History stored in DNA

    imageOn February 13, 2014, Nature magazine published an article entitled “The Late Pleistocene Human Genome (based on the remains found in the Clovis culture burial site in Western Montana)”. Clovis is a prehistoric American culture named after a city in the state of New Mexico, in the area of ​​which stone tools of this culture were found in the 1920s and 30s. Representatives of Clovis lived here at the end of the last ice age, that is, about 13–12.6 thousand years ago, and many American paleontologists consider it the progenitor of all indigenous tribes of North and South America. At the time of publication of the article, scientists have not yet reached a consensus regarding the origin of Clovis culture. Most believed that its representatives came to America from Asia, but some suggested an alternative route through South-Western Europe along the margins of the ice caps that covered the Atlantic Ocean. The historical significance of the Montana burial was immediately apparent. It was discovered in 1968 on land belonging to the Anzik family, at the foot of the Rocky Mountains near Wilsola. In the burial were found the skull and remains of the bones of a boy aged from a year to a year and a half, which the researchers named Anzik-1. In addition, in the only known science of the burial of the Clovis culture, there were many stone tools and fragments of bone tools. In the burial were found the skull and remains of the bones of a boy aged from a year to a year and a half, which the researchers named Anzik-1. In addition, in the only known science of the burial of the Clovis culture, there were many stone tools and fragments of bone tools. In the burial were found the skull and remains of the bones of a boy aged from a year to a year and a half, which the researchers named Anzik-1. In addition, in the only known science of the burial of the Clovis culture, there were many stone tools and fragments of bone tools.

    Radiocarbon analysis showed that the age of the bones of the child was 12 700 years. Thus, the Montana burial turned out to be the oldest discovered in North America. This fact, as well as the presence in the burial of characteristic tools, proved that Anzik-1 died at the very early stage of the Clovis migration. Sequencing of its genome could provide scientists with valuable information about the ethnic and geographical origin of the first Americans. This task was undertaken by a team of evolutionary biologists from Denmark, together with experts from the National Historical Museum and the University of Copenhagen.

    So, what exactly were the scientists looking for in the genome of a boy who died during the last glaciation of the Earth?

    They wanted to learn more about our origins and human migrations at a time when their survival depended on hunting and gathering, when all tools and weapons were made of wood, bone and stone, and when borders, empires, cities and farmlands did not exist.

    To better understand what they were looking for, you need to know the term “single nucleotide polymorphism,” or SNP. It sounds difficult, but, as we will see later, in fact there is nothing easier. So welcome to our magical train that runs along the DNA tracks. Today, the route is laid along the DNA segment of the germ cell (spermatozoon or egg) during its formation. I want to draw your attention to the process that sometimes occurs during DNA replication. I think I do not need to be reminded that the sections of our railway track consist of complementary nucleotides. C always joins G, A and T with the help of hydrogen bonds. Observing replication, you can see how the rails begin to diverge. Hydrogen bonds weaken and split, the process of copying begins. I direct our train to the lowest branch - the so-called antisense thread. We drive east for a long time, until finally I stop the engine. Let's get out of the cars and consider one railway train.

    - So, you have a section of DNA in the so-called non-coding part of the genome. It is not an element of the gene that encodes a protein.
    - What are we looking for?
    - Copy error.

    As before, you easily notice it. The error occurred where, when the web was re-formed, the G and the complementary to it Ts should have joined. In place of C (cytosine), T (thymine) appeared. So, we have another point mutation. It is obvious that G and T cannot connect with each other, therefore this section of the web is damaged. But in the course of subsequent replication cycles, T who is not in his place will attract complementary A (adenine) when copying to a new coding thread. This change in the DNA sequence will be transmitted to germ cells, inherited by the child that has formed from them, and then by all its descendants. It is this change that is called single nucleotide polymorphism, or snip (according to the English abbreviation SNP).

    Mutation occurs in non-coding sequence, so it will not affect the health of the child. Natural selection ignores such snipes. In scientific terms, we can say that they are selectively neutral. This means that all subsequent generations inherit them without harm or advantage for themselves. Over time, single nucleotide polymorphisms accumulate in the population of a species, creating genetic markers in certain regions of the chromosomes. These markers then become pointers to specific genetic lines.

