Ancient DNA analysis reveals some anthropological discoveries of 2022

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This year, the news of ancient human DNA analysis has been in the media a lot. Svante Pabo's Nobel Prize win in evolution in October added more oil to that coil. The study of the genomes of various human species that walked the ancient earth has opened the door to a new success in biology, which is being considered as a revolutionary milestone.

Ancient DNA analysis is now one of the most successful tools in anthropological research. Scientists are working day and night to find out about extinct animals through genome sequencing. Today's event is about 10 remarkable discoveries made by ancient DNA analysis in 2022.

Location of DNA in the nucleus, the heart of the cell; Image Source: Labster.

Neanderthal family of Russia

Scientists have discovered a Neanderthal family living in prehistoric times in the Chagiraska cave in Russia. Although they did not leave much physical evidence in the cave. Notable among the finds were dozens of teeth, and some bone fragments. Carbon dating suggests that they are around 59,000 to 51,000 years old. It should be noted that the Neanderthal species disappeared from the world about 40 thousand years ago. In October, a team of scientists provided genetic data from sixteen pieces of bone.

Handicrafts found in Chagiraska Cave; Image Source: Science Direct.

Analysis of the bone fragments revealed evidence of kinship or group similarity. Some of them have two or three teeth and bone structure found to be similar. DNA analysis of a piece of vertebrae and a molar tooth identified the father and daughter. Father's name can be described as 'A' for ease of understanding. Scientists also found that two relatives of 'A' from his mother's side lived there. Because, all of them are descended from a specific mitochondrial DNA. In biology, this phenomenon is called mitochondrial heteroplasmy. Mitochondria are transferred only from the mother to the child, not from the father, during the formation of the zygote from the sperm and egg. Thus, two of A's relatives come from his mother's side. A finger bone and a canine tooth were also found there, possibly belonging to A's uncle or niece.

Chagiraska Cave; Image Source: Bence Viola.

Ancient DNA

In December, scientist Kurt Zeier and his team shocked the scientific community with the discovery of mastodon DNA. This DNA found in Greenland was about 2 million years old. This is the oldest DNA found so far. The mastodon is the ancestor of mammoths and elephants, which became extinct about 10,000 years ago. According to scientists, Greenland 2 million years ago was different than Greenland today. At that time the temperature was around 20-34 degrees Celsius, and there was greenery all around. Greenland's shell changed after the Earth entered the Ice Age due to massive climate change. However, the temperature is extremely low, allowing DNA to survive for millions of years.

Greenland 200,000 years ago, which was much warmer than today; Image Source: Beth Zaiken.

Another scientific paper this year found that about 5,000 years ago, Greenland was the meeting place of three distinct nation-states, ancient fishers and hunters. One of these tribes is the 'Sakkak', who were the first to settle here. Another race was the 'Thule', who were the ancestors of the present-day inhabitants of Greenland, and the third was the 'Norse' race, who set foot in Greenland around 1000 AD.

Bones of a Norse people who settled in Greenland; Image Source: Le musée Vert/Le Mans.

Denisovan genes in defense

Denisovans were a human branch as ancient as Neanderthals. According to science, the people living in the world today i.e. Homo sapiens have been carrying some genes of Neanderthals and Denisovans in their bodies. But detailed information about the function of these genes has emerged this year. According to the researchers, people from Southeast Asia have the most Denisovan genes. Hence, research is conducted on them.

Geneticist David Vespasiani and his colleagues conducted a study among Indonesian and Papuan people. The study found that the genes carried over from Neanderthals and Denisovans to modern humans had less impact on coding sequences than on non-coding sequences. From there, after collecting data from ancient alleles in different cells, they learned that the Denisovan genes are involved in immune cells.

They then tested the 'OAS2' gene and the 'OAS3' gene. These two genes are important for building the body's defenses against viruses. In that experiment, they saw for the first time that alleles carried over from Denisovans to Homo sapiens were directly responsible for the expression of those two genes.

DNA analysis suggests a Denozoan in artist's drawing; Maayan Harel.

Genome of Anatolia

Deciphering the genome of early humans has been a huge challenge for scientists. A decade has passed since the publication of whole-genome-data papers on people from the Stone Age and beyond. The year 2014 was a milestone in the analysis of ancient human genomes.

This summer, Iosif Lazaridis and his colleagues published three papers showing just how rich this vast field of data generation has become. Together, these three papers include genome data from more than 700 ancient human skeletal remains from Anatolia and adjacent regions.

According to DNA analysis obtained in the last seven years, today's scattered Indo-European speakers in different parts of the world originated from the Yamnaya culture of the Copper Age. But now that research has been shaken up a bit by Lucif Lazaridis and his colleagues. Because, the previous DNA data is not the result of research conducted on the whole of Anatolia. Therefore, those data do not include results from places where some of the earliest Indo-European speakers existed.

