Japanese Archipelago during the last glacial maximum (LGM) when sea-levels were at their lowest. Grey areas were land which is now submerged.
Belief in the literal truth and inerrancy of the Bible’s origin myths somehow staggers on, despite their complete lack of supporting evidence and the repeated contradiction of their testable claims by evidence from the real world. It survives through the careful avoidance of inconvenient facts, a steady supply of misinformation and an assortment of strategies for dismissing evidence and suppressing the cognitive dissonance between what believers have been taught and what the evidence shows.
Within this intellectually impoverished and parochial culture, changing one’s mind in response to new information is treated as weakness rather than intellectual honesty, while ignorance of societies beyond the Bible’s narrow geographical horizon makes their histories easier to disregard. One such history is that of the Jōmon people of Japan—a population whose origins, migrations and adaptations extend far back into that immense expanse of human history before creationism’s supposed ‘Creation Week’.
The genomes of ancient people can preserve evidence not only of ancestry and migration but also of the environments in which their distant ancestors evolved. Genetic variants that became unusually common in a population may reveal where natural selection acted, particularly when several independent signals affect biological pathways relevant to the same environmental challenge.
This is the approach taken by an international research team led by Yusuke Watanabe, Yoshiki Wakiyama and Hiroki Oota of the University of Tokyo. In a paper published in Science Advances, the researchers analysed genome-wide data from 42 Jōmon individuals: 25 newly sequenced for the study and 17 whose genomes had previously been reported.
The individuals themselves lived during the Holocene, not during the Last Glacial Maximum. What their DNA preserves, however, is the genetic legacy of a much older population. The researchers estimate that the ancestral Jōmon lineage separated from continental East Eurasian populations sometime between approximately 27,000 and 19,000 years ago—broadly coinciding with the coldest part of the last Ice Age. After becoming established in the Japanese archipelago, this population remained comparatively isolated and later differentiated into regional Jōmon lineages.
The genomic history was not one of absolute separation. The analysis also detected gene flow from northern Upper Palaeolithic Siberians, adding another strand to the already complex history of East Asian populations. Conversely, the researchers found no evidence of Denisovan ancestry unique to the Jōmon lineage, suggesting that any such ancestry had entered the ancestors of East Asian populations before the Jōmon lineage diverged from continental groups.
Who were the Jōmon? Jōmon refers both to a long prehistoric period in the Japanese archipelago and to the diverse peoples and cultures that occupied it. The name means “cord-marked”, after the patterns made by pressing twisted fibres or cords into the surface of wet clay vessels.Whole-genome scans also identified patterns consistent with positive natural selection in regions associated with non-shivering thermogenesis, brown adipose tissue, lipid metabolism and sensitivity to cold. Among the implicated regions were those containing UCP1, FTO and APOA5. The authors propose that variants affecting heat production and the use of fats may have helped the ancestors of the Jōmon survive the severe conditions of the Last Glacial Maximum and possibly exploit diets rich in marine and freshwater resources.
The Jōmon period is usually dated from approximately 14,000–13,000 BCE to about 400–300 BCE, although its beginning and end varied between regions. It followed the Japanese Palaeolithic and overlapped at its end with the arrival of rice-farming populations associated with the Yayoi culture.
How did Jōmon people live?
Jōmon communities were principally hunter-gatherer-fishers, but this description can conceal the sophistication and diversity of their societies. Depending on location and season, they exploited:
- deer, wild boar and other terrestrial animals;
- fish, shellfish, seals and other marine resources;
- nuts, fruits, roots and edible plants; and
- in some areas, managed or cultivated useful plants.
Abundant coastal, riverine and woodland resources allowed many communities to live in relatively permanent settlements rather than continually following migrating game. Archaeologists have found pit dwellings, storage pits, cemeteries, shell middens and large communal settlements. Jōmon people also produced elaborate pottery, stone and bone tools, lacquerware, ornaments and distinctive clay figurines known as dogū. Official Japanese archaeological sources describe hunting, fishing and gathering as central to their subsistence and document the growth of settled communities and formal burial practices during the period. (Jōmon Prehistoric Sites in Northern Japan)
Were the Jōmon a single people?
Not in the sense of a single, uniform tribe or nation. The term covers thousands of years and an archipelago extending more than 3,000 kilometres. Jōmon communities consequently differed in diet, technology, customs and patterns of settlement. Genomic evidence now indicates that their shared ancestral population also divided into regional lineages after becoming established in the archipelago.
The Jōmon individuals analysed in the new study lived during the Holocene, but their genomes retained ancestry from Upper Palaeolithic people whose lineage had become distinct during the Last Glacial Maximum. “Jōmon genome” therefore does not mean that the sampled individuals themselves lived at the height of the Ice Age; it means that their DNA preserved part of that much older population history.
What happened to them?
From roughly the first millennium BCE, migrants from continental East Asia introduced intensive wet-rice agriculture and new technologies, initiating the Yayoi period in much of Japan. Jōmon populations were not simply exterminated or replaced. They mixed to differing degrees with incoming populations, and later migrations added further continental ancestry.
