Researchers develop a new method to analyze the genetic mixture of populations

Researchers at the HSE International Laboratory for Statistical and Computational Genomics together with their international colleagues have proposed a new statistical method for analyzing population admixture that allows the time and number of migration waves to be more precisely determined. The history of Colombians and Mexicans (descendants of Amerindians, Spaniards and Africans) presents two episodes of miscegenation that occurred about 350 and 200 years ago for Mexicans and 400 and 100 years ago for Colombians. The results were published in PLOS Genetics.

When Francis Crick and James Watson deciphered the structure of DNA in 1953, they declared that they had “found the secret of life.” In fact, all life on Earth reproduces by constantly dividing cells and copying their genetic material. DNA is passed down from generation to generation. from generation to generation, and Human genome it is a mosaic of genetic fragments from our ancestors from different times. To understand the origins of genetic diversity in modern humans, it is necessary to study the history of populations: where our ancestors lived, when and where they migrated, when and how they mixed.

The story of population admixture can be discovered by analyzing the connections between human genetic variants. Our genome has genetic material of our father and mother; then we pass on new combinations of genetic variants, a mosaic made up of our parents’ genomes, to our offspring. This phenomenon is called recombination.

For example, a Spanish mother and a Native American father will have a child with one Spanish and one American set of chromosomes. Her son, in turn, will pass on a set of chromosomes that includes a combination of sections of Spanish and American origin to his descendants (the second set of chromosomes will be inherited from the other parent). The origin of these sections can be determined by the sequences of genetic variants typical of a particular population. in each new generation, recombination will mix more and more sections from different origins, breaking these typical genetic sequences. Over time, they disintegrate and eventually mix with each other.

Therefore, by calculating the correlation between genetic variants on different parts of the chromosomes and analyzing the strength of their connections, we can tell how many generations ago population admixture occurred.

Previous methods of analyzing the genetic admixture of populations were able to estimate the time of the last admixture event. The algorithm was based on the analysis of the connection strength between pairs of genetic variants. Researchers at the HSE International Laboratory for Statistical and Computational Genomics and their international colleagues proposed to analyze triplet variants. East statistical method makes it possible to model more complex population admixture scenarios, for example, to identify two admixture episodes and determine how many generations ago they occurred.

“Imagine that ships with European settlers land on the shores of America for the first time. Europeans begin to explore new territories and mix with the indigenous population of America. However, after a few generations, more ships with Europeans arrive in America. Our method allows us to see that there were two waves of resettlement, two episodes of miscegenation in different periods of time”, explains Mikhail Shishkin, co-author of the article, research assistant of the laboratory and MIEM student.

As an example, the authors of the work analyzed genetic samples from the population of Colombians and Mexicans from the 1000 Genomas genetic database. Both populations appeared as a result of the mixture of Native Americans, Spanish and Africans. The results showed that the history of both populations had two waves of miscegenation, which occurred 13 and 8 generations ago (350 and 200 years) for the Mexicans and 15 and 4 generations ago (400 and 100 years) for the Colombians.

“Our method requires large amounts of data; if the previous algorithms required dozens of samples, then we need hundreds. And today we can get them. In our case, we used the genetic database of the 1000 Genomes project. During the last 10 years, the possibilities of genome sequencing and data processing have expanded significantly, so the number of available samples no longer limits us,” says Vladimir Shchur, director of the International Laboratory for Statistical and Computational Genomics at HSE University.

Provided by the Higher School of Economics of the National Research University