Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea

Pere Gelabert; Asta Blazyte; Yongjoon Chang; Daniel M Fernandes; Sungwon Jeon; Jin Geun Hong; Jiyeon Yoon; Youngmin Ko; Victoria Oberreiter; Olivia Cheronet; Kadir T Özdoğan; Susanna Sawyer; Songhyok Yang; Ellen McRae Greytak; Hansol Choi; Jungeun Kim; Jong-Il Kim; Choongwon Jeong; Kidong Bae; Jong Bhak; Ron Pinhasi

doi:10.1016/j.cub.2022.06.004

Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea

Pere Gelabert, Asta Blazyte, Yongjoon Chang, Daniel M Fernandes, Sungwon Jeon, Jin Geun Hong, Jiyeon Yoon, Youngmin Ko, Victoria Oberreiter, Olivia Cheronet, Kadir T Özdoğan, Susanna Sawyer, Songhyok Yang, Ellen McRae Greytak, Hansol Choi, Jungeun Kim, Jong-Il Kim, Choongwon Jeong, Kidong Bae, Jong BhakRon Pinhasi

Research output: Contribution to journal › Article › Academic › peer-review

Abstract

The genetic history of prehistoric and protohistoric Korean populations is not well understood because only a small 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 comprise eight shotgun-sequenced genomes from ancient Korea (0.7×-6.1× coverage). They were derived from two archeological sites in Gimhae: the Yuha-ri shell mound and the Daesung-dong tumuli, the latter being the most important funerary complex of the Gaya confederacy. All individuals are from between the 4th and 5th 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.

Original language	English
Pages (from-to)	3232-3244.e6
Number of pages	20
Journal	Current Biology
Volume	32
Issue number	15
DOIs	https://doi.org/10.1016/j.cub.2022.06.004
Publication status	Published - 8 Aug 2022
Externally published	Yes

Bibliographical note

Funding Information:
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 (University of 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 with the archeological context and information. This work was supported by the Promotion of Innovative Businesses for Regulation-Free Special Zones funded by the Ministry of SMEs and Startups (MSS, Korea) (P0016193). This work was also 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 Institute of 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. 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. Clinomics paid for the eight TK period sample's face prediction to the Parabon NanoLabs.

Funding Information:
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 (University of 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 with the archeological context and information. This work was supported by the Promotion of Innovative Businesses for Regulation-Free Special Zones funded by the Ministry of SMEs and Startups (MSS, Korea) ( P0016193 ). This work was also 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 Institute of 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.

Publisher Copyright:
© 2022 Elsevier Inc.

Keywords

Korea Three Kingdoms period genomes
Korean ancient genomes
ancient DNA
ancient diploid genomes
phenotypic analyses
population continuity
population genetics

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10.1016/j.cub.2022.06.004

Cite this

Gelabert, P., Blazyte, A., Chang, Y., Fernandes, D. M., Jeon, S., Hong, J. G., Yoon, J., Ko, Y., Oberreiter, V., Cheronet, O., Özdoğan, K. T., Sawyer, S., Yang, S., Greytak, E. M., Choi, H., Kim, J., Kim, J.-I., Jeong, C., Bae, K., ... Pinhasi, R. (2022). Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea. Current Biology, 32(15), 3232-3244.e6. https://doi.org/10.1016/j.cub.2022.06.004

@article{d1bc7cd996654aaab4bb6f66f6089ccf,

title = "Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea",

abstract = "The genetic history of prehistoric and protohistoric Korean populations is not well understood because only a small 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 comprise eight shotgun-sequenced genomes from ancient Korea (0.7×-6.1× coverage). They were derived from two archeological sites in Gimhae: the Yuha-ri shell mound and the Daesung-dong tumuli, the latter being the most important funerary complex of the Gaya confederacy. All individuals are from between the 4th and 5th 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.",

keywords = "Korea Three Kingdoms period genomes, Korean ancient genomes, ancient DNA, ancient diploid genomes, phenotypic analyses, population continuity, population genetics",

author = "Pere Gelabert and Asta Blazyte and Yongjoon Chang and Fernandes, {Daniel M} and Sungwon Jeon and Hong, {Jin Geun} and Jiyeon Yoon and Youngmin Ko and Victoria Oberreiter and Olivia Cheronet and {\"O}zdoğan, {Kadir T} and Susanna Sawyer and Songhyok Yang and Greytak, {Ellen McRae} and Hansol Choi and Jungeun Kim and Jong-Il Kim and Choongwon Jeong and Kidong Bae and Jong Bhak and Ron Pinhasi",

