Paleolithic Contingent in Modern Japanese: Estimation and Inference using Genome-wide Data

Area of Science:

• Population Genetics
• Human Origins
• Ancient DNA Analysis

Background:

• The genetic origins of Japanese populations, particularly the ancient Jomon people, remain a subject of debate.
• Jomon people inhabited the Japanese islands independently for over 10,000 years before continental migrations around 2,000 years ago.
• Previous studies using mitochondrial DNA and Y chromosomes provided limited insight into Jomon origins and their genetic contribution.

Purpose of the Study:

• To infer the origin of the Jomon population.
• To estimate the genetic contribution of the Jomon people to contemporary Japanese populations.
• To clarify the ancestral components of modern Japanese by analyzing genome-wide data.

Main Methods:

• Utilized an admixture model with missing Jomon data.
• Analyzed genome-wide data from 94 worldwide populations.
• Inferred Jomon allele frequencies to determine population origins and contributions.

Main Results:

• The Jomon genetic contribution to Ryukyuans was estimated at 54.3% to 62.3%.
• The Jomon genetic contribution to mainland Japanese was estimated at 23.1% to 39.5%.
• Inferred Jomon allele frequencies indicated a Northeast Asian origin for this Paleolithic contingent.

Conclusions:

• The Jomon people represent a significant Paleolithic component in the ancestry of modern Japanese.
• Modern Japanese populations exhibit varying degrees of Jomon genetic admixture, with higher proportions in Ryukyuans.
• The findings support a Northeast Asian origin for the Paleolithic Jomon population, shaping Japanese genetic landscape.