1. Denisova Cave: A New Human Group Found from One Finger Bone
Denisova Cave is located in southern Siberia. In 2010, scientists extracted DNA from a finger bone found in this cave and read its genome. A genome is the complete set of information that builds a body. The analysis showed that this bone belonged to a group that shared a common ancestor with Neanderthals but was neither Neanderthal nor modern human. This group was named the "Denisovans." [3]
It was also reported that the mitochondrial genome of a tooth found in the cave was very similar to that of the finger bone. [3] Svante Pääbo, a doctor who pioneered the field of ancient DNA, received the 2022 Nobel Prize in Physiology or Medicine for reading the Neanderthal genome and discovering the Denisovans. [1]
The mystery here is how scientists could identify a "new kind of human" with only a small bone fragment as a clue. The next section looks at how these people are connected to us.
2. Neanderthal Genomes: Extinct Humans Live On in Our Genes
In 2010, a draft genome of over 4 billion bases was published from the bones of three Neanderthals. Neanderthals disappeared by about 30,000 years ago, but modern humans in Eurasia share more genetic differences with Neanderthals than modern humans in Africa south of the Sahara do. [2] This suggests that genes flowed between the ancestors of people who left Africa and the Neanderthals. However, this does not mean Neanderthals are our direct ancestors. The proportion of their genes in us is only a small part, less than a few percent.
Did Denisovan genes help people live in high mountains? It was estimated in 2010 that Denisovan genes contributed 4 to 6% to the genomes of Melanesian people. [3] The type of the EPAS1 gene, which is related to living at high altitudes in Tibetan people, is also said to come from Denisovans. A 2021 study estimated that this gene was introduced about 48,700 years ago and began to spread about 9,000 years ago. [4] However, this is a rough estimate with a wide range. The confidence interval for when it was introduced is about 16,000 to 59,500 years ago, and for when it spread, about 2,500 to 42,000 years ago. These ranges vary by study.
It is said that these old gene flows also affect how our current immune systems respond to infectious diseases. [1] So, how can DNA from bones tens of thousands of years old be read without breaking down?
3. The Challenge of Reading DNA from Fragile Bones Contaminated by Modern People
Old bones are often contaminated with the DNA of modern people who touched them while they were stored in museums for decades. By the time they reach the lab, they are already mixed. In 2014, researchers at Uppsala University showed a statistical method to separate and extract old DNA from a computer, even if it was outnumbered by modern DNA. However, this method requires the DNA to be at least 1,000 years old. [5]
Which bones are used? The petrous bone, which houses the inner ear deep inside the skull, is popular because ancient DNA remains very well in it. In one comparison, the average percentage of the original person's own DNA was 40.0% in the petrous bone and 2.2% in the parietal bone. [6] This is an average from one study, showing that the difference depends heavily on the part of the bone. With these techniques, how far back can we read DNA?
4. Mammoth Teeth Over 1 Million Years Old Yield Genomes
In 2021, it was reported that genome-scale DNA was extracted from three mammoth teeth found in northeastern Siberia in the 1970s. Two of these teeth were more than 1 million years old. Before this, the oldest genome data was from horses, dating back 780,000 to 560,000 years. [7]
This old mammoth revealed a lineage that had not been known before. It is called the Krestovka mammoth and is the ancestor of the mammoths that first crossed into North America. The Columbia mammoths in North America were born from a mix of this lineage and another lineage during the Middle Pleistocene, with the mixing ratio being almost half and half. [7] It was also shown that most of the protein changes that help woolly mammoths withstand cold were already present 1 million years ago. [7]
So far, we have talked about bones and teeth. Can the past be read from soil even without bones?
5. Soil DNA Shows a Forest in Greenland 2 Million Years Ago
In 2022, a study examined environmental DNA in soil from layers about 2 million years old in North Greenland. Environmental DNA is DNA left in soil or water, not from the body of the living thing itself. From this, researchers reconstructed an open northern forest mixed with poplar, birch, and alder trees. [8]
For animals, mitochondrial DNA from hares, mastodons, reindeer, rodents, and geese was confirmed, and horseshoe crabs were also found. The Arctic at that time was warmer than it is now, and the reconstructed ecosystem has no parallel in the present day. [8]
Why did such old DNA remain? It is thought that it probably stuck to the surface of minerals. This is still at the "probably" stage. [8] However, this study showed the possibility of tracing past communities of living things with DNA even in places where fossils are scarce. [8] So, what does DNA tell us about the past right next to us in Japan?
6. The Genome of a Jomon Woman and Its Link to Modern Japanese People
A team including the National Museum of Nature and Science read the full genome of a Jomon woman (No. 23) from the Funadomari site on Rebun Island, Hokkaido, with high precision. This was published in 2019. They could estimate her earwax type and tolerance to alcohol. They also found a mutation in the CPT1A gene, which is considered advantageous for metabolizing high-fat diets. This type is common in Arctic groups but is almost absent in modern Japanese people. [9]
How much Jomon DNA is in modern Japanese people? According to reports of the National Museum of Nature and Science's announcement, the proportion of inherited Jomon genomes varies by region. It is about 10% for people from Honshu sampled in Tokyo, about 30% in Okinawa, and about 70% for Ainu people in Hokkaido. [10] These are rough estimates from a small-scale study based on news reports. Modern Japanese people are said to be a mix of Jomon people and people who migrated after the Yayoi period.
Also, analysis of the genome of a Jomon-related person (IK002) from Honshu about 2,500 years ago showed that they are positioned in an old lineage among East and Northeast Asian people. It may represent early migrants who moved north from Southeast Asia. They are genetically close to indigenous people in Taiwan, and a coastal route has been suggested. [11]
7. Finding Out Where Jomon Objects Were Found at a Museum
If there is a Jomon period exhibition at a nearby museum, go see it. Next to the exhibits, there is usually a note saying "where it was found." Look at what kind of place that was and what era it is from. Think about what clues might remain in the soil or bones. This changes how you see the items. One of the sources for this article is an introduction to the results of the team that studied the Jomon genome, published by the National Museum of Nature and Science. You can find other articles through news reports and explanatory pages. [9]