434: High‑coverage genomes recast Japan's prehistoric demography

Ishiya K et al., PNAS - This episode examines a PNAS study that reports two high-coverage ancient human genomes from mainland Japan (an Initial Jomon >67× and a Middle Yayoi >46×). The genomes enable diploid genotyping, demographic reconstructions, ancestry modeling, and AMY1 copy-number analysis that reshape understanding of Jomon and Yayoi histories. Key terms: ancient DNA, Jomon, Yayoi, AMY1, population history.

Study Highlights:
The authors sequenced two low-contamination, high-coverage genomes from mainland Japan (IY1, Initial Jomon; DO, Middle Yayoi) enabling diploid analyses and CNV inference. Demographic reconstructions show divergent post-LGM trajectories: long-term stability with no expansion in the Jomon lineage and gradual sustained growth in the Yayoi-related ancestral population. Admixture and f-statistics indicate substantial continental Northeast Asian ancestry in the Yayoi individual and genetic continuity between the Yayoi and present-day mainland Japanese. High AMY1 copy numbers (~9–10) in both individuals suggest starch-relevant variation existed before large-scale rice farming.

Conclusion:
High-coverage ancient genomes from mainland Japan reveal contrasting population histories for Jomon and Yayoi lineages and show that elevated AMY1 copy-number variation relevant to starch consumption predates intensive rice agriculture, refining models of Japanese population formation.

Music:
Enjoy the music based on this article at the end of the episode.

Article title:
High-coverage ancient genomes reveal divergent population histories and prehistoric starch-related genetic variation in Japan

First author:
Ishiya K

Journal:
PNAS

DOI:
10.1073/pnas.2606162123

Reference:
Ishiya K., Mizuno F., Gojobori J., Kumagai M., et al. High-coverage ancient genomes reveal divergent population histories and prehistoric starch-related genetic variation in Japan. Proc Natl Acad Sci U S A. 2026;123(30):e2606162123. doi:10.1073/pnas.2606162123

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) – https://creativecommons.org/licenses/by/4.0/

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Episode link: https://basebybase.com/episodes/high-coverage-ancient-genomes-japan

QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-08-06.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript sections describing (1) sampling of two high-coverage genomes (IY1 and DO), (2) authenticity checks and sequencing depth, (3) demographic inferences (PSMC/SMC++), (4) AMY1 copy-number findings, (5) ancestry and admixture contexts, (6) admixture timing, and (7) the dual-structure model; excluded n
- transcript topics: Two high-coverage mainland Japan genomes (IY1 Jomon, DO Yayoi); Petrous bone sampling and ancient DNA authentication; PSMC/SMC++ demographic inferences post-LGM; AMY1 copy-number variation and starch-diet adaptation; Ancestry and continental admixture in Yayoi vs Jomon; Admixture timing via LD decay and related methods

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 5
- claims flagged for review: 0<...