Consequently, Jōmon ancestry survives in people throughout Japan today, although its proportion varies geographically. Genetic studies generally find a stronger Jōmon contribution among the Ainu of Hokkaido and the Ryukyuan peoples of the southern islands than among people of the main Japanese islands. Modern Japanese populations are therefore products of repeated migration and mixture, not descendants of one isolated, unchanging ancestral population.
That interpretation requires appropriate caution. The researchers did not measure the physiology or diet of people who lived 20,000 years ago. Instead, they detected unusual patterns of genetic variation and compared the functions associated with those regions with what is known from modern biology. Cold adaptation and dietary adaptation are therefore well-supported evolutionary hypotheses derived from selection signals, environmental history and archaeological evidence—not direct observations of ancient metabolism.
Even with that qualification, the study presents a thoroughly evolutionary account of human history. Populations migrate, become isolated, exchange genes, divide into regional groups and change genetically as environmental pressures alter which inherited variants are most likely to be passed on. Nothing appears suddenly in its finished form, and no population remains biologically untouched by its history.
For creationists, the chronology alone is fatal. The ancestral Jōmon lineage was already diverging, mixing with other Eurasian populations and apparently adapting to Ice Age conditions tens of thousands of years before a Young-Earth chronology allows the world—or any humans—to have existed. The Jōmon genome is therefore more than a record of the ancestry of the Japanese archipelago: it is a surviving molecular archive of human evolution during a period that creationist mythology simply erases.
The paper in Science Advances was accompanied by a University of Tokyo news release:
Machine translated by DeepL which may contain errors.
Cold-Climate Adaptations of East Eurasian Hunter-Gatherers Who Lived During the Ice Age, as Revealed by the Jomon Genome
Ancient DNA Sheds Light on the Evolutionary Legacy of the Late Paleolithic
Summary
Yusuke Watanabe, Project Assistant Professor; Yoshiki Wakiyama, Graduate student ; and Professor Hiroki Oota of the Graduate School of Science, The University of Tokyo; Professor Yasuhiro Yamada and Associate Professor Masami Izuho of the Graduate School of Humanities at Tokyo Metropolitan University; Associate Professor Takayuki Nishimura of the Graduate School of Design, Kyushu University, and others have used the genomes of Jomon people to reveal the history of the formation of Late Paleolithic hunter-gatherer populations in East Eurasia and evidence of their adaptation to cold environments.
In this study, we integrated the ancient genomes of 42 Jomon individuals—comprising 25 individuals newly extracted and sequenced by our team and 17 previously reported individuals—and performed data analysis using high-performance computing. The results showed that the ancestral population of the Jomon people originated from a lineage that diverged from East Eurasian populations on the continent approximately 27,000 to 19,000 years ago. Archaeologically, this period corresponds to the Late Paleolithic era and coincides almost exactly with the coldest phase of the Last Glacial Maximum.
Through a whole-genome natural selection scan, we identified traces consistent with adaptation to cold environments in multiple gene regions associated with thermogenesis in brown adipose tissue, lipid metabolism, and cold sensitivity. In particular, the APOA5 gene region showed evidence of a rapid increase in mutation frequency during the period corresponding to the Last Glacial Maximum. This study demonstrates that the Jōmon genome is not only a clue to understanding the origins of the people of the Japanese archipelago but also a valuable record for deciphering the evolution and adaptation of East Eurasian populations who lived through the Ice Age. These findings present a new framework for reconstructing past environmental adaptations from ancient genomes.
Population History and Cold Adaptation in Paleolithic Populations of the Japanese Archipelago
Publication:
What the researchers have recovered from these ancient genomes is not merely a list of genetic differences, but a record of population history written in inherited variation. It tells of an ancestral East Eurasian population diverging during the Last Glacial Maximum, becoming comparatively isolated in the Japanese archipelago, receiving genes from northern peoples and eventually separating into regional Jōmon lineages. This is precisely the complex pattern of descent, migration, isolation and interbreeding expected under evolution—not the sudden appearance of separately created peoples.
The proposed adaptations to cold and diet should, of course, be regarded as informed inferences rather than direct observations of Ice Age physiology. Nevertheless, the convergence of selection signals in several genetic regions associated with thermogenesis, cold sensitivity and lipid metabolism provides a biologically coherent hypothesis that can be tested and refined as more ancient genomes become available. That cautious, evidence-led approach contrasts sharply with creationism, in which the conclusion is fixed in advance and contrary evidence must somehow be ignored or explained away.
The timescale presents an even more fundamental problem. The ancestral Jōmon lineage was already diverging from continental East Eurasian populations between about 27,000 and 19,000 years ago—during an Ice Age that itself forms part of a much longer geological and climatic history. These people had ancestors, neighbours and descendants; they migrated, exchanged genes and adapted to changing conditions many millennia before creationism permits either humans or the planet to have existed.
The Jōmon genomes therefore preserve something that no origin myth can provide: an independently testable account of real people living through real environmental change. Their history does not begin with a magical creation, a mythical first couple or the survivors of an impossible global flood. It emerges from the accumulated evidence of archaeology, palaeoclimate and genetics—a human history shaped by evolution and extending far beyond the cramped chronology of Genesis.
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