Article

Northeastern Asian and Jomon-related genetic
structure in the Three Kingdoms period of Gimhae,
Korea
HighlightsdEight 1,700-year-old ancient Korean genomes weresequenced to the depths of 0.73–63d

The genetic diversity in the Gaya Kingdom region is linked toJomon-related ancestryddAuthors
Pere Gelabert, Asta Blazyte,
Yongjoon Chang, ..., Kidong Bae,
Jong Bhak, Ron Pinhasi

Correspondence

The genetic diversity of the eight genomes is not linked tosocial statuspere.gelabert@univie.ac.at

There is substantial genetic continuity in Korea since the TK
periodGelabert et al. report the first
paleogenomic data from the Korean
Three Kingdoms period. All individuals
are modeled as an admixture between anorthern-China Bronze Age genetic
source and a Jomon-related ancestry.
Phenotypically relevant SNPs show
genetic continuity with modern Koreans.

Gelabert et al., 2022, Current Biology 32, 1–13
August 8, 2022 ª 2022 Elsevier Inc.
https://doi.org/10.1016/j.cub.2022.06.004

In briefllPlease cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
ArticleNortheastern Asian and Jomon-related
genetic structure in the Three Kingdoms
period of Gimhae, Korea
Pere Gelabert,1,2,15,16,* Asta Blazyte,3,4,15 Yongjoon Chang,5,15 Daniel M. Fernandes,1,2,6 Sungwon Jeon,3,7
 an,1,2
Jin Geun Hong,8 Jiyeon Yoon,9 Youngmin Ko,10 Victoria Oberreiter,1,2 Olivia Cheronet,1,2 Kadir T. Özdog
1,2
10
11
3
12
Susanna Sawyer, Songhyok Yang, Ellen McRae Greytak, Hansol Choi, Jungeun Kim, Jong-Il Kim,13
Choongwon Jeong,14 Kidong Bae,10 Jong Bhak,3,4,7 and Ron Pinhasi1,2,15
1Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
2Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
3Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919,
Republic of Korea
4Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology(UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea
5Daegu National Museum, 321 Cheongho-ro, Suseong-gu, Daegu 42111, Republic of Korea
6CIAS, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
7Clinomics Inc., UNIST-gil 50, Ulsan 44919, Republic of Korea
8Jeonju National Museum, 249 Ssukgogae-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 55070, Republic of Korea
9Gongju National Museum, 34 Gwangwangdanji-gil, Gongju-si, Chungcheongnam-do 32535, Republic of Korea
10National Museum of Korea, 137 Seobinggo-ro, Yongsan-gu, Seoul 04383, Republic of Korea
11Parabon NanoLabs, Inc., 11260 Roger Bacon, Reston, VA 20170, USA
12Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Cheongju 28160, Republic of Korea
13Department of Archaeology and Art History, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
14Seoul National University, School of Biological Sciences, 599 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
15These authors contributed equally
16Lead contact*Correspondence: pere.gelabert@univie.ac.athttps://doi.org/10.1016/j.cub.2022.06.004

SUMMARY

The genetic history of prehistoric and protohistoric Korean populations is not well understood because only asmall number of ancient genomes are available. Here, we report the first paleogenomic data from the Korean
Three Kingdoms period, a crucial point in the cultural and historic formation of Korea. These data compriseeight shotgun-sequenced genomes from ancient Korea (0.73–6.13 coverage). They were derived from twoarcheological sites in Gimhae: the Yuha-ri shell mound and the Daesung-dong tumuli, the latter being themost important funerary complex of the Gaya confederacy. All individuals are from between the 4th and5th century CE and are best modeled as an admixture between a northern China Bronze Age genetic source
and a source of Jomon-related ancestry that shares similarities with the present-day genomes from Japan.
The observed substructure and proportion of Jomon-related ancestry suggest the presence of two genetic
groups within the population and diversity among the Gaya population. We could not correlate the genomic
differences between these two groups with either social status or sex. All the ancient individuals’ genomic
profiles, including phenotypically relevant SNPs associated with hair and eye color, facial morphology,
and myopia, imply strong genetic and phenotypic continuity with modern Koreans for the last 1,700 years.
INTRODUCTION
Recent studies reveal that East Asian populations have genetic
continuity that can be traced back to the Neolithic.1–8 Presentday Koreans are an East Asian group with distinct genetic andlinguistic traits. The Korean language is often classified as an
isolate, having no other closely related modern language,9 andmight have been introduced to the Korean peninsula by millet
farmers during the Neolithic.10 A recent study of the genomesof 1,094 present-day Koreans indicates that they are a

genetically homogeneous group11 due to genetic drift resulting
from possible isolation during the last centuries. However,
Korean maternal and paternal markers suggest that presentday Korean genetic structure was formed through a processthat involved several past admixture events,11,12 with researchshowing that modern Korean genomes can be modeled as a
combination of ancestries belonging to ancient populations
from the West Liao River (China) and the Japanese archipelagoor, alternatively, from the admixture between Miaozigou_MNJapan_Jomon.1 Several recent low coverage captured genomes
Current Biology 32, 1–13, August 8, 2022 ª 2022 Elsevier Inc. 1

Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
ArticleFigure 1. The sites of the Three Kingdoms
period analyzed in this study
Geographical location and images of the sites of
Daeseong-dong and Yuha-ri sites. The image of theYuha-ri shell mound aerial view and the panoramicview of Daeseong-dong tumuli show a generalperspective of the archeological sites.
See also Figure S1 and Data S1.

from Neolithic and Bronze Age Korea10 suggest a significant
level of dilution of this Jomon-related ancestry, which happenedin Korea during the Bronze Age, akin to what is observed in the
Kofun people from Japan, who are contemporary with the Three
Kingdoms (TK) period (57 BCE–668 CE) in Korea.13 However, amajor knowledge gap remains due to the lack of ancient DNA
studies on Koreans from the TK period, when the Korean
ethnicity and culture were formed through the unification of all
TK (Goguryeo, Baekje, and Silla) by the Silla Kingdom. This
was then succeeded by the Korea Kingdom, which endowed
the present-day Korean national identity.
Agriculturally complex societies emerged in Korea during theBronze Age (1,400–300 BCE).14 Both the genetic study ofrice14 and archeological fieldwork10,15 suggest that rice andvarious legumes were introduced from the Liao River region
with their cultivation subsequently intensifying in the Korean
peninsula around 1,300–800 BCE.10,15 From Korea, rice spreadto the Japanese archipelago10,16 together with the genetic ancestries related to Bronze Age northeast Asian populations.13,16
In parallel, iron production arrived in Korea from China during the
4th century BCE17,18 and then expanded to Japan from Korea
during Japan’s Yayoi period (10th century BCE–3rd centuryCE).19 However, it is unclear whether the spread of iron technology in the Korean peninsula was accompanied by human migration or was transferred only via trade and cultural diffusion (STAR
Methods). Recently analyzed ancient genomes from the
Neolithic and Bronze Age periods from Korea10 and the Japanese Kofun period13 suggest a notable dilution of Jomon-related
ancestry in both regions during the 4th–7th centuries CE.
The TK period of Korea saw the extensive development of irontechnology and trade with neighboring populations during whichtime the Korean peninsula was ruled by the aforementioned
TK.17 The Gaya confederacy, which was the last independent
territory, lasted until the 6th century CE before being assimilated
by neighboring Silla.20 Gaya had the most developed iron production and trading infrastructure during the early Korean TK
period, which included the exchange of goods, and possibly
also the movement of people, such as the Wa (Wae) inhabitantsof the Japanese archipelago and northern China.21 This suggests that Gimhae, the political center of Gaya, was an important
trading center, and as such its populace may have included a
2 Current Biology 32, 1–13, August 8, 2022

level of cosmopolitanism, similar to thatfound in a recent genetic study of theancient inhabitants of Rome.22
At the end of the 3rd century CE, archeological sites from the Gimhae area
exhibit changes in funerary rituals that
include the replacement of stone-lined
pit tombs and jar coffin tombs withwooden-chambered burials.23 Also introduced during thisperiod was a mortuary practice that involved human sacrifices(STAR Methods), the inclusion of grave goods such as weapons,mirrors, and other items made of bronze and iron, and severed
heads of livestock that accompanied the deceased.21 The
most important excavated center of the Gaya culture is amassive 3,700 m2 burial complex of rulers in Daeseong-dong
in Gimhae, dated to the 1st–5th centuries CE. It consists of
219 tombs, 69 of which are complexes with multiple burials
that include human sacrifices and various mortuary goods
such as pottery, iron armors, and items related to archery.24,25
More modest burials are found throughout the TK period in shellmounds in the same Gyungsangnamdo province, including
areas such as Busan and Gimhae. None of these shell mounds
include human sacrifices or a family grave rather a single burial.26
RESULTSWe screened 27 petrous bones or teeth obtained from 22 individuals from two archeological sites in Gimhae City, Gyeongsangnam-do: Daeseong-dong and Yuha-ri, both dated to the
4th–5th centuries CE (Figure 1; Figures S1A–S1D).27 The genomic
libraries of eight individuals had over 7% of sequencing reads
that aligned to the human reference genome (range from 7.3%
to 68.9%; Data S1A), with whole-genome coverage depths between 0.73 and 6.13 (Table 1). All seven Daeseong-dong individuals were associated with specific mortuary practices linked
to social status, specifically, main burials (grave owners) and human sacrifices (STAR Methods). Only the single grave of a child(AKG_3420) from the Yuha-ri shell mound (Table 1; Data S1A;
Figures S1B and S1C) could not be assigned any social status
due to the lack of mortuary elements. All eight genomes exhibited typical deamination patterns28 at read ends, with deamination rates ranging between 12% and 33% (Data S1A). Five of
the individuals were identified as females and three as males
based on sex chromosomes and autosome depth coverage ratios (Data S1A). We generated two base-calling sets with thesegenomes: first, we called pseudo haploid positions of the
1,240k dataset29 (a standard call set that is used in most downstream analyses involving ancient samples), and second, we
generated imputed diploid calls that were used to identify

Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
ArticleTable 1. Main descriptive information of the eight Korean Three Kingdoms period individuals
Individual

Cluster

mtDNA haplogroup

Y- haplogroup

Date

Typology

Cover age

AKG_10203 (_)

Korea-TK_2

D4e2

D1a2a1

350–500 CE

Daeseong-dong-burial

1.583

AKG_10204 (_)

Korea-TK_1

D4e2a

O1b2a1a2a1b1

350–500 CE

Daeseong-dong-sacrifice

0.793

AKG_10207 (\)

Korea-TK_2

B4c1a1a1a–

350–500 CE

Daeseong-dong-sacrifice

6.113

AKG_10209 (\)

Korea-TK_1

M10a1b–350–500 CE

Daeseong-dong-sacrifice

1.783

AKG_10210 (\)

Korea-TK_1

F1b1a1a1–

350–500 CE

Daeseong-dong-sacrifice2.723

AKG_10218 (_)

Korea-TK_1

D4a1

O

300–500 CE

Daeseong-dong-burial

0.643

AKG_3420 (\)

Korea-TK_1

D4a1

–

300–500 CE

Yuha-ri shell mound3.203

AKG_3421 (\)

Korea-TK_1

D5a2a1a1–

300–500 CE

Daeseong-dong-sacrifice

0.743

See also Data S1.

haplotype-based connections with present-day populations,following previously described methodologies.30
There were no identifiable close familial relationships among
the sequenced individuals, given the normalized proportion of
non-matching alleles (P0) being greater than 0.906, indicating
no relationship as close as second degree.31 Two applied runsof homozygosity (ROH)-calling methods indicate that the ancient
Korean Gimhae genomes (AKGs) show only a small fraction of
the genome being homozygous (Figures S2A and S2B). All the
AKG individuals show values located within the diversity of present-day populations. From the Korean individuals, AKG_10207
shows the highest amount of long ROH, pointing to more recent
inbreeding.
Uniparental markers
All individuals had typical East Asian mitochondrial DNA (mtDNA)
haplogroups (Table 1; Data S1A), D (n = 5), B, F, and M, when we
determined the haplogroups from the consensus. All of theseprevail among present-day Koreans,9,12 with the most common
being haplogroup D4, which we identified in four of the eight
AKGs. This haplogroup was also common among ancient Japanese Yayoi farmers but was absent in the Jomon.32 Out of thethree male individuals, we successfully called Y chromosome
haplogroups (Table 1; Data S1A) for two: AKG_10203 (D1a2a1)
and AKG_10204 (O1b2a1a2a1b1). The third male, AKG_10218,
due to his lower coverage, was assigned to the major haplogroup O (Table 1; Data S1A). Haplogroup O is the most common Y haplogroup in present-day Korea and is shared by morethan 73% of Korean males,9 whereas haplogroup D is morecommon in the present-day Japanese population.33
Population genetics
A principal component analysis (PCA) was carried out using
modern East Asian individuals restricted to positions fromthe human origins (HOs)30 panel of SNPs (Data S1B). The
eight Gaya individuals were projected onto their principal components (PCs) alongside other previously published ancient individuals.1–8,10,13,34–36 A list of the individuals used for population

genetic analysis and their groupings and labels can be found in
Data S1B. The results showed the presence of four differentiatedgenetic groups in ancient East Asia: (1) Amur River, (2) northern
China, (3) southern China and Taiwan, and (4) Jomon-related
populations (Figure 2A; Data S1B). The eight individuals fromthe Korean TK period are positioned within the diversity of East
Asian individuals, particularly close to present-day Koreans
and Japanese, ancient Kofun from Japan, and several Neolithic
Koreans (Figure 2A). However, two individuals (AKG_10203 andAKG_10207) clustered rather closely with present-day Japaneseand closer to Japanese Jomon individuals (Figure 2A), a patternthat distinguishes them from the other six individuals. Next, we
further explored the ancestral compositions of the eight individuals using a pairwise qpWave analysis37 to formally identify individuals who might not form a clade with the others. When using a
set of ten outgroup populations described in the STAR Methods
section, which included the ancient Japanese Jomon, most individuals formed a clade with each other. However, AKG_10203
and AKG_10207 did not form a clade with any of the remaining
individuals. Therefore, we separated the eight TK individuals
into two groups: (1) the two outliers (Korea-TK_2) and (2) the remaining six individuals (Korea-TK_1) (Figure S2C). One individualfrom the Korea-TK_1 cluster (AKG_3421) is positioned slightly
toward Korea-TK_2 in the PCA and does not form a clade withthe five other individuals from Korea-TK_1 (Figure 2A). This
individual is nevertheless grouped as part of Korea-TK_1, as all
statistics f4(Mbuti, Japan_Jomon; AKG_3421, Korea-TK_1_individual) for each individual within Korea-TK_1 have a Z scorebelow |2.45|. The same pattern is observed when comparing
this individual with Yellow_River_LBIA. None of the comparisonsshow a Z score higher than |2.59| (Data S1C). Lastly, theobserved clustering pattern could not be linked to mortuary
status, as there are individuals within both Korea-TK_1 and Korea-TK_2 that were part of either grave owners or sacrificial
burials (Table 1).
Next, we assessed the genetic structure of the Gimhae Korean
individuals with ADMIXTURE,38 which included 2,283 presentday and ancient individuals (Figure S3), and a pruned SNP set
Current Biology 32, 1–13, August 8, 2022 3

Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
ArticleFigure 2. Three Kingdoms period Korean
genomic context

A(0.7%)(A) Principal components analysis performed withpresent-day East Asian populations and 96 projected ancient individuals, including eight TK
period Korean samples. We used principal components, PC1 and PC2, that account for (1.2%)and (0.7%) variation, respectively.
(B) ADMIXTURE plot (K = 12) of the most representative populations used in the analyses show ashared genomic profile across ancient and modern East Asians, including TK Koreans and present-day Koreans.
See also Figures S2 and S3 and Data S1.
Korea-TK_1
Korea-TK_2(1.2%)

K=12

B

of the HO dataset (extended methods). At K = 12, the Korea-TK
individuals are best represented by three main genetic components: two shared with the majority of other ancient and modern
East Asian populations, and the third represented mostly as theJapanese Jomon (Figure 2B; Figure S3). The analysis also suggests that the Korea-TK_2 individuals, AKG_10203 andAKG_10207, may have more Jomon-related ancestry than theother six TK individuals. This component is absent in presentday Koreans, but it is present among present-day Japanese.

Differential genetic affinities of the Three-Kingdomsperiod Koreans
We computed outgroup f3 statistics that measure the amount ofshared genetic similarity between populations by comparing Korea-TK_1 and Korea-TK_2 with ancient (Data S1D) and presentday populations (Figures 3A and 3B; Data S1D). The results
indicate that Korea-TK_1 shares the highest affinity to modern
Korean, Japanese, and present-day Han populations and ancient
populations from the Liao and Yellow Rivers, as well as Kofun. Korea-TK_2, however, appears to be closer to the present-day Japanese, the ancient Kofun, and other ancient Japanese populations
with Jomon ancestry (Figures 3A and 3B; Data S1D).
4 Current Biology 32, 1–13, August 8, 2022

