Autosomes Are Roots as a Surface, Mitochondrial DNA and the Y Chromosome Are Roots as a Line

In 1990, just before I was born, the Human Genome Project began. It was an attempt to read, from one end to the other, the blueprint inscribed in the creature we call human, and it took thirteen years. Its completion was declared in April 2003.

In other words, only a little more than twenty years have passed since humankind first held its own blueprint in its hands.

Of all the fields that benefited from the door genetic analysis opened, anthropology gained the most. Archaeology produced explosive results throughout the twentieth century, but pottery and the remains of structures are extremely difficult to date precisely, and while their styles can suggest lines of influence, they never had the power to reveal a history of migration with any confidence. Archaeology also, by and large, can speak only of those who stayed on land. The footprints of those who moved across the sea were erased by the waves, and whatever they carried was swept away by the tide. Even so, over the course of the twentieth century, archaeology, folklore studies and anthropology, entangled as they were with nationalism and ethnic nationalism, cut the first paths toward vast questions such as “What is a people?” and “What is humankind?”

Yet however high the findings piled up, something was missing. Artifacts and remains are made by human beings, and without information about those human beings themselves, one can say little more than that this people resembles that one. The success of the Human Genome Project was a great step toward filling exactly this missing piece.

And yet the more ancient skeletons with surviving DNA were excavated, and the more peoples were tested, the clearer it became that humankind is an extraordinarily plural being. Interestingly, DNA carries within our bodies the memory of great migrations that by rights should never have survived, and every one of us holds a memory that is ours alone. Where our ancestors passed and which seas they crossed, the history of migrations from ages that left behind neither writing nor artifacts, had been stored all along as an immense body of data inside our cells. Genetic testing then became gradually democratized, but the decisive turn was the arrival of AI. Today individuals can hold their own genetic information at a depth that was once far beyond anyone’s understanding.

However, when the focus falls on roots, there is something many people overlook. Depending on what you test, the era that comes into view and the breadth of space it covers turn out to be entirely different things. To begin with, genetic ancestry research has two entrances of very different character. One is the autosomes, and the other is mitochondrial DNA together with the Y chromosome. The two look alike but are not, and their results differ at the root.

The autosomes are the twenty-two pairs of chromosomes in the cell nucleus, the main body of information, so to speak, that determines our build and our constitution. We inherit half of them from our father and half from our mother, and with every generation, the fragments that came from a grandfather and those that came from a grandmother are randomly cut, pasted and mixed together. The share we inherit from any particular ancestor therefore thins with each generation, to 50 percent, then 25, then 12.5, like a ball rolling down a slope. An autosomal test therefore reveals the mixture of populations each of us stands as, and in what proportions. It is also why such a test can track down relatives across every line, paternal and maternal alike. The autosomes, in other words, are a mosaic spread out as a surface.

Mitochondrial DNA and the Y chromosome are entirely different in nature. Mitochondrial DNA passes from mother to child and the Y chromosome from father to son, and they are inherited one hundred percent intact, never mixing with the DNA of the other parent. Only mutations, which occur at the low rate of once in several thousand to several tens of thousands of years, are inscribed as new markers and preserved unchanged in the descendants. That is precisely why following them reveals the path by which humans left Africa, crossed Eurasia, moved through Asia, and finally crossed the sea to the Japanese archipelago. Because the information never thins, however many generations pass, these lines carry within them, intact, the movements of ancient populations from the Pleistocene into the Holocene. They are, so to speak, a “line.” They are a single, unimaginably long line.

Since this is hard to picture, let us think about ten generations back.

Ten generations ago means roughly three hundred years ago, the middle of the Edo period. Go back that far, and every one of us has 1,024 ancestors. Yet mitochondrial DNA and the Y chromosome can trace, without exception, only two of them. Countless ancestors enter along the way, but their lines break off, and in the end only these two threads are handed down. The maternal line runs mother’s mother’s mother, and on back. The paternal line runs father’s father’s father, and on back. What can be known is only the two people at the far ends of these two threads, and of the remaining 1,022 we have no information whatsoever. This is the biological course of human life.

The autosomes, meanwhile, are shuffled and halved over and over, so that by about five to seven generations back, some 150 to 200 years, the fragments that come from any specific ancestor have grown too small and vanish altogether. A person who is, as a matter of historical fact, undeniably our ancestor may thus have left us not a single fragment of DNA at the molecular level. We are certainly connected on the family tree, and yet nothing of them remains inside our bodies. This gap is the greatest paradox in what genes can tell us about roots.

What, then, do these “two threads” actually refer to? If you take a test while leaving this vague, you will misread the results.

