipelago, but there are over 3,000 smaller islands.

Based on craniofacial analyses, Hanihar proposed that the first people to come to the Japanese archipelago were from Southeast Asia, arriving in the Upper Paleolithic age. These individuals were ancestors of the indigenous Jōmon people, a hunter-gatherer population that are believed to have inhabited sunken pit dwellings near bodies of water so that they could hunt and fish. The Jōmon population is estimated to have occupied the Japenese archipelago from ~16,000 years ago to 3,000 years ago. A second wave of migration – as suggested by Hanihara – took place in a time known as the Yayoi period. This ancient population were farmers, and their time in the Japanese archipelago – between 300 and 700 AD – is associated with the introduction of rice cultivation to the country.

A new study by researchers from Dublin, Ireland and Japan suggests that the long held dual-ancestry model needs an update. Their evidence? DNA collected from ancient Japanese bone samples.

Ancient DNA analysis

The research team, led by Shigeki Nakagome, assistant professor in psychiatry in Trinity College Dublin's school of medicine, collected petrous bones – one of the densest bones in the body – from nine Jōmon individuals and three Kofon individuals.

"We extracted DNA from the petrous bones that have been shown to preserve high levels of human endogenous DNA," Niall Cooke, a student in Nakagome's lab and first author of the paper, said. "The range of human DNA content is 20-70%, and the rest are non-human DNA, which could be bacteria or some other environmental DNA."

Extracting DNA from ancient artefacts or human samples is often challenging because, until the sample is sequenced, researchers cannot guarantee how much DNA has been preserved. Luckily for Nakagome and colleagues, they were able to obtain sufficient DNA for sequencing from their samples.

Rewriting Japan's history with DNA code

Using the human DNA and next-generation sequencing methods, the researchers generated whole-genome sequence data from the samples. "These samples represent a time series of data spanning 8,000 years of Japanese prehistory. Using current bioinformatic modeling and statistical approaches, we were able to track the changes in the genomic profile of Japan over time and interpret these changes in the context of the climatic and archaeological record."

The genomic data suggest that a third influx of East Asian ancestry occurred during the Kofun period, which lasted from 300-700 AD, challenging the dual-ancestry model. In addition, the study highlighted a high affinity between the Jōmon samples, which suggests that this population likely spent a prolonged period of time living in isolation.

The study provides a window into the history of Japan's population and the influence of its ancestors. "The movements and interactions of the earliest humans were formative events in shaping the world we live in today and are of interest to a wide variety of disciplines beyond genomics, such as archaeology, anthropology and linguistics to name a few," Cooke said. Japan is a particularly interesting region to study in this context, Cooke added, because its population spent thousands of years seemingly isolated from the rest of Asia prior to rice farming. "The genomic impact of these cultural changes has not been fully explored prior to our study," he said.

A powerful tool to understand the past

Ancient genomics has witnessed significant research interest over recent years due to technological advances in sequencing methods and DNA extraction. While this is great news for the field, it can prove challenging for scientists that are keen to make and publish novel discoveries. "Many papers are published each week that describe a newly sequenced ancient dataset or a shiny new piece of software to analyze them. You need to constantly keep your ear to the ground as you never know what effect someone else’s work may have on your own research and analysis – but it’s a good complaint as it keeps things interesting," Cooke said.

The study is the most comprehensive analysis of the Japanese archipelago published to date, but the researchers show no signs of slowing down in their quest to understand history through DNA analysis. There are many outstanding questions and further areas to explore.

"Ancient genomics on the Japanese archipelago, geographically isolated islands, provides a unique opportunity to observe the magnitude of the effects of major cultural transitions on the genetic makeup of human populations. We will further strengthen this interdisciplinary and highly collaborative research to understand the complex history of the Japanese archipelago," Cooke concluded.

Niall Cooke was speaking to Molly Campbell, Science Writer for Technology Networks.

Reference: Cooke N, et al. Ancient genomics reveals tripartite origins of Japanese populations. Sci Adv. 2021. doi: 10.1126/sciadv.abh2419.