In order to observe differential affinities
between Korea-TK_1 and Korea-TK_2,
we calculated the statistic f4(Mbuti,Pop
A; Korea-TK_1, Korea-TK_2), generating
30 combinations with the highest |value|(Figure 3C; Data S1C). We observed acloser relationship of Korea-TK_1 to the
populations from the Neolithic andBronze Age Liao and Yellow rivers innorthern China and other historical populations from Nepal, Vietnam, and China.
We identified allelic share between
Korea-TK_2 and ancient populations
from Korea, Japan, and the Amur
River basin. However, the test f4(Mbuti,
Korea-TK_1; Yellow-River_LBIA, LiaoRiver_BA) yielded statistically nonsignificant results (Z < |3|), and, therefore, wecannot detect a clear source for the north
Asian Bronze Age ancestry, which follows
the same pattern of f4(Mbuti, X; YellowRiver_LBIA, Liao-River_BA), where X are
the different Korean Neolithic individuals from Robbeets
et al.10 (Data S1C), and with no excessive allele sharing toward
these two populations (Z < |3|). Although Korea-TK_2 has significantly more Japan_Jomon-related ancestry than Korea-TK_1(f4(Mbuti, Japan_Jomon; Korea-TK_1, Korea-TK_2), Z = 14.31),
the nonsignificant statistic f4(Mbuti, Korea-TK_2; Korea-TK_1,
Japan_Jomon) (Z = 1.40) suggests that Korea-TK_2 does
not share statistically more derived alleles with Korea-TK_1
or Japan_Jomon. Additionally, we observe significantly moregene flow between Korea-TK_1 and Liao_River-BA/
Yellow_River-LBIA over Korea_MN (Z = |3.38| and |4.37|, respectively). Neither test is significant for Korea-TK_2 (|1.29| and |0.97|
respectively) (Data S1C). Taking into consideration the low
coverage of the ancient Korean individuals from Robbeets
et al.,10 we merged three Middle Neolithic individuals with thehighest sequence coverage from the sites of Yeondaedo andGadeokdo (Changhang) islands with up to 20% Jomon-related
ancestry (GDI002, GDI008, and TYD007) as Korea_MN to reducebias related to data sparsity. We also included individual TYJ001
from Korea_LN_Yokchido, which has more Jomon ancestry inRobbeets et al. analyses.10 The remaining samples from thisstudy10 were not included, as they all have low coverage.
Furthermore, Korea-TK_1 is more closely related to Korea_MN

Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
ArticleFigure 3. f-statistics(A and B) f3-statistics of present-day Asian populations with Korea-TK populations Korea-TK_1(A) and Korea-TK_2 (B) in the combinationf3(Mbuti; Korea-TK,X). Korea-TK_2 has more affinity to the Japanese than to Koreans. KoreaTK_1 is associated with populations from Korea,
Japan, and eastern China, whereas Korea-TK_2
has the closest affinity to the Japanese.
(C) f4-statistics emphasize differential genetic affinities of Korea-TK_1 and Korea-TK_2 using thestatic f4(Mbuti, X; Korea-TK_2, Korea-TK_1). Korea-TK_2 has the closest affinity to the ancientJapanese populations with substantial Jomon
ancestry, and Korea-TK_1 shows affinity to Liaoand Yellow River Bronze Age populations. The
colors in the sample name denote the region as
follows: dark red, Liao River; orange, Yellow River;
red, Southern China and Taiwan; purple, Amur
Basin; gray, Nepal; black, Russia (Russian Far
East, Siberia); light brown, Vietnam; and green,
Japan.

than to Jomon-related ancestry (f4(Mbuti, Korea-TK_1;
Korea_MN, Japan_Jomon), Z = 8.10), whereas Korea-TK_2
has the inverse correlation (Z = 2.30). When compared with
Korea_LN_Yokchido, both groups have more shared derived
SNPs with Korea_LN_Yokchido, without being significant( 0.000960, Z = 2.50 for Korea-TK_1 and 0.000347, Z =0.76 for Korea-TK_2). The little difference in this case is probably linked with the larger Jomon affinity of Korea_LN_Yokchido.
Lineage analyses based on ancestry composition
We applied qpAdm37 to investigate the overall ancestry composition of the two groups and to confirm the observed Jomonrelated ancestry. We used a total of ten possible sources thatwere close to Korea-TK, both geographically and temporally.
We also included Korea_MN from Robbeets et al.10 as the only
source of pre-TK Korean ancestry due to the fact that mostancient Korean genomic data from Robbeets et al. do not pass
our qpAdm threshold of 150,000 SNPs; therefore, they were
excluded from this analysis to ensure unbiased and more

confident admixture models. Applying a
two-step model competition approach,39
Korea-TK_1 could only be modeled ascomposed of 93% ± 6% ancestry related
to Yellow_River_LBIA and 7% ± 6%
related to Japan_Jomon (p = 0.42),
whereas Korea-TK_2 could be modeledusing a single model as Korea_MN (p =0.06) (Figure 4; Data S1E). To quantify
the amount of Jomon-related ancestryin Korea-TK_2 and how it compareswith Korea_MN, we modeled both using
the same sources as above, but thistime with Korea_MN as one of the test
populations as well. The results showthat Korea-TK_2 and Korea_MN could
be modeled with Liao_River-BA as theproxy for northern China ancestry(66% ± 7% and 70% ± 8%, respectively), with the remaining
ancestry from a Jomon-related source (34% ± 7% and 30% ±8%, respectively) (Data S1E). The amount of Jomon-related
ancestry in Korea_MN is, therefore, about twice as much as
the percentage reported in the original publication (average of
Yeondaedo and Changhang individuals 15%10) but is arguably
a more powerful estimate due to the substantial increase in data
used as the result of merging these individuals into a single population. In order to compare our genomes with the previously reported analyses on Japanese ancient individuals,13 we repeatedthe qpAdm analysis using the same right and left set (Data S1E),
which indicates that Korea-TK_1 can be modeled as 28% NEasia, 63% Han, and 8% Jomon. Korea-TK_2 can be modeled as
32% NEasia, 43% Han, and 25% Japan Jomon. In comparison
with the contemporary Japan_Kofun, Korea-TK_2 shows more
Jomon ancestry than Japan_Kofun, which is compensated byless Han ancestry.13
Based on the evidence that Korea-TK_2 could be modeled asa single source as Korea_MN, suggesting genetic continuity inCurrent Biology 32, 1–13, August 8, 2022 5

Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
ArticleFigure 4. qpAdm analysis
Results of the qpAdm analyses at a group level(TK_1 and TK_2). We represent the ancestral components of the eight TK individuals by their minimum
number of source populations. The complete results
are displayed in Data S1E. The shell represents theindividual from the shell mound, whereas crowns
represent the grave owners.

the Korean peninsula (Data S1E), we tested the possibility of Korea-TK_2 representing the source population for Korea-TK_1, in
addition to other north-China related sources. This led to theqpAdm result of Korea-TK_1 modeled as 87.5% Yellow_RiverLBIA and 12.5% Korea-TK_2. These proportions are very similar
to the proportions when Korea_MN is used as a source (Data
S1E). However, we cannot discard the scenario in which Korea-TK_2 represents a recent admixture between Korea-TK_1
or a population with similar ancestry and a Jomon-related
source.
When we performed the same qpAdm modeling on an individual basis, we found that four of the six individuals in the KoreaTK_1 cluster could be modeled with a single source, as
Yellow_River-BA or Liao_River-BA, whereas individuals
AKG_10218 and AKG_4321 could be modeled with a single
source as Korea_MN/Japan_Kofun and Korea_MN, respectively(Data S1F). These models, however, might be overrepresenting
the Jomon-related ancestry in these individuals, as the statistics
f4(Mbuti, Japan_Jomon; AKG_3421/AKG_10218, Other_KoreaTK_1_Individual) suggest nonsignificant affinities to Japan Jomon when compared with the other Korea-TK_1 individuals(Z < |2.4|) (Data S1C). Additionally, we did not observe a clear genetic affiliation of Korea-TK_1 to either the Yellow_River-BA or
Liao_River-BA population as a close Chinese source.
The findings of Robbeets et al.10 restrict the Jomon presencein Korea to the Neolithic. Furthermore, given the very low
coverage of the Bronze Age individual from Taejungni (9,747
SNPs), it is possible that the qpAdm analyses presented in Robbeets et al.10 lacked the statistical power for simpler one-way
models to be rejected and that this individual did, in fact, have
Jomon-related (or other) ancestry.39 Indeed, we obtained biased
results by randomly subsampling our Korea-TK_2 individual
AKG_10203 to four independent sets of 10,000 SNPs andmodeling it with both allsnps: YES/NO options. We foundthat for each replicate, between five and eight populations
worked as one-way models with p values above 0.05
(0.064 < p < 0.924; Data S1F), whereas AKG_10203’s full SNP
set models required substantial amounts of Jomon-related
ancestry above 30% (Data S1F). It is also worth noting that allmodels with subsampled data using two or three source populations failed due to their having standard errors higher than theancestry amounts (higher than 1 or p value < 0.05).
We also investigated with ancestry modeling the similarity between the Korea-TK and the contemporaneous Japan Kofun genomes. When not considering either of the two TK groups as
possible sources, the Japan Kofun individuals, dated to 600–
700 CE, can be modeled as requiring a source of northern China
ancestry related to Liao_River-BA (78% ± 7%) and another
6 Current Biology 32, 1–13, August 8, 2022

