Geographic regions in Japan from which the samples were recruited are described. These regions include the Japan archipelago, commonly known as Hondo, and the Ryukyu archipelago, which is termed as Okinawa in this study.
From: Xiaoxi Liu et al (2024).
In my previous post, I showed how scientists, unlike creationists, can and do change their minds when the facts change, using the example of revised dates for the repopulation of the post-glacial British Isles. In this post, I will use another example: a recent revision in our understanding of the origins of the population of the Japanese archipelago.
It had long been believed that a two-part model could largely explain modern Japanese people: indigenous Jomon hunter–gatherer–fishers and later migrants from continental East Asia, associated with rice farming and the cultural transformations that followed. However, whole-genome analysis of 3,256 people from across Japan has shown that the picture is more complex.
The new study identified three major ancestral components: Jomon, East Asian, and a north-east Asian component, most strongly represented in north-eastern Japan and possibly connected with the historical Emishi people. The study was conducted by researchers from RIKEN’s Center for Integrative Medical Sciences. RIKEN is Japan’s National Research and Development Agency and its leading national comprehensive research institute. The research was published, open access, in April 2024 in Science Advances.
The fact that the population history of the Japanese archipelago is best explained by multiple ancestral components, regional structure, migration and admixture is, of course, utterly incompatible with the childish creation and global flood genocide of Bible mythology. It is not a history of people magically created without ancestry, followed by a population reset from a single family of flood survivors. It is the history of an evolved species, carrying in its DNA the record of earlier populations, migrations, interbreeding and selection.
Nor was that the only embarrassing finding for creationists. The researchers also identified DNA inherited from archaic humans, including Neanderthals and Denisovans, in modern Japanese genomes. Some of these introgressed segments are medically relevant. For example, a Denisovan-derived region within the NKX6-1 gene is associated with type 2 diabetes and may influence sensitivity to semaglutide, a drug used to treat the condition. The researchers also identified 11 Neanderthal-derived segments associated with conditions including coronary artery disease, prostate cancer, rheumatoid arthritis and four other diseases. By way of comparison, the RIKEN article also notes earlier research showing that a Neanderthal-inherited cluster on chromosome 3, present in roughly half of all South Asians, is linked to a higher risk of respiratory failure and other severe effects of Covid-19.
In other words, the genomes of modern Japanese people, like the genomes of all modern human populations, contain the traces of real ancestry: migration, admixture, archaic introgression, natural selection and inherited vulnerabilities. This is exactly the sort of messy, contingent history that evolution predicts, and exactly the opposite of what creationists need if their mythology is to be treated as real history.
Who Were The Jōmon? The Jōmon were the prehistoric hunter-gatherer-fisher peoples of the Japanese archipelago, living long before the arrival of large-scale rice farming from mainland Asia. The name “Jōmon” means “cord-marked”, referring to the characteristic pottery decorated by pressing cords into the wet clay before firing. Jōmon pottery is among the oldest pottery traditions in the world, and the period is generally dated from roughly 13,000 years ago until the first millennium BCE, although dates vary by region and archaeological convention. [1.1]The research paper was later summarised in a research news feature from RIKEN:
Unlike the popular image of hunter-gatherers as necessarily small, wandering bands, many Jōmon communities were relatively settled, especially where forests, rivers and coastlines provided dependable food. Their diet included fish, shellfish, deer, boar, nuts, acorns, chestnuts, berries and other wild foods. In coastal areas, shell middens preserve evidence of a highly successful maritime and fishing economy, while inland sites show adaptation to forest and river environments.
Jōmon society was not a single uniform culture frozen in time. It lasted for thousands of years and varied greatly from Hokkaido in the north to Kyushu and the Ryukyus in the south. Over that long period, Jōmon communities developed regional styles of pottery, tools, ornaments and ritual objects. Some sites, such as those in northern Japan, show substantial settlements, storage pits, burial areas, trade goods and evidence of long-distance exchange. The World Heritage Jōmon sites in northern Japan preserve a record of increasing sedentism, craft production and complex social life over about 10,000 years. [2.1]
Their material culture included stone tools, bone and antler implements, fishing equipment, lacquered items, beads, ornaments and the famous clay figurines known as dogū, many of which appear to have had ritual or symbolic significance. Far from being a primitive prelude to “real” civilisation, Jōmon culture represents one of the world’s most enduring and sophisticated hunter-gatherer-fisher traditions.