    In the genome of each person there are millions of snaps. They point to differences between individuals and between entire populations. Some snaps form clearly defined clusters in certain regions of the chromosomes. Such clusters are called haplotypes and are inherited as a whole. They are not damaged even by the exchange of elements of coinciding chromosomes during sexual recombination, which occurs during the formation of eggs or spermatozoa. Here I should note that initially the concept of "haplotype" denoted gene clusters that tend to co-inheritance. However, the definition of the haplotype had to be changed when we found out that most of the human genome is not genes. If you are a man, your Y chromosome will have the same haplotype your father and all the male ancestors on the paternal side. The same applies to the mitochondrial haplotype, which both men and women receive through the mother.

    Genetics use another way of grouping - into haplogroups, which are used to unite haplotypes according to a common ancestor. However, here I must urge you to be attentive, as some genetics ignore the differences and use the concepts of “haplogroup” and “haplotype” as if they meant the same thing. For example, men of Celtic descent, that is, Irish, Welsh, and Basque, are united by a Y-chromosomal haplogroup, as are men of German-Scandinavian origin. But if we go even further, most European men (or women) can be combined into a haplogroup of even earlier origin, for example, from Asian roots. For this reason, haplotypes are usually used when working with close relatives and family trees,

    A haplogroup (or haplotype) begins with a root, or basic, mutation, which is found during archaeological and paleontological research in a specific human population. Then, additional selectively neutral mutations are added to it within the same region of chromosome propagation, which over time creates distinct genetic subgroups. The root mutation is usually denoted by a capital letter, and the subsequent mutations arising due to additional snaps are denoted by numbers or lower case letters. Genetic lines form something like a tree - branches that are getting thinner and thinner depart from a single trunk. These branches denote subgroups diverging from the main group over thousands, tens or even hundreds of thousands of years.

    One such ancient haplogroup, found exclusively in mitochondrial DNA, is called the D-clade, or monophyletic taxon D. It originated as a root snip in a population that lived in Northeast Asia, including modern Siberia, about 48 thousand years ago. Over time, the descendants of the D population introduced into the mitochondrial DNA and other snakes, which led to the emergence of four branches, or clades, from D1 to D4. Additional mutations within the branches that continued to migrate caused the appearance of subgroups. Each new branch, or subgroup, corresponded to a specific geographic location or a time period of population movement, which could be confirmed using archeology, for example, by radiocarbon analysis.

    But back to the child Anzik-1. We know that radiocarbon analysis determined its age as 12,600–13,000 years. This means that this child was alive at the very beginning of the colonization of both Americas. Its mitochondrial haplogroup is D4h3a, a rare genetic line characteristic of the indigenous peoples of America. Given the dating and haplogroup, the researchers concluded that Anzik-1 belonged to an ethnic group close to the founder of the D4h3a line, that is, members of his ethnicity were the ancestors of 80% of Native Americans and close relatives of the remaining 20%. The study of the Anzik-1 genome also showed a distant resemblance to some European haplotypes.

    In the journal, the same group of geneticists and archaeologists described the remains of a 24 thousand-year-old boy discovered in an early Paleolithic burial in Siberia. This is the most ancient remains of modern man, found today. The study of his haplotype showed that he belonged to an even older mitochondrial haplogroup than Anzik-1, more precisely, to the baseline of the haplogroup R. Today, it includes people living in Western Eurasia, South Asia and Altai in southern Siberia. Related to the haplogroup R-lines form the Q haplogroup, which is common among the indigenous people of America. In Eurasia, its branches closest to the US are also found in Altai. According to the Danish paleontologist Eske Villersleva, who led the genome sequencing of both findings, "At some point in the past, a group of East Asian people and a group from Western Eurasia met, and their descendants spread widely around the world." In particular, they headed eastward over the land bridge between Asia and North America and found two huge rich continents not inhabited by people. From them came most of the indigenous American peoples who are known to us today, including the Anzik-1. Let not everyone agrees with Villerslev, the remains of these two boys explain why Native Americans and Western Eurasians have from 14 to 38% of the genome. From them came most of the indigenous American peoples who are known to us today, including the Anzik-1. Let not everyone agrees with Villerslev, the remains of these two boys explain why Native Americans and Western Eurasians have from 14 to 38% of the genome. From them came most of the indigenous American peoples who are known to us today, including the Anzik-1. Let not everyone agrees with Villerslev, the remains of these two boys explain why Native Americans and Western Eurasians have from 14 to 38% of the genome.

    An excerpt from the book "The Mysterious Human Genome"

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