Ancient DNA tool “ancIBD” reveals distant genetic ties uncovering hidden relatives across millennia

In the realm of biological relationships, individuals who share common ancestry possess extended stretches of DNA known as “Identity by Descent” (IBD) segments. These almost identical genomic segments, inherited from a recent common ancestor, serve as a genetic fingerprint of relatedness. Personal genomics companies like 23andMe and Ancestry routinely leverage this phenomenon to identify biological relatives among their customers, detecting IBD segments in their DNA databases.

A recent breakthrough, detailed in a study published in Nature Genetics by researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, and Harvard University, introduces a powerful tool named “ancIBD.” This innovative tool aims to extract IBD segments from the genomes of individuals who lived hundreds, thousands, or even tens of thousands of years ago.

The primary challenge faced by the researchers was the often degraded state of ancient genomes, presenting lower quality compared to contemporary DNA. To overcome this hurdle, the authors devised a clever strategy involving the use of modern reference DNA panels to fill in gaps in the ancient genomes.

This advancement opens up unprecedented avenues for the analysis of ancient DNA data. “By precisely measuring the regions of shared genome, we can now identify pairs of up to sixth-degree relatives in ancient genomes. Previous ancient DNA methods, relying on genomic average similarities, were limited to detecting only up to third-degree relatives,” explains Yilei Huang, a first author of the study and Ph.D. researcher at the Max Planck Institute for Evolutionary Anthropology.

The development of ancIBD not only extends the scope of identifying genetic relatedness in ancient populations but also underscores the ingenuity required to overcome the challenges posed by the degraded nature of ancient DNA. This tool promises to enhance our understanding of familial relationships among ancient individuals, shedding new light on the genetic interconnectedness of human populations across different epochs.

Researchers identified hundreds of new pairs of relatives

Utilizing their innovative tool, ancIBD, the researchers applied it to a dataset featuring 4,248 ancient genomes spanning Eurasia over the past 50,000 years. This groundbreaking approach led to the identification of numerous previously unnoticed pairs of relatives, unraveling fascinating insights into the mobility of ancient populations.

A particularly intriguing instance revealed two Early Bronze Age nomads from Central Asia, living around 5,000 years ago, who were fifth-degree relatives despite being buried approximately 1,500 kilometers apart. This discovery underscores the remarkable journeys undertaken by these individuals or their immediate ancestors, traversing vast distances from birth to burial.

The versatility of the new tool also empowered the investigation of even more distant relatives with unprecedented precision. While not all relatives beyond the tenth degree exhibited long shared IBD, the authors could quantify the average rate of long DNA sharing between groups of ancient individuals. This approach unveiled previously undiscovered connections, unveiling exciting links between ancient cultures and showcasing close relationships over considerable distances and time spans.

Harald Ringbauer from the Max Planck Institute for Evolutionary Anthropology, the lead researcher, emphasizes the significance of these findings. “We found exciting links between ancient cultures, and the signal of long shared segments allowed us for the first time to specifically demonstrate close relationships between important ancient cultures, sometimes over vast spaces over the order of only a few hundred years.”

This novel method for scrutinizing ancient DNA for parental relatedness provides researchers with a versatile computational tool. As the field of ancient DNA continues to rapidly evolve, with thousands of ancient genomes generated annually, this tool promises to shed new light on the lives of our ancestors. It operates on both a small scale, providing insights into individual life stories and their familial connections, and on a larger scale, contributing to our understanding of significant cultural-historical events.

Source: Max Planck Society

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