Genetically, the Jōmon are important because they contributed ancestry to later populations of the Japanese archipelago, including modern Japanese people. Earlier models tended to explain Japanese origins as a mixture between Jōmon people and later continental migrants associated with agriculture, but recent ancient and modern DNA studies show a more complex picture, with Jōmon ancestry forming one component in a broader history of migration, admixture and regional population structure. [3.1]
That makes the Jōmon especially significant in the study of human evolution and population history. They were not people without ancestry, nor were they a separate creation. They were part of the wider human story: descendants of earlier populations, adapted to the environments of prehistoric Japan, and ancestors in turn of later peoples who inherited part of their genetic and cultural legacy.
DNA study challenges thinking on ancestry of people in Japan
By studying the genomes of more than 3,000 people across Japan, researchers have shed light on the population’s complex ancestry. The work may also pave the way for future precision medicine.
A genetic study led by researchers from RIKEN’s Center for Integrative Medical Sciences has uncovered evidence that people in Japan descend from three ancestral groups1.
The findings, published in Science Advances in April 2024, challenge the longstanding belief that there were two main ancestral groups in Japan: the indigenous Jomon hunter–gatherer–fishers and the rice-farming migrants from east Asia.
Instead, the researchers identified a third group with potential ties to north-east Asia—the so-called Emishi people, thus lending further credence to a ‘tripartite origins’ theory first suggested in 20212. The Japanese population isn’t as genetically homogenous as everyone thinks, says RIKEN’s Chikashi Terao, who led the study.
Our analysis revealed Japan’s subpopulation structure on a fine scale, which is very beautifully classified according to geographical locations in the country.
Chikashi Terao, senior author.
Laboratory for Statistical and Translational Genetics
RIKEN Center for Integrative Medical Sciences
Yokohama, Japan.
Combing for clues
Terao’s team arrived at their conclusions after sequencing the DNA of more than 3,200 people across seven regions of Japan, running the length of the country from Hokkaido in the north to Okinawa in the south. It is one of the largest genetic analyses of a non-European population to date.
The researchers used a technique called whole-genome sequencing, which reveals an individual’s complete genetic makeup—all three billion DNA base-pairs. It provides roughly 3,000 times more information than the DNA microarray method, which up until now has been used more widely.
Whole-genome sequencing gives us the chance to look at more data, which helps us find more interesting things.
Chikashi Terao.
To further enhance the data’s usefulness and examine the potential links between genes and certain diseases, he and his collaborators combined the DNA information obtained with relevant clinical data, including disease diagnoses, test results and information on both medical and family history. They collated all of this into a database known as the Japanese Encyclopedia of Whole-Genome/Exome Sequencing Library (JEWEL).
One topic of particular interest to Terao’s was the study of rare gene variants.
We reasoned that rare variants can sometimes be traced back to specific ancestral populations, and could be informative in revealing fine-scale migration patterns within Japan.
Chikashi Terao.
Their hunch proved right, helping to reveal the geographic distribution of Japanese ancestry. Jomon ancestry, for instance, is most dominant in the southern, subtropical shores of Okinawa (found in 28.5% of samples) while lowest in the west (just 13.4% of samples). By contrast, people living in western Japan have more genetic affinity with Han Chinese people—which Terao’s team believes is likely associated with the influx of migrants from east Asia between the year 250 and year 794, and is also reflected in the comprehensive historical adoption of Chinese-style legislation, language and educational systems in this region.
Emishi ancestry, on the other hand, is most common in northeastern Japan, decreasing to the west of the country.