source carrying Jomon-related ancestry (22% ± 7%) (Data
S1E), revealing that these individuals had less Jomon ancestry
than Korea-TK_2 but more than Korea-TK_1. The statisticf4(Mbuti, Japan_Jomon; Japan_Kofun, Korea-TK_2) supports
this finding (Z = 4.01). When using Korea-TK as possible sources,
Japan Kofun could be modeled as 71% ± 10% Korea-TK_2 and
29% ± 10% Yellow-River_LBIA (Data S1E).
Lastly, we applied qpAdm to model present-day Koreans using the same ancestry sources that were used for modeling theancient Koreans, including the two TK groups as separate
possible sources. We found that the simplest working models
were with a source related to Yellow_River-LBIA (p = 0.75)(Data S1E). However, when present-day Koreans were modeledusing each Korea-TK period individual as a source, at least threeout of the six individuals from Korea-TK_1 were sufficient as asingle source, just like Yellow_River-LBIA (0.15 < p < 0.69)(Data S1E).
We estimated the dates of the admixture events identified
through the qpAdm analyses using DATES.40 No combinations
yielded significant results for Korea-TK_2, and only KoreaTK_1 modeled as the admixture of Yellow_River-LBIA and Japan
Jomon yielded significant results (Data S1G), modeled as 47.93
generations with a CI of 13.7 generations. Assuming 28 years per
generation, this corresponds to an admixture that happened
1,400–600 BCE.40
Genetic and phenotypic continuity
The results obtained with fineSTRUCTURE and identity-bydescent (IBD) analyses, which were based on the imputed
genotypes dataset (STAR Methods), support a clear separation between the Korea-TK_1 and Korea-TK_2 groups.
FineSTRUCTURE suggested that the Korea-TK_1 individuals
were related to present-day Koreans and Han Chinese (Figure 5A). On the other hand, Korea-TK_2 individuals had a closer
genetic affinity to present-day Japanese, Japan Kofun, and theJapan Jomon representatives (Figures 5A and 5B; Data S1H)
than modern Korean or Chinese. The shared IBD between the
Korea-TK_1 and Korea-TK_2 individuals with modern andancient populations show clearly differentiated trends. The
normalized length of the shared IBD between the Korea-TK_2
and the Japan Jomon is 3.37 on average, which is 5.16 times
higher than that of the Korea-TK_1 (0.65). When comparedwith present-day populations, we observe a similar trend. Korea-TK_2 and modern Japanese share 2.52 per individual, while
Korea-TK_1 shares 0.51. The shared average length withmodern Koreans is more similar between both groups: 0.67 for
Korea-TK_2 and 0.38 for Korea-TK_1, which suggests that the
Jomon-related ancestry explains the observed differences,Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
Article
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Figure 5. Imputed genotypes analyses(A) fineSTRUCTURE. The plot shows that Korea-TK_2 clusters with modern Japanese and JpIw32 individuals, whereas Korea-TK_1 shows connections with Han
Chinese and Korean individuals.
(legend continued on next page)

Current Biology 32, 1–13, August 8, 2022 7

Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
Articleshowing more connections between Japan Jomon and KoreaTK_2. Very few IBD blocks have been observed between TK individuals (Figure 5C; Data S1H). This can be explained by the low
coverage of our individuals, which does not allow for the assessment of clear tendencies.
In order to use our data to explore possible differences frompresent-day Koreans, we selected 160 relevant variants thatreflect morphology as well as other characteristics from the literature (Data S1I) to estimate whether Koreans changed phenotypically in the last 1,700 years. The small sample size did not enable
us to draw any statistically significant inferences; thus, we limited
our analysis to the presence/absence of the relevant variants.
Based on our eight individuals, we conclude that all the relevant
variants present in the modern Korean population were alreadyestablished in the Korean TK period at least 1,700 years ago,showing deep genetic continuity (Data S1I). Some East Asian
traits were detected among all the analyzed individuals, including
dry earwax, no body odor (SNP -rs17822931),41,42 and no homozygous alleles associated with excess sweating.43 Seven of
the eight individuals carried the canonical ectodysplasin A receptor (EDAR) gene variant (rs3827760) associated with Asian hairstraightness/thickness44 (except AKG_10207), which is homozygous in six of them (Data S1I). The HirisPlex system,45 a phenotype prediction protocol, predicted that all the individuals had
brown eyes, most likely black hair, and a variation in skin tone
ranging from intermediate to darker (Data S1H), a result whichis also in agreement with the phenotypes of present-day Koreans.
Surprisingly, the genetic makeup of the eight Gaya Korean individuals also included a common present-day Korean healthphenotype: all individuals have multiple (four or more) ‘‘susceptibility-to-myopia-risk’’ alleles. Myopia is highly prevalent inmodern Korea, reaching values of 95% in adult males fromSeoul.46 In several individuals we detected variants associatedwith alcohol flush reaction.47,48 Also, all individuals had, on
average, at least one homozygous balding risk allele or eight
androgenic alopecia risk variants,49 with individual AKG_10209
having five of these homozygous risk alleles. The eight genomes
also captured the diversity of SNP profiles related to eyelidmorphology, hair curliness, and other phenotypic features (Figure 6; Figure S4). The female individual, AKG_10207, from the
Korea-TK_2 group, stood out with a reference allele ‘‘A’’ in the
EDAR gene (rs3827760) (Data S1J), which is generally uncommon in East Asians, except for the Jomon in Japan. Although it
is difficult to assess hair morphology, in addition to reference
allele homozygosity in EDAR (rs3827760), AKG_10207 had multiple SNPs related to hair curliness, two of them homozygous,
suggesting she may have had wavy hair, whereas the other individuals most likely had straight hair.
All the phenotypic features assessed by the HirisPlex phenotype prediction protocol and our selected forensically relevant
facial-morphology-related SNPs were independently validated
by the Parabon NanoLabs (https://snapshot.parabon-nanolabs.
com/) (STAR Methods). Unfortunately, due to the poor preservation of all TK individuals’ skeletal remains, the standard skull-based facial reconstruction was not possible at the time of thisstudy. Therefore, to illustrate our analysis beyond the basic
phenotypic features and to comprehensively reconstruct the
facial characteristics of the studied individuals, we used Snapshot facial prediction based on the imputed calls, which, again,
showed phenotypic diversity indistinguishable from the present-day Koreans (Figure 6; Figure S4).
DISCUSSION
Our study presents several novelties in comparison with the previous research on Korean genomes. First, we present samples with
sufficient coverage to obtain confident statistics that permit precise comparison of the retrieved samples with the remaining available datasets. Second, we confirm the presence of Jomon
ancestry in Korea until the 5th century CE. Third, we demonstratewith confident qpAdm results that present-day Koreans are closely
related to the TK period individuals. Finally, we report the existenceof two genetic groups that do not present the same genetic history,
pointing toward population diversity in the past.
Several recent studies have reported genomic data of ancientindividuals from China, Japan, Mongolia, Philippines, andVietnam1–4,6,8,10,50 and also ancient low coverage capture datafrom the southeastern Korean region close to Gimhae.10 Here,
we provide shotgun data from the Korean TK period, which allowed us to genetically characterize the population of Gimhae atthat time, as well as to shed light on the genetic history of Korea.
However, the lack of Neolithic and Bronze Age high-coverage
Korean samples does not allow the in-depth assessment of the Jomon-related diversity dilution in the Korean peninsula. Therefore,
future studies with more samples from these protohistoric periods
will be interesting for understanding the Korean TK period genetic
dynamics. Moreover, it should be noted that all the currently available ancient Korean genomes, including those presented in thisstudy, are only from the southeastern part of Korea and may notreflect the general picture of the origin, migration, and admixtureof ancient and modern Koreans.
The genetic variability seen among the Gaya TK period individuals points to population diversity in the Gimhae region during
this time. It is interesting that some individuals are genetically close
to previously reported Neolithic individuals from the Korean
coastline,10 while others do not share this affinity, pointing toward populations with different genetic histories. The individuals of
the Korea-TK_1 cluster had comparable amounts of Jomon
ancestry with Korean Middle Neolithic Ando population, but
not Yeondaedo or Gadeokdo (Changhang). This can be explainedby Yeondaedo and Gadeokdo (Changhang) islands being not only
physically closer to Japan10 but also genetically closer, as KoreaTK_2 affinity may suggest.. This suggests that the presence ofJapan Jomon ancestry in Korea varied over time. Although in Gimhae we observed diversity within the same area, previous Neolithic
data suggest geographic differences in Jomon-related ancestry.10
Individuals of the Korea-TK_2 cluster share more Jomon-related
ancestry than contemporary Japan Kofun-related ancestry, which(B) Shared IBD segments (>1 cM). Korea-TK_2 shows the highest number of shared IBD with Japan Jomon, whereas Korea-TK_1 shows very little IBD with therest of the dataset.
(C) IBD (cM) shared among the pairs of TK individuals. Even though none of the pairs indicate familial relationship, the highest IBD sharing is between AKG_10207
and AKG_10210.