First, the Y chromosome. It passes only from male to male, from father to son, so a female, a daughter, has no Y chromosome at all. A woman who wants to know her paternal line will find nothing by testing herself, and has no choice but to ask a male relative, her father, a brother, or an uncle on her father’s side, for help.

Next, mitochondrial DNA. It passes from mother to child, to sons and daughters alike. Not only women but men as well do receive the mitochondrial DNA of a woman, their mother. A son, however, cannot pass it on to his own children, because at fertilization the mitochondria from the sperm are broken down and only those from the egg remain.

Here a strange asymmetry arises.

A man can trace two lines on his own, because he carries both the Y chromosome of his paternal line and the mitochondrial DNA of his maternal line. Yet that maternal line is fated to end with him. He can receive it, but he cannot pass it on. To put it in terms of my own case, my mother was an only child and we are three brothers, so the mitochondrial DNA we inherited from her will, sadly, end with my brothers and me.

A woman, a daughter, cannot trace her paternal line from her own body, but she can keep handing the maternal line on to the next generation. This is the decisive difference between the maternal and the paternal lines. Narrowed to the question of what is passed on, it looks like this.

◯ Maternal line | woman → woman → woman → woman → woman → woman → woman → woman → woman
◯ Paternal line | man → man → man → man → man → man → man → man → man

What is fascinating is that there are those who receive but cannot pass on, and those who cannot trace but keep passing on. Our bodies share these two roles between them.

So when you look into your roots through the autosomes, you can see every line, paternal and maternal, but you can go back only about five to seven generations, 150 to 200 years at most. You can roughly work out your ethnic makeup and use the results to find relatives, but as a view of roots it is far too shallow. In a country like the United States, with a short history and a population made up largely of immigrants, this is the kind of service that has become popular, but for the Japanese, with their long history, it offers almost nothing.

Mitochondrial DNA and the Y chromosome, by contrast, can be called the pure maternal and paternal lines. However many generations back you go, the information is preserved one hundred percent, and only mutations accumulate. And as noted above, those mutations basically occur only once in several thousand to several tens of thousands of years. Because of this property, the grand history of migration can be worked out to a certain degree, reaching from ancient times back tens of thousands of years, and telling how modern humans who set out from Africa traveled, arrived in the Japanese archipelago, and came down to us.

Of course, ancestry research using mitochondrial DNA and the Y chromosome has only just begun in earnest, and its resolution cannot yet be called high. Such research does not rest on genetic information alone. It presupposes the human bones excavated by archaeology, enough samples in enough number, and accurate data, and it comes to be understood only by combining all of these. For the Japanese in particular, wide-ranging cooperation is indispensable with neighboring countries such as China, Korea (South and North), Russia, Tibet, Central Asia, Turkey, Southeast Asia and South Asia. Without working together with China, South Korea, North Korea and Russia above all, countries with which Japan has many diplomatic problems, the research cannot move forward.

Even so, anyone can go back through their genetic data as far as the first mother and father from whom they descend. I call them the “Progenitor Mother” and the “Progenitor Father,” and it is here that the vast archaeological and anthropological achievements accumulated by those before us since the twentieth century can at last come into force in the true sense.

Last weekend, I received an enormous set of my own genetic data and, with it, a map. My mitochondrial DNA and Y chromosome, which matter most to me, also produced intriguing results, so I am now planning a new journey toward my roots on my own terms, combining them with the latest anthropological and archaeological data, with the ancient history of Asia, and with the research on ancient Japan that I have carried out myself.

Of course, mitochondrial DNA and the Y chromosome alone cannot answer the question “Who are you?” Every Japanese person carries in their genes three layers, laid down by the Jomon people, the Yayoi people and the people of the Kofun period. The precise question, then, concerns the Progenitor Mother and the Progenitor Father, the origins of the mitochondrial DNA and the Y chromosome we inherited from our mother and father. Where were they born, and by what migrations did their descendants reach the Japanese archipelago?

Once AI begins replacing human labor in earnest, people who no longer need to work will find themselves with time on their hands and will be driven, more and more, toward introspection. When that happens, the question “Who am I?”, intertwined with the democratization of genetic testing, will inevitably turn into a question of roots. At the same time, a new ethnic nationalism for the twenty-first century, grounded in genes, will rise and, for a while, sweep the world.

With that era in view, I intend to be among the first to dig into my own roots. Will the journey, in the end, reach the African continent, which gave birth to humankind’s first mother?

Data filled with masses of cryptic code will come together into a single story. Another personal journey is about to begin. The first findings will probably be published in the 2030s at the earliest.