Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations

Takashi Gakuhari,Blánaid Ní Chuinneagáin,Morten E Allentoft,Osamu Kondo,Hiromi Shitara,Hiromi Matsumae,Tadayuki Masuyama,Ryosuke Kimura,Hajime Ishida,Atsushi Tajima,Takehiro Sato,Kae Koganebuchi,Minoru Yoneda,Yasuhiro Yamada,Tetsuaki Wakebe,Tsunehiko Hanihara,Martin Sikora,Atsushi Toyoda,Thorfinn Sand Korneliussen ,Eske Willerslev,Nobuo Shigehara,Simon Rasmussen,Shigeki Nakagome,Toshiyuki Tsurumoto,Souichiro Mizushima,Ryan Schmidt,Hiroki Shibata,Hiroki Oota

doi:10.1038/s42003-020-01162-2

Abstract

Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia.

Highlights

Modern humans reached East Asia more than 40,000 years ago
Taking advantage of the earliest divergence of the IK002 (Fig. 1c & Supplementary Fig. 8), we address a question if the UpperPaleolithic people who took the northern route of the Himalayas mountains to arrive east Eurasia made genetic contribution to populations migrated from Southeast Asia
IK002 is modeled as a basal lineage to East Asians, Northeast Asians/East Siberians, and Native Americans after the divergence between Tiányuán and the ancestor of hunters-gatherers in Southeast Asia (Fig. 4)[7,17]

Summary

Introduction

Modern humans reached East Asia more than 40,000 years ago. key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. After the major Out-of-Africa dispersal of Homo sapiens around 60,000 years ago (60 kya), modern humans rapidly expanded across the vast landscapes of Eurasia[1] Both fossil and ancient genomic evidence suggest that groups ancestrally related to present-day East Asians were present in eastern China by as early as 40 kya[2]. To identify the origin of the Jomon people, we sequenced the genome of a 2500-year-old Jomon individual (IK002) excavated from the central part of Honshu to 1.85-fold genomic coverage Comparing this IK002 genome with ancient Southeast Asians, we previously reported genetic affinity between IK002 and the 8000 years old Hòabìnhian hunter-gatherer[17].

Methods

Results

Conclusion