8 Current Biology 32, 1–13, August 8, 2022

Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
ArticleFigure 6. Facial predictions of Three Kingdoms period Korean individuals
Face reconstruction of the Korean TK period individuals AKG_10218, AKG_10203, AKG_3420,
and AKG_10207 shows a diversity in phenotypicfeatures commonly observed in present-day Koreans. Face morphology differences are emphasized relative to a baseline face prediction madeusing sex and ancestry. The facial reconstruction
was performed with the imputed calls dataset.
See also Figure S4 and Data S1.

also evidences the existence of differential Jomon-related
ancestry at a regional level. This would be primarily influenced by
the amount of incoming northeastern China ancestry.
Similarly, we demonstrated that the reported lack of Jomonrelated ancestry in the previously published single Bronze Age
Korean genome may not be statistically supported with such
low amounts of data10 and with the analytical tools used (i.e.,
qpAdm). Nevertheless, our results show that Jomon-related
ancestry persisted at high levels in South Korea until at least
the TK period, around 500 CE. Moreover, the fact that Jomon
has not been identified as a dominant cultural component in
the Gimhae area at any time and that present-day Koreansshow high genetic homogeneity with no Jomon-related ancestry
implies that the Korea-TK populations bearing Jomon-related
ancestry were probably completely absorbed by incoming populations originating from northern China who entered along the
Korean peninsular coastlines, leading to the genetic homogeneity observed in present-day Koreans. A recent archeologicalreport51 on the southeastern islands (Yokji-do and Yeondaedo)of Korea confirms the presence of Jomon in Korean territory, citing finds like obsidian tools, which were traded before the Bronze
and Iron Ages. These artifacts originated from Koshidake(obsidian source, Nagashaki in Japan) and indicate Gaya’s
cosmopolitanism and an established trade network with the Japanese archipelago up until that time.51 The evidence of Jomonrelated ancestry during the Neolithic suggests that this ancestry
would be local in Korea and probably not associated with the Jomon culture from Japan. Therefore, pan-peninsular paleogenomics is required to precisely resolve the origin and extent ofJomon admixture in the whole Korean peninsula. With the current data, we are not able to point toward specific source populations in northern China. In the near future, larger sample sizes
and more advanced informatic tools based on individual genetic
histories may allow us to differentiate between these similar populations to uncover the origin of this ancestry.
Despite the genetic variability and the two genetic subgroups
identified among the eight TK period Gaya individuals, we could

not point out any consistent phenotypic
differences between the groups. Instead,our phenotypic analysis suggests strong
genetic continuity in modern Koreans,including important SNPs, such as an intronic variant rs1534480 in PLB1 and the
ABCC11 G538A (rs17822931), whichhave already been found in Tianyuan
man and suggest the genetic continuityof these variants in East Asia for the last 40,000 years.52 The
analysis of the diploid calls also evidences a connection between
Korea-TK_1 and modern Koreans as well as Korea-TK_2 andmodern Japanese. However, the relatively low coverage of oursamples has proven insufficient for high-resolution IBD analyses.
Our results also suggest that the grave owners and the humansacrifices were not associated with distinct genetic substructures, as both the Korea-TK_1 and Korea-TK_2 groups included
individuals associated with both burial types. However, the information inferred from the artifacts was limited due to tomb looting
and poor grave preservation. For example, the male AKG_10203
was identified as a grave owner, possibly a warrior class or alower-class noble, while the female AKG_10207 was possibly ahuman sacrifice. The remaining gilt bronze artifact and arrow
quiver ornaments are insufficient to accurately determine the social status of AKG_10203. Due to these issues, we could not
identify the owner of each grave, which is also the case for
AKG_10207, who was a sacrifice for a possibly high-class noble,
as indicated by the finding of an iron spear and bronze mirror.25
Among the Korea-TK_1 group, AKG_10218 was the grave
owner, while the rest were sacrifices for other grave owners.
Our evidence suggests that the ruling class of the Gaya Confederacy of the 5th–6th Centuries CE are characterized by genetic
diversity that may point toward a cosmopolitan society.
It is also notable that we could not ascertain the relationshipbetween sex and social status in the Daeseong-dong tumuli.
Even though the two grave owners were males, the human sacrifices in our study were associated with both sexes.
STAR+METHODS
Detailed methods are provided in the online version of this paper
and include the following:d KEY RESOURCES TABLE
d RESOURCE AVAILABILITY

B Lead contact

Current Biology 32, 1–13, August 8, 2022 9

Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
ArticleB Materials availability
B Data and code availabilityd EXPERIMENTAL MODEL AND SUBJECT DETAILSB Archeological context
d METHOD DETAILSB Sampling
B DNA extraction, library preparation, and sequencing
d QUANTIFICATION AND STATISTICAL ANALYSIS

B Bioinformatic analysis
B Facial prediction and ancestry analysis
B Data authenticity
B Uniparental markers
B Population genetic tools
B qpWave and qpAdm
B Dates
B Imputation
B Homozygosity
B Chromosome painting analysis (fineSTRUCTURE)
B IBD analyses
B Phenotypic variant analysis
SUPPLEMENTAL INFORMATION
Supplemental information can be found online at https://doi.org/10.1016/j.
cub.2022.06.004.
ACKNOWLEDGMENTS
We would like to thank Kendra Sirak and Éadaoin Harney for their help and discussions, Yeonsu Jeon for assistance in aesthetic visualization, Dan Bolser
and Whan-Hyuk Choi for giving critical feedback with editing, and Jaesu
Bhak for editing the manuscript. We are grateful to Gayoung Park (Universityof Washington), Su-Whan Kim (Gyeongnam Provincial Government, Gaya Cultural Heritage Division, Korea), Seong Won Cho (Pukyung National Museum),and Weon Young Song (Daeseong-dong Tombs Museum) for their help withthe archeological context and information. This work was supported by the
Promotion of Innovative Businesses for Regulation-Free Special Zones fundedby the Ministry of SMEs and Startups (MSS, Korea) (P0016193). This work wasalso supported by the Establishment of Demonstration Infrastructure for Regulation-Free Special Zones funded by the Ministry of SMEs and Startups (MSS,
Korea) (P0016191). This work was partially supported by the research project
funded by the Ulsan City Research Fund (2.201052.01) of UNIST (Ulsan National Institute of Science & Technology), the U-K BRAND Research Fund(1.200108.01) of UNIST (Ulsan National Institute of Science & Technology),
the Ulsan City Research Fund (1.200047.01) of UNIST (Ulsan National Instituteof Science & Technology), and the Clinomics internal fund. This work was also
funded by the internal funding of the National Museum of Korea. The Korea
Institute of Science and Technology Information (KISTI) provided us with the
Korea Research Environment Open Network (KREONET). Lastly, the project
was funded by the Research Plat-form MINERVA (AGB326800) of the University of Vienna.
AUTHOR CONTRIBUTIONS
D.M.F. and R.P. collected the samples. J.G.H., J.Y., Y.K., and S.Y. provided
the samples and archeological and historical context. D.M.F., O.C., K.T.Ö.,
S.S., and V.O. performed the lab work. P.G., A.B., S.J., H.C., and D.M.F.
analyzed the data. E.M.G. organized face predictions for ancient genomes.
P.G., A.B., D.M.F., J.B., and R.P. wrote the paper with input from all co-authors. Y.C. and K.B. organized sampling and archeological data.
DECLARATION OF INTERESTSClinomics paid for the eight TK period sample’s face prediction to the Parabon
NanoLabs.

10 Current Biology 32, 1–13, August 8, 2022

Received: December 19, 2021
Revised: April 5, 2022
Accepted: June 1, 2022
Published: June 21, 2022
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Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
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ArticleSTAR+METHODSKEY RESOURCES TABLEREAGENT or RESOURCESOURCEIDENTIFIER

Ancient Korean Genome

Gimhae National Museum

AKG_10203

Ancient Korean Genome

Gimhae National Museum

AKG_10204

Ancient Korean Genome

Gimhae National Museum

AKG_10207

Ancient Korean Genome

Gimhae National Museum

AKG_10208

Ancient Korean Genome

Gimhae National Museum

AKG_10209

Ancient Korean Genome

Gimhae National Museum

AKG_10202

Ancient Korean Genome

Gimhae National Museum

AKG_10210

Ancient Korean Genome

Gimhae National Museum

AKG_10212

Ancient Korean Genome

Gimhae National Museum

AKG_10213

Ancient Korean Genome

Gimhae National Museum

AKG_10214

Ancient Korean Genome

Gimhae National Museum

AKG_10215

Ancient Korean Genome

Gimhae National Museum

AKG_10216

Ancient Korean Genome

Gimhae National Museum

AKG_10217

Ancient Korean Genome

Gimhae National Museum

AKG_10218

Ancient Korean Genome

Gimhae National Museum

AKG_10219

Ancient Korean Genome

Gimhae National Museum

AKG_10220

Ancient Korean Genome

Gimhae National Museum

AKG_10221

Ancient Korean Genome

Gimhae National Museum

AKG_10206

Ancient Korean Genome

Gimhae National Museum

AKG_10211

Ancient Korean Genome

Gimhae National Museum

AKG_3420

Ancient Korean Genome

Gimhae National Museum

AKG_3421

This paper

PRJEB45573

Cutadapt 1.2.1

Martin53

https://cutadapt.readthedocs.io/en/stable/

BWA 0.7.5

Li and Durbin54

http://bio-bwa.sourceforge/

Picard Tools 2.21.4

Picard-Tools55

https://broadinstitute.github.io/picard/

Qualimap-2.2.1

Okonechnikov et al.56

http://qualimap.conesalab/

MapDamage-2.0.9

Jónsson et al.57

https://ginolhac.github.io/mapDamage/sequenceTools

Schiffels et al.58

https://github.com/stschiff/sequenceTools

Schmutzi

Renaud et al.59

Biological samples

Deposited data
Whole genome data of eight Korean
genomes from the TK period
Software and algorithms

https://github.com/grenaud/schmutzi
60

ANGSD 0.91.8

Korneliussen et al.

