Back
Table of Contents
Researchers can use ancient DNA to study the formation of populations, but determining paternal lineages in men has so far been difficult because the samples are often with low yield and degraded. Researchers in Tartu have developed a new method that makes it possible to obtain reliable results even from extremely small amounts of DNA.
Male ancestry can be studied using the Y chromosome, which is passed from father to son. The different branches of the male chromosome are called haplogroups, and their distribution helps researchers understand the formation and migration of populations. As the Y chromosome reflects only the paternal line, it can help to reveal whether historical migrations were associated more with the movement of men or women.
A major challenge in studying ancient DNA is that hereditary material breaks down over time into tiny fragments. Therefore, many samples only yield a small fraction of the entire genome. Standard methods that search for individual mutations require more and better-preserved DNA.
The Y-mer method, created as part of a doctoral thesis defended in the Institute of Molecular and Cell Biology of the University of Tartu, approaches the problem differently. Instead of searching for individual changes in DNA, it analyses short DNA sequence patterns across the entire Y chromosome. This allows haplogroups to be determined from extremely small amounts of data – less than 0.01x genome coverage. In practice, this means archaeogeneticists could work with datasets tens or even hundreds of times smaller than previously possible.
The method uses previously underutilised DNA
The idea for the method emerged from the question of how to determine patrilineality between remains from very old burial sites. It was proposed by Toomas Kivisild, Associate Professor of Population Genetics at the University of Tartu.
With ancient DNA, the conventional PCR method often performs poorly because it requires more intact DNA. Although the Y chromosome makes up about one per cent of total DNA, roughly half of it (heterochromatin) has not previously been used. It contains repetitive DNA sequences that were once considered unimportant.
However, Tarmo Puurand noticed patterns in precisely those regions considered to be ‘junk DNA’ that can be detected even from extremely small quantities of DNA.
In the study, I show that the k-mer method, previously developed by bioinformaticians at the University of Tartu, is well suited for analysing such repetitive sequences. The workflow for determining patrilineal haplogroups based on the k-mer frequencies of the Y chromosome was termed Y-mer.
Rapid advancements in genome research
The study of ancient DNA is closely tied to developments in sequencing technology. Y-mer analysis became possible after new sequencing machines were introduced to the market in 2007. Since then, the amount of ancient DNA data has increased dramatically.
Together with colleagues, we tested the method on samples whose Y-chromosome haplogroups were already known. The results showed that larger and older haplogroups can be identified with particular precision.
In addition to archaeological samples, we also tested the method on blood samples from pregnant women (NIPT tests). These samples primarily contain the mother’s DNA, but there are also small amounts of foetal DNA.
Because foetal DNA is limited and fragmented, it is difficult to say anything for certain using conventional methods, especially regarding the paternal lineage of male foetuses. The study demonstrated that the Y-mer method can successfully extract the necessary information even from such data.
Future plans
Researchers are planning to develop similar models for other chromosomes in the future. They also aim to create a system in which Y-chromosome haplogroups are determined during DNA sequencing itself, rather than later during data analysis.
The new method still needs broader introduction so that other scientists can begin using it in their own research.
The study was published in the journal Genome Biology.
Author of this article: Tarmo Puurand (University of Tartu). This article was originally published on the the Estonian Public Broadcasting online news portal.
What is “Junk DNA”?
