An infant named KS007 was found cradled in the chest of a woman, buried together in a shell mound in what is now Funabashi City, overlooking Tokyo Bay. She had died more than 4,000 years ago. Her bones, along with those of 41 other individuals from sites scattered across the Japanese archipelago, form the basis of a new genomic study that traces a lineage back through the last Ice Age and into questions that touch three continents.
The people in this study are the Jomon, hunter-gatherers who lived across the Japanese islands from roughly 16,000 to 3,000 years ago, known best for some of the world’s earliest pottery. But the genomes recovered from their remains carry a signal from much earlier. Researchers sequenced1 25 new individuals and combined them with 17 previously published genomes, then used that dataset to reconstruct what happened to a population of Homo sapiens that got cut off from the rest of Eurasia right around the coldest point in the last glaciation.
The story starts with geography. During the Last Glacial Maximum, sea levels sat about 100 meters lower than today, and the modern Japanese islands didn’t exist as separate landmasses. Honshu, Shikoku, and Kyushu were fused into one island the researchers call Paleo-Honshu, nearly touching the Korean peninsula. Hokkaido was welded to Sakhalin and the Kuril chain, forming a corridor straight into the Eurasian mainland. People had reached Paleo-Honshu with flake-based stone tools by around 38,000 years ago. Then, as the ice age deepened and seas rose at its end, those land bridges drowned. Paleo-Honshu split into the modern southern islands, and Hokkaido separated from the continent.
Genetically, something similar happened around the same time. The team estimates that the ancestors of the Jomon split off from mainland East Eurasian populations somewhere between 27,000 and 19,000 years ago, deep in the Upper Paleolithic. Their population size dropped sharply during this period of isolation, then rebounded once the Jomon culture took hold in the warmer post-glacial world. That decline and recovery lines up with what archaeologists have already pieced together from tool assemblages and site density, which makes the genetic and material records feel less like two separate stories and more like one.
Where those ancestors actually came from is where things get more interesting. Two competing routes have long been proposed for how people first reached eastern Eurasia: a northern path through Siberia, and a southern path through the Indian subcontinent into Southeast Asia. Stone tool evidence from Japan, dated to between 36,000 and 24,000 years ago, has shown blade technology that resembles northern traditions. But earlier genetic work hadn’t found much to back that up, leaving archaeologists and geneticists somewhat talking past each other.
This study finds a middle ground. The Jomon carry a strong southern signal overall, comparable to what’s seen in other East and Southeast Asians, consistent with descent from populations related to Southeast Asian Hòabìnhian foragers. But the researchers also detected a subtle, consistent northern contribution, one not reported before, that looks like limited gene flow from Upper Paleolithic Siberian groups. The signal shows up a bit more strongly in the small number of Hokkaido individuals in the sample, which tracks with archaeological evidence that the Ice Age toolmakers in that region had closer technological ties to Siberia than to communities further south.
