https://www.science.org/doi/10.1126/sciadv.abh2419 

以下に、8000年にわたる日本列島の先史時代および原史時代をカバーする12の新たに配列決定された古代日本人ゲノムを報告する（図1および表1）。我々の知る限り、これは日本列島からの年代を特定したゲノムセットとしては最大のものであり、最古の縄文人個体および初の古墳時代のゲノムデータを含んでいる。我々の解析には、既に発表された5つの先史時代の日本人ゲノムも含まれている：後期縄文時代のF5およびF23、および晩期縄文時代のIK002（12-14）、ならびに九州北西部の弥生文化に関連する2000年前の2人の個体で、これらの骨格遺物は移住者のタイプではなく縄文的な特徴を示しているが、他の考古学的資料は明らかに弥生文化との関連を支持している（15, 16）。この形態学的評価（16）にもかかわらず、これらの2人の弥生人は縄文人よりも現代日本人集団に対する遺伝的親和性が高く、弥生時代後期には大陸集団との混血が既に進行していたことを示唆している（15）。これらの日本人ゲノムを、中央および東部ステップ地域（17, 18）、シベリア（19）、東南アジア（12）、および東アジア（15, 20, 21）にまたがるより大規模な古代ゲノムデータセットと統合することで、本研究は縄文時代の農耕以前の集団の特徴をよりよく理解し、今日の日本列島の遺伝的プロファイルを形成した後続の移住および混血を明らかにすることを目指している。

Here, we report 12 newly sequenced ancient Japanese genomes spanning 8000 years of the archipelago’s pre- and protohistory (Fig. 1 and Table 1). To our knowledge, this is the largest set of time-stamped genomes from the archipelago, including the oldest Jomon individual and the first genomic data from the imperial Kofun period. We also include five published prehistoric Japanese genomes in our analysis: three Jomon individuals (F5 and F23 from the Late Jomon period and IK002 from the Final Jomon period) (12–14), as well as two 2000-year-old individuals associated with the Yayoi culture from the northwestern part of Kyushu Island, where skeletal remains exhibit Jomon-like characters rather than immigrant types but other archaeological materials clearly support their association with the Yayoi culture (15, 16). Despite this morphological assessment (16), these two Yayoi individuals show an increased genetic affinity to present-day Japanese populations compared with the Jomon, implying that admixture with continental groups was already advanced by the Late Yayoi period (15). Integrating these Japanese genomes with a larger ancient genomic dataset spanning the Central and Eastern Steppe (17, 18), Siberia (19), Southeast Asia (12), and East Asia (15, 20, 21), our study aims to better characterize the preagricultural populations of the Jomon period, as well as the subsequent migrations and admixtures that have shaped the genetic profile of the archipelago today.

Fig. 1.

Sampling locations, dates, and genome coverage of ancient Japanese individuals.

(A) Archaeological sites are marked with circles for individual genomes newly sequenced in this study and triangles if previously reported (see Table 1 and table S1). The colors represent three different periods of Japanese pre- and protohistory: Jomon, Yayoi, and Kofun. (B) Each individual is plotted with whole-genome coverage on the x axis and median age (years before present) on the y axis. The nine Jomon individuals are split into five different subperiods on the basis of their ages (see note S1): Initial (JpKa6904), Early (JpOd274, JpOd6, JpOd282, JpOd181, and JpFu1), Middle (JpKo2), Late (JpKo13, JpHi01, F23, and F5), and Final (IK002).

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Associated culture	Sample ID	Date range and median (cal B.P.)	Coverage	mtDNA contamination rate (%)	Molecular sex	mtDNA haplogroup	Y chromosome haplogroup	Ref.
Newly sequenced in this study
Jomon	JpKa6904	8646–8991; 8819	7.51	1.46	XX	N9b3	–	–
	JpOd274	6119–6289; 6204	1.56	1.13	XY	M7a	D1b1d1	–
	JpOd6	5934–6179; 6057	1.18	1.55	XX	N9b3	–	–
	JpOd181	5751–5917; 5834	1.83	0.91	XY	N9b1	D1b1d1	–
	JpOd282	5737–5902; 5820	0.96	1.38	XY	M7a1	D1b1d1	–
	JpFu1	5478–5590; 5534	1.13	2.15	XX	M7a1	–	–
	JpKo2	4294–4514; 4404	2.47	1.44	XX	N9b	–	–
	JpKo13	3847–3978; 3913	1.81	1.50	XX	N9b1	–	–
	JpHi01	3685–3850; 3768	0.88	1.45	XX	M7a1a	–	–
Kofun	JpIw32	1347–1409; 1378	4.80	0.41	XY	B5a2a1b	O3a2c	–
	JpIw31	1303–1377; 1340	1.44	0.63	XX	D5c1a	–	–
	JpIw33	1295–1355; 1325	1.54	0.75	XX	M7b1a1a1	–	–
Previously published
Jomon	F23	3550–3960; 3755	34.82	1.20	XX	N9b1	-	(14)
	F5	–	3.74	2.45	XY	N9b1	D1b2b	(14)
	IK002	2418–2720; 2569	1.85	0.50	XX	N9b1	–	(12)
Yayoi	Yayoi_1	–	0.01	2.92	XX	M7a1a4	–	(15)
	Yayoi_2	1931–2001; 1966	0.07	2.33	XY	D4a1	O	(15)

Table 1. Summary of ancient Japanese data.

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