Traces of the past
The clay figurine at the left, which was found in Japan, has been linked to the Jomon people, one of the most dominant ancestries on the southern, subtropical island of Okinawa, while people living in western Japan share more genetically with Han Chinese people, represented by the figurine on the right.Left: © Penta Springs Limited / Alamy Stock Photo;
Right: © cai liang / Alamy Stock Photo.
The researchers also examined JEWEL for genes inherited from Neanderthals and Denisovans, two groups of archaic humans that interbred with Homo sapiens.
…such genes are sometimes associated with certain traits or conditions.We are interested in why ancient genomes are integrated and kept in modern human DNA sequences.
Chikashi Terao.
For instance, other researchers have shown that people in Tibet have Denisovan-derived DNA within a gene called EPAS1, which is believed to have aided their colonization of high-altitude environments3. More recently, scientists discovered that a cluster of Neanderthal-inherited genes on chromosome 3—a trait that is present in roughly half of all south Asians—is linked to a higher risk of respiratory failure and other severe symptoms of Covid-194.
The analysis by Terao’s team shed light on 44 ancient DNA regions present in Japanese people today, most of which are unique to East Asians. These include a Denisovan-derived one, located within the NKX6-1 gene, known to be associated with type 2 diabetes, which the researchers say could affect a person’s sensitivity to semaglutide, an oral medication used to treat the disease. They also identified 11 Neanderthal-derived segments linked to coronary artery disease, prostate cancer, rheumatoid arthritis and four other conditions.
Toward personalized medicine
The RIKEN-led team also used data on rare genetic variants to uncover the potential causes of diseases. For example, they found that one variant of a gene called PTPRD has the potential to be “highly damaging” because it could be linked with hypertension, kidney failure and myocardial infarction, says Xiaoxi Liu, a senior scientist in Terao’s lab and the study’s first author.
Additionally, the team noted significant incidence of variants—also called loss-of-function variants—in the GJB2 and ABCC2 genes, which are associated with hearing loss and chronic liver disease, respectively.
Teasing out the relationship between genes, their variants, and how these impact traits, including disease predisposition, could one day play a role in helping scientists develop personalized medicine, says Terao.
What we’ve tried to do is to find and catalog loss-of-function gene variants that are very specific to Japanese people, and to understand why they are more likely to have some specific traits and diseases. We’d like to connect population differences with differences in genetics. […it’s] quite important to expand this to the Asian population so that in the long run, the results can benefit us too.
Chikashi Terao.
In the future, he hopes to expand JEWEL and include even more DNA samples in the dataset. For the longest time, large-scale genomic studies have focused on analyzing data from people of European descent.
Publication:
The important point here is not merely that scientists have revised an earlier model. It is that they have done so because new evidence required it. The older two-part model of Japanese ancestry was useful while it fitted the available data, but whole-genome sequencing has now revealed a more complex history involving Jōmon, East Asian and north-east Asian ancestral components, together with traces of archaic human introgression from Neanderthals and Denisovans. So the model changes, not because science has failed, but because science is working exactly as it should.
And that is precisely what creationism cannot do. It begins with a conclusion and then tries to force the evidence to fit it. There is no mechanism in creationism for admitting that the evidence has overturned the story, because the story is held to be sacred and unchangeable. Science, by contrast, is provisional, self-correcting and evidence-led. When better evidence arrives, honest scientists alter their conclusions accordingly, and, as we see here, by revising their understanding scientists almost invariably refute creationism with even greater precision.
The genomes of modern Japanese people, like the genomes of every human population, are not the product of a magical act of special creation, still less of a global population reset a few thousand years ago. They are historical documents written in DNA: records of migration, isolation, admixture, selection, survival and interbreeding with other human species. They reveal a deep, complex and fascinating human past extending far beyond the cramped chronology of Bible literalism.
So once again, the evidence points in the same direction as it always does: to humans as evolved African apes whose descendants spread, diversified, mixed and adapted over tens of thousands of years. And once again, the creationist alternative contributes nothing to our understanding. It predicts none of this, explains none of it, and is contradicted by all of it.
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