FASTQC 0.11.8

Andrews61

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

READ v3

Monroy Kuhn et al.31

https://bitbucket.org/tguenther/read

Yleaf

Ralf et al.62

https://github.com/genid/Yleaf

Eigensoft 7.2.1

Alexander et al.63

https://guix.gnu.org/packages/eigensoft-7.2.1/

R 4.1.1

R Core Team64

https://cran.r-project.org/

ADMIXTURE 1.3.0

Alexander et al.63

https://dalexander.github.io/admixture/download.html

PONG 1.4.9

Behr et al.65

https://pypi.org/project/pong/1.4.9/

admixtools 5.1

Patterson et al.37

https://bioweb.pasteur.fr/packages/pack@AdmixTools@5.1

DATES 753

Patterson et al.37

https://github.com/priyamoorjani/DATESGATK 3.7

McKenna et al.66

https://gatk.broadinstitute.org/

samtools 1.9

Li and Durbin54

http://www.htslib.org/doc/1.9/samtools.html

http://www.popgen.dk/angsd/index.php/ANGSD(Continued on next page)e1 Current Biology 32, 1–13.e1–e6, August 8, 2022

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Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
ArticleContinued
REAGENT or RESOURCESOURCEIDENTIFIER
54

bcftools 1.6

Li and Durbin

Beagle 4.0

Browning et al.67

https://faculty.washington.edu/browning/beagle/b4_0.html

Plink 1.9b6.13

Purcell et al.68

https://www.cog-genomics.org/plink/

vcftools 0.1.13

Danecek et al.69

http://vcftools.sourceforge.net/

KING v.2.2.4

Manichaikul et al.70

https://bioweb.pasteur.fr/packages/pack@king@2.2.4

ChromoPainterv2

Lawson et al.71

https://github.com/sahwa/ChromoPainterv2

Refined IBD version ‘‘17Jan20.102

Browning and Browning72

https://faculty.washington.edu/browning/refined-ibd.html

https://github.com/samtools/bcftools/releases/

RESOURCE AVAILABILITY
Lead contact
Questions regarding further information on materials, datasets, and protocols should be directed to and will be fulfilled by the leadcontact, Pere Gelabert (pere.gelabert@univie.ac.at).
Materials availability
The raw genomic data used in all the analyses can be accessed at the European Nucleotide Archive (ENA) under the accession
number: PRJEB45573.
Data and code availability
Sequencing data and the filtered sequences are available at the European Nucleotide Archive (ENA) under the accession number:
PRJEB45573. All code used in this study and other previously published genomic data is available at the sources referenced in
the key resources table.
EXPERIMENTAL MODEL AND SUBJECT DETAILSWe studied several genomic sequences from ancient Korean individuals from the Three-Kingdoms period.
Archeological context
The practice of human sacrifices
Human sacrifice was a common practice in several ancient societies, and is usually interpreted as evidence for the existence of a
wealthy class that sought political benefits at the expense of victims belonging to the general population (i.e., the non-wealthy).73,74
The practice of human sacrifice was known as sunjang in the southern part of Korea during the first half of the first millennium CE. It
has been hypothesized that this practice lasted for centuries during the Three Kingdoms period. In Silla, these practices lasted until
the 4th to 5th centuries CE and are connected to the appearance of the stone-piled wooden chamber burials. In these graves there isa main burial chamber which housed the grave owner, and an auxiliary chamber with numerous grave goods; in both chambers thebodies of human sacrifices are also found.75 There are controversies regarding the status of the human sacrifices; several authors
have hypothesized that some of the sacrificed individuals may have enjoyed relatively high status in Silla society based on the
numerous ornaments found with their bodies, although this evidence is indirect, and the written records do not clarify their status.76,77
Identification of human sacrifices and grave owners in Daeseong-dong funerary complex
The Daesong-dong samples were excavated during the second (AKG-10203, AKG-10204, AKG-3421; 03 Sep. 1990 – 14 Apr. 1991)
and the third excavation (AKG-10207, AKG10209, AKG-10204, AKG-10218; 08 Oct. 1991 – 08 Mar. 1991) in the Gimhae tumuli area.
The determination of grave owners was carried out by the excavation team and advisory committees. The excavation teams werecomposed of ten experts in Korean archaeology during the second excavation, and seven during the third excavation (researchersand professors in the Museums, Universities, and Cultural Heritage Administration). In both cases, the advisory committees werecomposed of five experts in Korean archaeology (current and former Korean national cultural heritage research fellows or archaeology professors). The advisory committee members were different in each of the excavations.
A common belief in Korean archaeology is that the formation of social hierarchy stretches back to the Bronze Age. During the Three
Kingdoms period of Korea, the hierarchy became increasingly evident. The human sacrifices found in the tombs of nobility demonstrate the existence of social and economic hierarchies. The most important factor in determining whether the samples were humansacrifice was the location where they were excavated within the tomb. A commonly accepted view among archeologists and theadvisory committee in Korea, is that main burials, in our manuscript referred to as ‘‘grave owners’’, are buried in the center of atomb or in a separate special room in a tomb (Figure S1D). As a side note, even though there is a possibility of two individuals being
buried side-by-side and owning the same tomb (husband and wife), there were no such cases in Daesong-dong. Therefore, if morethan one person other than the owner of a tomb were buried together, they were regarded as human sacrifices.25,26,78,79
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Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
ArticleDaeseong-dong
The archeological site of Daeseong-dong, Gimhae in Gyungsangnamdo province, is situated on the hill facing the southeastern
coastline of South Korea between the Gujibong Peak and Bonghwangdae, and east of the Surowangneung Tomb (Tomb of KingSuro). The tombs of this site were built during the Geumgwan Gaya period (42–532 CE). The burial complex of Daeseong-dong,
together with the complex of Bokcheon-dong, are the most well-known sites of the Gaya Royal Class. The funerary complex covers
3,700 m2. Since fieldwork started in 1990, 219 individuals have been recovered,27 69 of which are buried in large tombs made ofwooden coffins that are believed to belong to the ruling classes. Most of these burials include human sacrifices and grave goods.
During the Korean Three Kingdoms period, Gimhae was a major trading port, as is evident from the multiple Chinese and Japanese
artifacts recovered from the tombs (Figure S1A). One example is the mortuary finds from Tomb 91, dating to the early 4th century CE,
which included a bronze vessel made in northeast China, a gilt bronze harness made from Conidae shells imported from Japan,
bronze horse bells, a chamfron, and cylindrical bronze implements from Japan. Substantial Japanese bronze ornaments werealso unearthed from Tomb 88 which dates to the early 5th century CE. These two tombs are the only ones with absolute dates.
For Tomb 88, there are two dates: (KRKD-1:*Oxcal v4.4/IntCal 20;1700±20 330-415calCE (78.8%) (from Ottchil)) and (KRKD-2:*Oxcal v4.4/IntCal 20;1610±20 415-540calCE (95.4%) (from bone)). There are also two dates for Tomb 91 (*Oxcal v4.4/IntCal
20;1770±20 275-350calCE (72.4%) (from Ottchil)) and *Oxcal v4.4/IntCal 20;1740±20 245-385calCE (95.4%) (from bone)).80 Basedon matching relative chronology records and artifacts it is clear that the remaining burials are dated between the 4th–5th
centuries CE.
Iron artifacts, including armors, helmets, and coins, were very common in most tombs. Some of the most remarkable finds were thegrave goods from Tomb 29. The owner of Tomb 29 was buried inside a large wooden coffin built in the mid 3rd century CE that lies
over more than 100 iron ingots. Additionally, this tomb consisted of multiple pieces of pottery and bronze pots which are stylistically
typical of a northern-style culture. This culture was introduced to the Gimhae area at the end of the 3rd century CE, probably from thenorthern nomadic steppe tribes.81,82 The high-status burials of this culture are characterized by Gimhae-type wooden-chamberedburials, Dojil pottery, Ordos-type bronze pots, and iron armors and trappings for horse riding typical of nomadic tribes. This has
been understood as a signal of intensive trade between the northern East Asian region and Gimhae area. However, it is unclear
whether this could also indicate the migration of northern tribes, especially from the Buyeo Tribe (an ancient Korean Kingdom locatedin Middle Manchuria),83 as no anthropological or genetic studies have been carried out to test this hypothesis. The appearance of
these non-local objects also corresponds to the timing of the appearance of human sacrifices in the complex at the end of the
3rd century CE, and to the burial division starting from the 4th–5th centuries CE, as indicated by the appearance of Gimhae-type
