Nav: Home

Archaeological mystery solved with modern genetics

June 20, 2019

Researchers at the University of Tokyo conducted a census of the Japanese population around 2,500 years ago using the Y chromosomes of men living on the main islands of modern-day Japan. This is the first time analysis of modern genomes has estimated the size of an ancient human population before they were met by a separate ancient population.

"Evidence at archaeological dig sites has been used to estimate the size of ancient human populations, but the difficulty and unpredictability of finding those sites is a big limitation. Now we have a method that uses a large amount of modern data," said Associate Professor Jun Ohashi, an expert in human evolutionary genetics and leader of the research team that performed the analysis.

Archaeological mystery

The current theory on human migrations into Japan is that the original inhabitants, the Jomon people, were met about 2,500 years ago by a separate group coming mainly from the Korean Peninsula, the Yayoi people.

Archaeologists have identified fewer Jomon sites from the Late Jomon Period, the era immediately before the Yayoi arrival. Global temperatures and sea levels dropped during that period, which could have made life more difficult for the hunter-gatherer Jomon people.

When the Yayoi people arrived, they brought wet rice farming to Japan, which would have led to a more stable food supply for the remaining Jomon people living with the new Yayoi migrants.

The lesser amount of archaeological remains from the Late Jomon Period could be evidence of an actual population decline, or just that the archaeological dig sites have not yet been found.

Genetic evidence

Ohashi's research team decided to start digging through the human genome to address this archaeological mystery. They began by comparing the Y-chromosome sequences of modern Japanese men to those of Korean and other East Asian men. Y chromosomes are passed on from father to son with very little change over generations, so modern Y-chromosome sequences can reliably estimate the Y chromosomes of men thousands of years ago.

Researchers used DNA samples collected before 1990 from 345 men whose families were from the three main islands of Honshu, Shikoku, and Kyushu in Japan.

The research team identified one group of DNA sequences that only Japanese men had. That unique sequence group likely came from the Jomon people. The researchers identified six sequence groups common to both Japanese men and men with other East Asian heritage (Korean, Vietnamese, Chinese), which likely came from the Yayoi people or other ancestors common to Japanese and East Asian people.

DNA confirms archaeology

Researchers built evolutionary family trees using the Y-chromosome sequences and saw a pattern indicative of a population decrease and sudden increase: a remarkable decrease in the number of ancestral Y-chromosome sequences around 2,500 years ago.

Interestingly, modern Japanese men seem to have a greater percentage of Jomon ancestral DNA in their Y chromosomes than the rest of their genomes.

Previous genetic analyses concluded that modern ethnically Japanese people get about 12 percent of their entire genomes from Jomon ancestors and the rest from Yayoi ancestors. Ohashi's research team calculated that the one group of Jomon sequences they identified accounted for 35.4 percent of the entire Y chromosome, indicating that the specific sequence would have been extremely common in Jomon men.

Since it is easier for a sequence to become common in a small population, this is another indication that the size of the Jomon population decreased during the Late Jomon Period before the arrival of the Yayoi people.

"We hope this method might be useful to confirm other ancient human dynamics not fully explained by archaeology," said Ohashi.
-end-
Research Article

Yusuke Watanabe, Izumi Naka, Seik-Soon Khor, Hiromi Sawai, Yuki Hitomi, Katsushi Tokunaga, Jun Ohashi. 2019. Analysis of whole Y-chromosome sequences reveals the Japanese population history in the Jomon period. Scientific Reports (in press). DOI: 10.1038/s41598-019-44473-z

https://www.nature.com/articles/s41598-019-44473-z

Related Links

Ohashi Lab website (Japanese only): http://www.bs.s.u-tokyo.ac.jp/~humgendiv/

Department of Biological Sciences: http://www.bs.s.u-tokyo.ac.jp/english/

Graduate School of Science: https://www.s.u-tokyo.ac.jp/en/index.html

Research contact

Associate Professor Jun Ohashi
Department of Biological Sciences, Graduate School of Science, The University of Tokyo
7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 JAPAN
Tel: 03-5841-8395
Email: juno-tky@umin.ac.jp

Press Contacts

Ms. Caitlin Devor
Division for Strategic Public Relations, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, JAPAN
Tel: +81-3-5841-0876
Email: press-releases.adm@gs.mail.u-tokyo.ac.jp

Office of Communication, Graduate School of Science, The University of Tokyo
7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 JAPAN
Tel: +81-3-5841-8856
E-mail: kouhou.s@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 2,000 international students. Find out more at http://www.u-tokyo.ac.jp/en/ or follow us on Twitter at @UTokyo_News_en.

University of Tokyo

Related Chromosomes Articles:

Andalusian experts indicate new elements responsible for instability in chromosomes
The researchers state that RNA joins with DNA by chance or because of a disease, the structure of the chromatin, the protein envelope of the chromosomes is altered, causing breaks in the DNA.
Reconstruction of ancient chromosomes offers insight into mammalian evolution
Researchers have gone back in time, at least virtually, computationally recreating the chromosomes of the first eutherian mammal, the long-extinct, shrewlike ancestor of all placental mammals.
Newly discovered DNA sequences can protect chromosomes in rotifers
Rotifers are tough, microscopic organisms highly resistant to radiation and repeated cycles of dehydration and rehydration.
For keeping X chromosomes active, chromosome 19 marks the spot
After nearly 40 years of searching, Johns Hopkins researchers report they have identified a part of the human genome that appears to block an RNA responsible for keeping only a single X chromosome active when new female embryos are formed, effectively allowing for the generally lethal activation of more than one X chromosome during development.
Researchers assemble five new synthetic chromosomes
A global research team has built five new synthetic yeast chromosomes, meaning that 30 percent of a key organism's genetic material has now been swapped out for engineered replacements.
More Chromosomes News and Chromosomes Current Events

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Anthropomorphic
Do animals grieve? Do they have language or consciousness? For a long time, scientists resisted the urge to look for human qualities in animals. This hour, TED speakers explore how that is changing. Guests include biological anthropologist Barbara King, dolphin researcher Denise Herzing, primatologist Frans de Waal, and ecologist Carl Safina.
Now Playing: Science for the People

#534 Bacteria are Coming for Your OJ
What makes breakfast, breakfast? Well, according to every movie and TV show we've ever seen, a big glass of orange juice is basically required. But our morning grapefruit might be in danger. Why? Citrus greening, a bacteria carried by a bug, has infected 90% of the citrus groves in Florida. It's coming for your OJ. We'll talk with University of Maryland plant virologist Anne Simon about ways to stop the citrus killer, and with science writer and journalist Maryn McKenna about why throwing antibiotics at the problem is probably not the solution. Related links: A Review of the Citrus Greening...