note = "Funding Information: We would like to thank Kendra Sirak and {\'E}adaoin 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 (University of 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 with the archeological context and information. This work was supported by the Promotion of Innovative Businesses for Regulation-Free Special Zones funded by the Ministry of SMEs and Startups (MSS, Korea) (P0016193). This work was also 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 Institute of 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. 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.{\"O}. 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. Clinomics paid for the eight TK period sample's face prediction to the Parabon NanoLabs. Funding Information: We would like to thank Kendra Sirak and {\'E}adaoin 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 (University of 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 with the archeological context and information. This work was supported by the Promotion of Innovative Businesses for Regulation-Free Special Zones funded by the Ministry of SMEs and Startups (MSS, Korea) ( P0016193 ). This work was also 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 Institute of 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. Publisher Copyright: {\textcopyright} 2022 Elsevier Inc.",

year = "2022",

month = aug,

day = "8",

doi = "10.1016/j.cub.2022.06.004",

language = "English",

volume = "32",

pages = "3232--3244.e6",

journal = "Current Biology",

issn = "0960-9822",

publisher = "Cell Press",

number = "15",

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Gelabert, P, Blazyte, A, Chang, Y, Fernandes, DM, Jeon, S, Hong, JG, Yoon, J, Ko, Y, Oberreiter, V, Cheronet, O, Özdoğan, KT, Sawyer, S, Yang, S, Greytak, EM, Choi, H, Kim, J, Kim, J-I, Jeong, C, Bae, K, Bhak, J & Pinhasi, R 2022, 'Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea', Current Biology, vol. 32, no. 15, pp. 3232-3244.e6. https://doi.org/10.1016/j.cub.2022.06.004

TY - JOUR

T1 - Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea

AU - Gelabert, Pere

AU - Blazyte, Asta

AU - Chang, Yongjoon

AU - Fernandes, Daniel M

AU - Jeon, Sungwon

AU - Hong, Jin Geun

AU - Yoon, Jiyeon

AU - Ko, Youngmin

AU - Oberreiter, Victoria

AU - Cheronet, Olivia

AU - Özdoğan, Kadir T

AU - Sawyer, Susanna

AU - Yang, Songhyok

AU - Greytak, Ellen McRae

AU - Choi, Hansol

AU - Kim, Jungeun

AU - Kim, Jong-Il

AU - Jeong, Choongwon

AU - Bae, Kidong

AU - Bhak, Jong

AU - Pinhasi, Ron

N1 - Funding Information: 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 (University of 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 with the archeological context and information. This work was supported by the Promotion of Innovative Businesses for Regulation-Free Special Zones funded by the Ministry of SMEs and Startups (MSS, Korea) (P0016193). This work was also 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 Institute of 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. 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. Clinomics paid for the eight TK period sample's face prediction to the Parabon NanoLabs. Funding Information: 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 (University of 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 with the archeological context and information. This work was supported by the Promotion of Innovative Businesses for Regulation-Free Special Zones funded by the Ministry of SMEs and Startups (MSS, Korea) ( P0016193 ). This work was also 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 Institute of 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. Publisher Copyright: © 2022 Elsevier Inc.

PY - 2022/8/8

Y1 - 2022/8/8

N2 - The genetic history of prehistoric and protohistoric Korean populations is not well understood because only a small 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 comprise eight shotgun-sequenced genomes from ancient Korea (0.7×-6.1× coverage). They were derived from two archeological sites in Gimhae: the Yuha-ri shell mound and the Daesung-dong tumuli, the latter being the most important funerary complex of the Gaya confederacy. All individuals are from between the 4th and 5th 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.

AB - The genetic history of prehistoric and protohistoric Korean populations is not well understood because only a small 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 comprise eight shotgun-sequenced genomes from ancient Korea (0.7×-6.1× coverage). They were derived from two archeological sites in Gimhae: the Yuha-ri shell mound and the Daesung-dong tumuli, the latter being the most important funerary complex of the Gaya confederacy. All individuals are from between the 4th and 5th 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.

KW - Korea Three Kingdoms period genomes

KW - Korean ancient genomes

KW - ancient DNA

KW - ancient diploid genomes

KW - phenotypic analyses

KW - population continuity

KW - population genetics

UR - http://www.scopus.com/inward/record.url?scp=85135768117&partnerID=8YFLogxK

U2 - 10.1016/j.cub.2022.06.004

DO - 10.1016/j.cub.2022.06.004

M3 - Article

C2 - 35732180

SN - 0960-9822

VL - 32

SP - 3232-3244.e6

JO - Current Biology

JF - Current Biology

IS - 15

ER -

Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea

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Bibliographical note

Keywords

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