Yusuke Watanabe, Yoshiki Wakiyama, Daisuke Waku, Guido Valverde, Akio Tanino, Mizuki Hayashi, Izumi Naka, Yuka Nakamura, Tsubasa Suzuki, Kae Koganebuchi, Takashi Gakuhari, Takafumi Katsumura, Motoyuki Ogawa, Atsushi Toyoda, Pornlada Nuchnoi, Suwanna Chaorattanakawee, Hathairad Hananantachai, Jintana Patarapotikul, Soichiro Mizushima, Tomohito Nagaoka, Kazuaki Hirata, Minoru Yoneda, Midori Motoi, Hideo Toyoshima, Takafumi Maeda, Takayuki Nishimura, Tadayuki Masuyama, Yasuhiro Yamada, Ryuzaburo Takahashi, Masami Izuho, Jun Ohashi, NCBN Controls WGS Consortium, Hiroki Oota
How did Homo sapiens thrive in extreme environments during their dispersal across Eurasia? Unraveling adaptations that enabled human survival during the Last Glacial Maximum (LGM) remains critical. Here, we analyze 42 genomes from Holocene hunter-gatherers (Jomon) in the Japanese archipelago, revealing their deep ancestry from an isolated Upper Paleolithic (UP) East Eurasian lineage. We detect gene flow from northern UP Siberians into Jomon, reconciling long-standing debates between bioanthropology and archaeology regarding East Asian peopling. We find no Jomon-specific Denisovan ancestry, suggesting shared introgression before their LGM divergence from mainlanders. Furthermore, we find evidence consistent with cold adaptation in Jomon UP ancestry, highlighting diverse physiological pathways. Our study provides one of the first paleogenomic frameworks for investigating ancient adaptations in UP East Eurasians, revealing an evolutionary legacy from a colder past in present-day humans.