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Genetics of origin. Haplogroups

Origin is one of the most interesting sections of the Atlas genetic test . From it you can find out your haplogroup, population structure and how much you are Neanderthal. In a series of articles, we decided to talk about genetics of origin in more detail: how this area is investigated, what data we can get and what they mean. In the first article we talk about haplogroups.


Earth model with the migration of ancestors from the Atlas account

What are haplogroups


Before diving into the definition of haplogroups, let's first recall how children inherit the genetic material of their parents.

There are 23 pairs of chromosomes in our genome: one from each parent. In the case of girls, the 23rd pair consists of two X chromosomes, and in the case of boys, it consists of X and Y chromosomes. Every child also inherits mitochondrial DNA from the mother - one that is not in the nucleus, but in the mitochondria.

Each person has unique genetic information, which is obtained, inter alia, due to the recombination of parental genes. In this case, the Y chromosome and mt DNA remain unchanged until any random change in the gene occurs, for example, a single nucleotide polymorphism.

Such a change will be inherited, and we can determine the group of people that came from one ancestor. Such groups are called haplogroups. A group of alleles that is inherited unchanged is a haplotype.



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All men and women on earth have common ancestors - the Y-chromosome Adam and mitochondrial Eve. They were not the first and only people on Earth, just mt-DNA and Y-chromosomes of other people who lived 150-100 thousand years ago did not survive. The polymorphisms of the Y-chromosomal Adam and mitochondrial Eve are in every person on the planet.


Y-chromosome haplogroup migration pattern

Other changes in the Y chromosome and mt DNA are not so common, but they still occur in a large number of people. One haplogroup can be identified in tens of thousands of people, the second in thousands, and the third in only a hundred. The reason for this unevenness is the drift of genes. The fact is that due to random events, the frequency of alleles in a population changes. The group of people that went through the bottleneck will leave behind fewer defined changes than the other groups.



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All haplogroups except the root haplogroup have a parent haplogroup and one or more daughter haplogroups. For example, R1b1 is the “daughter” of the haplogroup R1b. The first letter in the name means the main group, while the remaining letters and numbers are used for later changes in DNA.


Haplogroup Tree with a Vertical Timeline

In the Atlas genetic test, we examine all the main haplogroups and their subclades - second-level branches. If we find polymorphisms of more specific subclades - the third, fourth level and lower - they will also be included in the report. From the open data we took information about haplogroups of famous personalities. For example, if the test shows that you have one haplogroup with Tom Hanks or Nikolai Copernicus, then you have a common ancient ancestor with him.

In Russia, the most common Y-chromosome haplogroups are R1a, N, I2, and mitochondrial haplogroups are   H, U5, J.

Haplogroups can be associated with human health, which is quite logical, because some populations are more susceptible to certain diseases than others. However, there has been little research on this topic.


Mitochondrial haplogroup migration pattern

One study revealed that ischemic cardiomyopathy is more often diagnosed in people with maternal haplogroup H than in the rest. And haplogroup J, on the contrary, was more common in healthy people. It is worth noting that the groups in the study were small, about 400 people each.

British study showed that coronary heart disease was more common among carriers of the paternal haplogroup I. This study was larger, it used data from 3200 Britons.


How haplogroups are determined


The data structure and calculation algorithm are the same for both the maternal and paternal haplogroups. The only difference is that for the first one, the mt DNA is counted, and for the second, the Y chromosome and mt DNA are used.

There are many different tools for determining haplogroups by polymorphisms. Various tools for calculating the paternal haplogroup can be found here , and for the maternal haplogroup here . In some cases, data on short tandem repeats (STRs) rather than polymorphisms can be used to determine the paternal haplogroup.



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To determine the haplogroup by microsatellites, a suitable combination of different short tandem repeats is selected. When they match the values ​​that correspond to a particular haplogroup, the user gets the final result.

The analysis for polymorphisms is different. Each node of the haplogroup tree is a set of specific polymorphisms. From open sources, we take the appropriate tree depending on whether the paternal or maternal haplogroup is calculated, and assign weight to each polymorphism. The less often an option is found in a tree, the greater its weight.

The path in the polymorphism tree from the root to each haplogroup must correspond to the maximum total weight. Thus we get the user tree, where the result is the bottom haplogroup in the tree. In your personal account, the user will also see the parent haplogroups that were previously met.


How it looks in your account


In the Geography section, the user sees his haplogroups and a description of them. In males, both maternal and paternal haplogroups are displayed, in women, only maternal.



Polymorphisms in the genome accumulate at a relatively constant rate. It is enough to divide the number of changes by speed to find out the approximate time of occurrence of the mutation. There is also open access data on the migration of maternal and paternal haplogroups.

We decided to combine all this with the results of the user and visualize the migration of his ancestors on the model of the Earth. You can see and twist it here . In one of the following articles we will describe in detail how the model was assembled and what problems it encountered.

From the open data we took information about haplogroups of famous personalities. For example, if the test shows that you have one haplogroup with Tom Hanks or Nikolai Copernicus, then you have a common ancient ancestor with him.



In the next article, the Atlas will explain why genetics use the concept of population, how it differs from nationality, and how the population composition of a person is determined by gene variants.

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