Three new papers confirm the influence of people from the plains among the inhabitants of Copper-Age Anatolia. The paper also describes the genealogy of the Y chromosome in the Mycenaean region of Anatolia and Greece. The study also provides a complex understanding of the pre-agriculture of Mesopotamia and Anatolia, and the pre-pottery and pottery of the Neolithic inhabitants of the region.

Skeletons found in Anatolia; Peter Jablonka.

Ancient flora of the cave

Primitive people used various types of plants for food, clothing, art, decoration, cosmetics. But there is very little evidence of plants from archaeological sites. Little is known about ancient plants other than the fact that humans used flowers and airborne pollen in ancient times. Because most DNA evidence is destroyed by time.

Anneke ter Scheuer and her colleagues fortunately discovered ancient plant DNA in the lining of the Aghitu-3 cave in Armenia. They were essentially pollen-cell chloroplast DNA. In the cave, they found plant DNA as well as various Paleolithic artifacts, which are between 43,000 and 26,000 years old. Later in November, they published the news in an article in the Journal of Human Evolution.

Aghitu 3 caves; Image Source: Science Direct.

Mixture of variants in Africa

Our knowledge of the genomes of ancient human species living in Africa is limited. DNA is relatively well-preserved in colder places, and scientists have been sorely lacking such well-preserved DNA in Africa for the past 20,000 years. According to anthropology, modern humans spread throughout the world from Africa.

Despite these limitations, scientists are working tirelessly to learn about the anthropology of mankind through DNA searches from Africa. In February Mark Lipson and his colleagues recovered the DNA of six ancient humans from archaeological sites in Malawi, Tanzania, and Zambia. They have been radiocarbon dated to between 16,000 and 5,000 years ago. They then compared these DNA samples with DNA samples obtained from other locations.

Differences in the skulls of modern humans, Neanderthals, and Denisovans; Image Source: Troy Lawrence.

At the outset, Lipson noted that the people of today's Africa originated from four distinct groups. In the new study, they added, three of these four groups were the ancestors of the original inhabitants of East Africa. Later the four groups bred within themselves to create different varieties. This different anthropological variation of humans from South Africa to East Africa began about 50,000 years ago. As the population density was low then, the distance between the different ethnic groups was relatively large. As the population grew, that gap closed.

An African man 20,000 years ago; Image Source: Shutterstock.

Introduction to Paleogenomics

Undoubtedly one of the most talked about news this year was the Nobel Prize winning in the category of 'Physiology' or 'Medicine' by Svante Pabo. He was awarded the Nobel Prize for his significant contributions to the genetics of extinct hominins and human evolution. He uncovered the genome sequence of Neanderthals, the extinct species closest to modern humans. He also discovered the unknown 'Denisova' hominin. Pebo showed through his research, Homo sapiens exchanged genes with these extinct hominins about 70,000 years ago.

Artist's drawing of a Neanderthal father and daughter, made similar to DNA analysis; Image Source: Tom Björklund.

Today's Homo sapiens carry genes from these ancient humans. Pabo's characteristic research gave birth to an entirely new branch of biology called paleogenomics. We still carry some of the genes of extinct hominins, Pabo said. An example is the Tibetan population. They have the Denisovan version of the EPSA1 gene, which allows them to survive in low oxygen conditions at high altitudes on mountains.

Nobel laureate Savante Pabo; Image Source: Alamy.

Footprints of the plague

Many of the rapidly evolving human genomes are involved in the immune system. Because epidemics span short periods of time, tracing their effects from gene frequencies is fairly difficult. By analyzing the DNA of ancient humans, geneticists try to figure out mortality and survival rates in ancient epidemics.

The Black Death, a European plague that lasted from 1346-1452, killed about half of Europe's population. Jennifer Clunk and her colleagues worked on the genotypes of some Black Death victims, who were buried in the Smithfield mass grave in central London. They then compared the DNA from some corpses that died before or after the Black Death with the information obtained from their genes. Jennifer Clunk obtained two types of genetic results from people who died of the pandemic and those who later succumbed to the effects of the pandemic and died naturally.

Europe's Black Death epidemic in artist's portrait; Image Source: Getty Images

They found many genes whose structure had undergone dramatic changes during and after the Black Death. Those genes have either helped people survive pandemics or pushed them to the brink of death. They experimented with immune cell lines that responded against the bacterium responsible for the pandemic (Yersinia pestis). Those experiments showed that when these genes, important during the Black Death, were exposed to the pathogen, immune cells responded. That is, if this gene was carried to the next generation, it could have developed a defense against the plague.