The Roots of the Japanese People—Ancient DNA Analysis and Notes on Some Confusing Terminology
Recently, I watched a television science program about where the Japanese people came from.
The Japanese archipelago was once uninhabited. So where did its first people come from, and how did they get there?
The program presented a hypothesis that people crossed the sea during the Paleolithic period, traveling from the direction of Taiwan through the Ryukyu Islands before reaching the Japanese archipelago.
This was during the Pleistocene, when the coastline differed from what it is today. Even then, however, reaching the Ryukyu Islands required a sea crossing.
It is fascinating simply to imagine what kind of boats people used tens of thousands of years ago and what those voyages were like.
Extracting DNA from Bones Tens of Thousands of Years Old
The part of the program I found especially interesting showed researchers extracting DNA from ancient human bones.
A researcher drilled into a bone and collected powder from inside it.
Over the centuries, various microorganisms attach themselves to the surface of a bone. Researchers therefore take samples from the less contaminated interior.
But that is where the real problem begins.
Most of the DNA extracted from the bone belonged to bacteria and other organisms that entered it later.
According to the program, only about 1% of the sample was DNA from the ancient person.
In other words, the researchers had to find the DNA they wanted amid nearly 99% irrelevant DNA.
Moreover, DNA that is tens of thousands of years old has broken into tiny fragments and suffered chemical damage.
Researchers read those fragments, analyze them with computers, and investigate genetic relationships among ancient people.
When you think about it, the task is extraordinary.
Genetically Close to the Jomon People but Distant from Modern Japanese People?
The figures presented as results of the analysis were also interesting.
The ancient person was described as having about a 50% genetic affinity with the Jomon people, but only about a 5% relationship with modern Japanese people.
However, it is necessary to confirm exactly what genetic measure those figures represent. A percentage of matching DNA and a percentage of genetic ancestry inherited from an ancestral population mean completely different things.
In any case, it is clear that modern Japanese people did not simply inherit the genes of the first people who reached the Japanese archipelago unchanged.
Over the long period that followed, many different groups migrated to the islands.
Although we speak of “the ancestors of the Japanese” as though they were a single group, the reality is a history of migration and intermixture extending across tens of thousands of years.
The more you investigate the roots of the Japanese people, the more interesting the subject becomes.
The Terminology Is Far Too Confusing
I was impressed by the program, but I also had a problem.
One technical term appeared after another.
Bone apatite, hydroxyapatite, collagen, sediment, microbial DNA, ancient DNA, and more.
I can more or less follow the explanation while listening, but by the next day I have forgotten it completely.
The structure of bone and the mechanisms that preserve DNA are especially difficult to remember from words alone.
So this time, I decided to organize the terminology as a reference for myself.
Ancient DNA Analysis Glossary
| Term | Meaning |
|---|---|
| Paleolithic | The prehistoric period primarily associated with the use of chipped stone tools |
| Neolithic | A prehistoric period characterized by developments including polished stone tools; its timing and features vary by region |
| Pleistocene | The geological epoch from about 2.58 million to 11,700 years ago |
| Holocene | The geological epoch from about 11,700 years ago to the present |
| Ancient DNA (aDNA) | DNA preserved in ancient bones, teeth, and other remains |
| Bone powder sample | Powder collected from inside a bone for DNA analysis |
| Bone apatite / Hydroxyapatite | Calcium phosphate minerals that give bone its hardness and may also play a role in DNA preservation |
| Collagen | The main structural protein found in bone |
| Sediment | Deposited material such as soil and sand found around archaeological remains and fossils |
| Microbial DNA | DNA from bacteria, fungi, and other microorganisms that have entered a sample |
| Exogenous DNA | DNA originating from something other than the individual being analyzed |
| DNA fragmentation | The process by which long DNA molecules break into shorter pieces |
| DNA sequencing | The process of reading the order of bases in DNA |
| Next-generation sequencing (NGS) | Technology that reads large numbers of DNA fragments in parallel |
| Genetic affinity | Genetic similarity between populations or individuals |
| Ancestry | The genetic origins inherited by an individual or population |
Once organized this way, the process is surprisingly easy to understand.
Researchers take a sample from an old bone, read data containing enormous amounts of irrelevant DNA, isolate the fragments they need, and compare them with data from other ancient people.
In IT terms, it is like recovering necessary data from a corrupted backup.
Except this backup is tens of thousands of years old, and 99% of it is filled with data from other organisms.
The fact that modern science can reconstruct the history of human migration from something like that is astonishing.
And yet, although we live in an age when scientists can decode DNA from tens of thousands of years ago, I cannot even remember the technical terms I heard on television yesterday.
My memory may be in worse condition than the ancient DNA.