wooden-chambered burials. The majority of the burials and objects associated with ruling class tombs date to the 4th and 5th centuries. The tombs of the rulers were placed on the upper parts of the hills.84
The ritual of human sacrifice as a funeral practice first appeared in the Gyeongsang province, particularly in Gimhae. No evidenceof sacrificial rituals was reported from other Korean regions. The first human sacrifices appeared in the Gimhae region at the end of
the 3rd century CE and became prominent during the 4th century, and then rapidly disappeared in the Gimhae area during the late 5th
century. The sacrificed persons in the Daeseong-dong tumuli were previously considered slaves, but recent studies suggest they
were warehouse keepers, concubines, horsemen, and guards related to the grave owner. It is not possible to discern the relationshipbetween the owner of a tomb and the associated sacrificial victims. Anthropological data suggest that human sacrifices in Gaya were
mostly in their 20s and 40s. Sacrifices of women are a bit more common than those of men, a pattern which may relate to division oflabor.26,79,81
Individuals from Daeseong-dong included in the study
Individual AKG_3421, Burial 11. Individual AKG_3421 (Ancient Korean Gimhae Genome 3421) is a female sacrifice found in Tomb 11.
Individual AKG_3421 was found together with the grave owner. The main buried individual was found in a single wooden coffin. The
tomb is indirectly dated to the early 5th century CE based on the coffin characteristics.
Individual AKG_10207, Burial 23. Burial 23 is a single wooden coffin with four human sacrifices dated to the late 4th century CE
based on the burial style. Individual AKG_10207 is female sacrifice B of this burial. Japanese and Chinese style relics were discoveredin the tomb. The funerary objects include a bronze mirror and iron spear suggesting that the burial owner was a high-class individual.
Individual AKG_10203, Burial 12. Individual AKG_10203 is the grave owner. He was found inside a wooden coffin together with goldand bronze artifacts from the early 5th century CE. This individual likely belongs to a warrior class or to the low nobility, as the tomb is
not one of the richest. He is therefore classified as a grave owner individual.
Individual AKG_10204, Burial 12. Male sacrifice of Tomb 12 representing a non-grave owner individual.
Individual AKG_10209, Burial 24. Individual AKG_10209 is the sacrifice B of Burial 24, of a non-grave owner female. The owner of
Burial 24 is buried in a wooden coffin together with three sacrifices dating to the early 5th century CE. One spindle was found in theburial, which is a rare object for the Deesong-dong site.
Individual AKG_10210, Burial 24. Individual AKG_12010 is the sacrifice C of Burial 24.
Individual AKG_10218, Burial 62. Individual AKG_10218 is the grave owner of Burial 62. The relics found in the burial date to the mid
4th century CE. The objects found in the tomb suggest a grave owner. This individual is a male.
Yuha-ri, Gimhae
The Yuha-ri site, also known as Monument Gyeongsangnam-do No. 45, is located on a slope about 15 m above the sea level in thecity of Gimhae (Figure 1). Multiple artifacts have been documented from this site, including Joseon Dynasty artifacts found in
Trenches 1 and 2 that include porcelain, pottery, and tiles.
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Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
ArticleTrench 3, situated along the southern walls of the complex, is 17 m long, 2 m wide and 60 cm deep. A shell-rich layer at theeastern section of the trench, at a depth of 20 cm, yielded (in addition to the numerous shells) Korean Three Kingdoms period vessels and soft earthenware. A five-year-old child (individual AKG_3420) was excavated at the western part of the trench; a Joseon
dynasty tomb was identified about 30 cm below the topsoil (Figure S1C). The ceramics and other artifacts unearthed surrounding
the body indicate that the burial dates to the 4th century CE (Three Kingdoms period). No other tombs were found at this site.85
An anthropological study was carried out in 2017 in the Bioanthropology Lab (Department of Anthropology, Seoul National University) using standardized anthropological methods.86 Based on the length of the long bones the age estimate is 3–6 years old.87 All thedeciduous teeth were erupted, with the dental analysis suggesting the child is at least 3 years old (±1 year). Considering the growth
status of the crowns of the permanent dentition the subject is estimated to be 4 years old (±1 year).
METHOD DETAILSSampling
All individuals were sampled with the permission of the local authorities at the Gimhae National Museum following preventive measures to avoid contamination. Six teeth were collected and twenty petrous bones were drilled using the protocol described in Sirak
et al.88 Tooth roots were cleaned and cut using a sandblaster and later pulverized using a mixer mill (Retsch Mixer Mill 400).89 For thisstudy we sampled all the available petrous bones and/or teeth.
DNA extraction, library preparation, and sequencing
All experimental work was performed in the dedicated ancient DNA laboratory of the University of Vienna. Personnel and facilities followed all the standard measures to guarantee the authenticity of the data. We included extraction of negative controls(no powder), library, and PCR negative controls (the extract was supplemented with water) in every batch of samples processedand carried them through the entire wet laboratory processing to test for reagent contamination. DNA was extracted
from 75 mg of powder using an optimized DNA extraction protocol.89 Illumina sequencing libraries were constructed using
12.5–25 ml of extract and amplified using Accuprime Pfx Supermix (Thermo Fisher Scientific), following Gamba et al.90; a protocol adapted from.91 Quality assessment of the amplified library was performed on an Agilent 2100 Bioanalyzer and a Qubit 2.0
Fluorometer. All the amplified libraries were initially screened using NovaSeq platform and further sequenced with NovaSeq
platform in the Vienna Biocentre.
QUANTIFICATION AND STATISTICAL ANALYSIS
Bioinformatic analysis
Sequencing reads were trimmed using cutadapt (version. 1.2.1) with a minimum length of 30 and removing polyA tails,53 and aligned
to the human reference genome (GRCh37), with the revised Cambridge reference sequence (rCRS) mitochondrial genome using
BWA54 (Version 0.7.5) disabling seeding and setting a gap penalty open of 2. Duplicate mapped reads were removed using Picard
Tools 2.21.455 with default parameters. Reads with mapping qualities below 30 were also removed. Unique and filtered reads wereanalyzed with Qualimap-2.2.156 to assess whole genome coverage depths. MapDamage-2.0.957 was used to estimate the level ofdeamination and the authenticity of the data. Reads used for the genotype-calling were trimmed again, 5 nucleotides in both ends, tominimize the genotyping errors in the downstream analyses.
Pseudo-haploid genotypes were called with a pileup caller of sequenceTools,58 filtering out bases with a base-quality score below
30. At this stage we called the positions of the 1240k dataset.29 These calls were merged with individuals from1,2,4,36,92–95 and the restof present-day genomes available from David Reich’s group website (reich.hms.harvard.edu). The full list of samples is available in
Data S1D. The final dataset is composed of 645 present-day Eurasian1,96 samples and 237 ancient individuals.
Facial prediction and ancestry analysis
Facial prediction and ancestry analysis were conducted by Parabon NanoLabs, Inc. based on genotyping data from 851,274 SNPs.
Facial prediction is based on autosomal SNPs and sex information to infer skin, eye, and hair color, as well as facial morphology using
the Snapshot DNA Phenotyping System (https://snapshot.parabon-nanolabs.com/). The ancestry analysis is based on the PCA
using Eigensoft v. 6.0.1 and Admixture v. 1.23, both run on a background dataset with approximately 13,000 individuals from
more than 150 different genetic/ethnic backgrounds (denoted here: https://snapshot.parabon-nanolabs.com/ancestry). Regarding
East Asians relevant to our analysis, the background population dataset included 163 Koreans and 341 Japanese that are divided intoeither ‘‘Japanese’’ (292 individuals) or ‘‘Ryukyuan’’ (49 individuals) ancestry. The map of all populations in the background dataset isavailable online (https://snapshot.parabon-nanolabs.com/img/populations-1.png).
Data authenticity
Contamination level was estimated from the mtDNA sequences using Schmutzi59 and by estimating the heterozygous content of themale X chromosomes using ANGSD 0.91.8.60 The estimates of both analyses are presented in Data S1A. Mapping qualities and read
length distribution were also examined with FASTQC 0.11.8,61 and the average genomic and mitochondrial depths were obtainedusing Qualimap 2.2.11.56
Current Biology 32, 1–13.e1–e6, August 8, 2022 e4

Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
ArticleUniparental markers
Reads aligned to mitochondria were processed with Schmutzi59 to generate a consensus sequence of the mitochondrial genomes.
We called the mitochondrial haplogroups of the mitochondrial consensus sequences using Haplogrep 2.097 and version 17 of Phylotree. Y chromosome haplogroups were estimated using Yleaf.62
We used READ31 to explore the presence of kinship relationships between the samples analyzed. We filtered the SNPs present in
the 1,240k dataset with an (Minor allele frequency) MAF of 0.01. There are four possible outcomes when running READ: unrelated(normalized P0R0.90625), second degree (0.90625Rnormalized P0R0.8125), first degree (0.8125Rnormalized P0R0.625).
Population genetic tools
All the subsequent analyses were performed with the 1,240K dataset. Principal component analysis was conducted using 597,573
SNPs and 645 present-day genomes using smartpca from Eigensoft package 7.2.137 with numoutlieriter: 0 and 10 eigenvectors. The
resulting data were plotted using R 4.1.1.64 Ancient samples were projected onto the PCA that was based on present-day samples
using the option ‘‘lsqproject’’. Two rounds of outlier removal were used. Results with ancient samples were plotted using R. We
excluded first-degree relatives from the population genetics analyses, and when founding it, we chose the one with higher coverage
according to the labeling publicly available.
An unsupervised ADMIXTURE analysis was performed with ADMIXTURE 1.3.063 with the modern genotypes from the publicly
available Human Origins (HO) panel37 together with the eight 1,700-year-old Korean TK individuals, restricting the analysis to the597,573 SNPs of the HO dataset.96 These SNPs were filtered for MAF < 0.05 and Missing sites > 0.05. Filtered SNPs were pruned
for linkage-disequilibrium (LD) using PLINK 1.968 flag –indep-pairwise with a window size of 200 SNPs, advanced by 50 SNPs andestablishing an r2 threshold of 0.4. A total of 282,896 SNPs were used in the analysis. The final ADMIXTURE was run with K ranging
from 2 to 15 and 100 bootstrap replications. The ADMIXTURE result was plotted with PONG 1.4.9 and in R.65
f3-statistics were run using admixtools 5.137 in the form f3(X, Test; Mbuti) using all the populations of the dataset, both present-day
and ancient. f4-statistics were also run using the same package. We used the form f4(X, Test; PopA, PopB) using all the multiple combinations. Only results with |Z| > 3 and supported by more than 100,000 SNPs were considered.
qpWave and qpAdm
We used the software qpWave98 from admixtools 5.137 with parameter ‘‘allsnps: NO’’ to investigate the homogeneity of the ancientindividuals and if any would require additional sources of ancestry to explain their genomes. All the samples included in our study
have sufficient SNPs to perform the qpAdm modeling (at least 50% of the 1240k set) without using the ‘‘allsnps: YES’’ option. Therefore, we prefer to avoid the bias that the option may introduce.39 To capture a wide range of distal ancestries we used the followingbase ‘‘Right’’ outgroup set of populations (‘‘R10’’): Mbuti.DG, Ami.DG, ONG.SG, Mixe.DG, Tianyuan, Iran_GanjDareh_N,
DevilsCave_N, Bianbian, Liangdao2, Yumin. We used a threshold of p=0.01.
In admixture modeling we used qpAdm,29 again with parameter ‘‘allsnps: NO’’, to find populations and potential admixture eventsfrom which the two ancient Korean subgroups could have descended. As the outgroup ‘‘Right’’ set we used the base R10. As sources
we used a set of populations based on the top results from the outgroup-f3 statistics of the form f3(X, Test, Mbuti), for Korea-TK_1
and Korea-TK_2: Amur_Basin-IA, Ekven_IA, Japan_Jomon, Japan_Kofun, LateXiongnu, LateXiongnu_Han, Yankovsky_IA,
Yellow_River-BA, Taiwan-IA, Liao_River-BA, Korea_LN_Yokchido, and Korea_MN. We applied a more stringent threshold of significance when compared with qpWave, of p=0.05. As part of a two-step model competition approach, models passing this thresholdwere re-evaluated and only accepted if they remained significant after moving all unused source populations to the ‘‘Right’’.
Dates
We used DATES 75399 to estimate the dates of different admixture events based on the results of qpAdm. We ran the program usingparameters as follows: bin size: 0.001, maxdis: 1.0, runmode: 1, qbin: 10 and jackknife: YES, setting a generation time of 28 years.
Imputation
The eight TK period genomes, together with other ancient shotgun genomes (NEO240_DevilsGate2, Kolyma_River, F5, F23,
JpKa6904, JpIw32) with a coverage greater than 1x have been imputed following the procedure described in Cassidy et al.30,100
We first processed the filtered mapped reads with RealignerTargetCreator from GATK 3.7,66 and realigned the indels from The Mills
and 1000 Genomes Project gold standard indels.101 Afterwards, we added MD tags to the bam reads using samtools 1.9 calmd.54
SNPs overlapping the 1000 Genomes Project dataset version 3101 were called in these reads using GATK UnifiedGenotyper, setting
the options-out_mode EMIT_ALL_SITES and –genotyping_mode GENOTYPE_GIVEN_ALLELES. Option -glm SNP was also used to
get the genotype likelihoods of the SNPs. Obtained calls were filtered to add equal likelihoods to both missing data and the sites
possibly affected by deamination, which corresponds to the transitions. Resulting files were split into chromosomes with bcftools
1.6102 and filtered for sites with MAF>0.05, and less than 10% of genotype missingness. Resulting files were split with splitvcf.jar
from Beagle in 100,000 SNPs files with 20,000 SNPs of overlap. We used Beagle 4.067 to impute the genotypes setting ‘‘gl’’ option,‘‘gprobs=true’’, ‘‘window=15000’’, ‘‘impute=true’’, providing genetic maps and reference files from Beagle. Imputed calls were
filtered by Genotype probability > 0.99 and MAF > 0.05, excluding transitions. The resulting datasets consist of 1,574,651 filteredand imputed calls.

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Please cite this article in press as: Gelabert et al., Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae,
Korea, Current Biology (2022), https://doi.org/10.1016/j.cub.2022.06.004ll
ArticleHomozygosity
We used two methods to call the ROH in our samples. First, we used the imputed transversions overlapping with the 1000 Genomes
Project phase 3 database (402,250 SNPs) to detect Runs of Homozygosity (ROH) using Plink 1.9b6.13,68 following the previous
parameter described in Gamba et al.,90 classifying ROH between long and short using a threshold of 1.6 Mb. using the –homozyg
command and the following options: -homozyg –homozyg-density 50 –homozyg-gap 100 –homozyg-kb 500 –homozyg-snp 50 –homozyg-window-het 1 –homozyg-window-snp 50, –homozyg-window-kb 5000 and –homozyg-window-threshold 0.05. Second, we
called ROH with the methodology described in Ringbauer et al.103 optimized for the study of aDNA with the same dataset used for the
population genetics analyses.
Chromosome painting analysis (fineSTRUCTURE)
We used vcftools 0.1.13 to merge our eight imputed samples with modern East Asian samples from the 1,000 Genome Project101(Han, Dai, Korean, Japanese, and Kihn_Vietnamese), a Korean set from Jeon et al.,11 and six additional ancient shotgun genomes
from east Asia at a high coverage (NEO240_DevilsGate2, Kolyma_River, F5, F23, JpKa6904, JpIw32 ).4,13,35,36 The total numberof SNPs after filtering out all the positions with genotype missingness ‘‘–max-missing 1’’, Hardy-Weinberg equilibrium ‘‘–hwe
0.000001’’, and minor allele frequencies ‘‘–maf 0.00000000001’’, to exclude fixed variants, was 402,250. Relatives were excluded
from the present-day populations utilizing KING v.2.2.470 with options ‘‘–related’’ and ‘‘–degree 3’’. The representatives for each present-day population were randomly downsampled to leave a) 10; b) 5; c) 3 representatives per each group. The finalized datasets
were converted to map and ped formats using plink v1.90 with option ‘‘–recode 12’’ to preserve the phasing information. We ran
scripts ‘‘plink2chromopainter.pl’’ and ‘‘makeuniformrecfile.pl’’ from the FineSTRUCTURE pipeline ‘‘fs_4.1.1’’ to generate phasing
and recombination information files. Effective population size (Ne) was estimated using ChromoPainter v2 with 10 random
samples and settings: ‘‘-a -i 20 -in -iM’’. The average Ne was estimated using ‘‘neaverage.pl’’ (in="3250.16016988007" andiM="0.000779866001166277). We ran FineSTRUCTURE v.4.1.1 in linked mode with options ‘‘-x 1000000 -y 1000000 -z 10000’’and ‘‘-y 10000 -m T’’. The results were visualized in FineSTRUCTURE GUI for Windows v.0.1.0 (https://people.maths.bris.ac.uk/
madjl/finestructure/finestructureGUI.html).
IBD analyses
IBD blocks were identified using a Refined IBD version ‘‘17Jan20.102’’ with default settings and a recombination map provided withthe program. As input, we merged our eight imputed ancient Korean genomes with East Asians from the 1,000 Genome Project,101 a
Korean set from Jeon et al.,11 and six additional ancient shotgun genomes from East Asia and filtered them as described in the‘‘Chromosome painting analysis’’ section above. Our eight imputed samples were generated and prefiltered as described in the‘‘Imputed Calls and imputation’’ section. Additionally, all the sites with missing variants and fixed alleles (MAF>0) had been excluded,
yielding 402,250 high-quality markers used as an input.
IBD segments with LOD>3 were analyzed excluding the few sporadic large-size segments (>39cM) that are most likely an artifact(shown in S19). We averaged the values of segment length and segment counts to reflect the pattern of genetic material shared between each ancient sample and present-day East Asian populations. The results were plotted using heatmap.2 in R.
Phenotypic variant analysis
We selected 160 variants with phenotypic implications from the imputed ancient genomes, retrieving the alleles and their ‘‘rs ID’’ fromdbSNP. The calls included in Data S1J correspond to the genotype probabilities imputed with the Korean Genome project and 1000
Genomes Project data overlap-based merged panel (denoted in black font) or the 1000 Genomes Project data alone (denoted in bluefont). Genotypes were filtered by genotype probabilities of 0.9. For reference, we included their allelic frequencies in East Asian
populations.

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