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Volume 11, Issue 6

Fine-scale population structure of Japanese provides new anthropological and epidemiological insights Open Access

Abstract

is considered to contribute to gastric cancer and is also used as a marker to trace human migration due to its co-evolution with humans. To understand the recently proposed tripartite model suggesting three ancestral origins for the Japanese population and address the enigma of the high incidence of gastric cancer in Northeast Hondo (Hondo is mainland Japan), we conducted a fine-scale population structure analysis using a large Japanese dataset, including 438 strains from 9 regions based on whole-genome sequences. As a result of fineSTRUCTURE analysis, it was found that in Northeast Hondo is genetically distinct from hspEAsia subgroup 7 (sg7), which is widely distributed elsewhere in Hondo. We named this new subgroup hspEAsia-sg8 (Northeast Hondo). Ancestry analysis using ChromoPainter revealed that, while a large proportion of the genomes of hspEAsia-sg8 strains were painted by donors from their own population, the ancestry components of hspEAsia-sg7 showed a high proportion of Chinese and Korean components, suggesting that they were formed through admixture with continental hspEAsia subgroups. These results align with human genome studies, which indicate an original ancestry component in Northeast Hondo and a higher proportion of East Asian components in West Hondo, supporting the tripartite model. This also suggests novel potential for biogeographic ancestry inference in forensic science, as the genome can distinguish Hondo populations. Furthermore, fixation index analysis comparing the genome of hspEAsia-sg8 with other Japanese hspEAsia subgroups revealed a high number of nonsynonymous mutations in () and (/). Because these genes are involved in cytochrome c maturation and disulphide bond formation, the detected mutations may affect bacterial survival, growth or pathogenicity. This study supports the tripartite model for the formation of modern Japanese people and suggests that the strain of prevalent in the Northeast Hondo region may contribute to the high incidence of gastric cancer there.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): ancestry analysis , gastric cancer , Helicobacter pylori , human migration and population structure
Funding
This study was supported by the:
  • Japan Agency for Medical Research and Development
    • Principle Award Recipient: YoshioYamaoka
  • Ministry of Education, Culture, Sports, Science, and Technology (MEXT) (Award 21K08010)
    • Principle Award Recipient: TakashiMatsumoto
  • Ministry of Education, Culture, Sports, Science, and Technology (MEXT) (Award 21K07898)
    • Principle Award Recipient: JunkoAkada
  • Ministry of Education, Culture, Sports, Science, and Technology (MEXT) (Award 23K24133)
    • Principle Award Recipient: YoshioYamaoka
  • Ministry of Education, Culture, Sports, Science, and Technology (MEXT) (Award 22H02871)
    • Principle Award Recipient: YoshioYamaoka
  • Ministry of Education, Culture, Sports, Science, and Technology (MEXT) (Award 21H00346)
    • Principle Award Recipient: YoshioYamaoka
  • Ministry of Education, Culture, Sports, Science, and Technology (MEXT) (Award 221S0002)
    • Principle Award Recipient: YoshioYamaoka
  • National Institute of Health (Award DK62813)
    • Principle Award Recipient: YoshioYamaoka
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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Fine-scale population structure of Japanese Helicobacter pylori provides new anthropological and epidemiological insights
M Gen 11, 001419 (2025); https://doi.org/10.1099/mgen.0.001419
/content/journal/mgen/10.1099/mgen.0.001419
/content/journal/mgen/10.1099/mgen.0.001419
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