Identity-by-descent method reveals hidden genetic ties in rhesus macaques

The GIST
Editors' notes

This article has been reviewed according to Science X's editorial process and policies. Editors have highlighted the following attributes while ensuring the content's credibility:

fact-checked

peer-reviewed publication

trusted source

proofread

Understanding biological relationships is often critical when studying animal populations. Researchers from the Max Planck Institute for Evolutionary Anthropology, Leipzig University, the German Centre for Integrative Biodiversity Research and the Freie Universität Berlin have now developed a transformative approach that identifies stretches of DNA that two individuals inherited from a common ancestor. The study is published in the journal Proceedings of the National Academy of Sciences.

The team successfully applied their new tool to a free-ranging population of rhesus macaques. The results show that even for low-quality sequencing data, this method can accurately determine relatedness among pairs of individuals, even without prior knowledge of pedigrees within the population. This breakthrough helps to reveal previously unknown pairs of relatives and provides rich insights into population structure in the wild.

Quantifying which individuals share genetic material from common ancestors plays a central role in several scientific disciplines, particularly animal behavior, conservation biology, and genetic evolution. While scientists initially relied on family trees (or pedigrees) to delineate these pairwise relationships, their inherent limitations prompted the search for more accurate techniques.

Recent technological advances have greatly accelerated this journey. Genetic testing and analysis of genetic markers called single nucleotide polymorphisms (SNPs), which represent individual variations in DNA sequence data, can help researchers directly infer biological relatedness.

A powerful new genetic tool identifies pairs of relatives

An international team of researchers has now developed a bioinformatics pipeline that breaks new ground in estimating genetic relatedness in animal populations. The software analyzes whole-genome sequencing data and works accurately even with very low-quality data.

"Our computational tool has opened the door to a more refined understanding of genetic relationships in ecology and evolution. It accurately identifies identical DNA fragments in pairs of individuals that were inherited from a common ancestor. These so-called identity-by-descent or IBD segments are an exceptionally powerful signal for detecting and quantifying biological relatedness that was previously only accessible in high-quality human data. Now we can do it in animal genomes, too," says one of the senior authors, Harald Ringbauer of the Max Planck Institute for Evolutionary Anthropology.

Variation in actual relatedness in a macaque population

In developing and evaluating this tool, the team ran computational experiments on a free-ranging rhesus macaque population from Cayo Santiago, Puerto Rico. The new tool provided superior insights compared to previous methods: while conventional methods estimate relatedness in categories, this method is able to precisely represent the continuous nature of relatedness. In addition, the team detected a higher level of shared genetic inheritance than expected, suggesting the presence of previously undetected relatives within the population.

"Through its application in a free-ranging primate population, our IBD method has proven its potential by providing more detailed insights into relatedness structures than traditional pedigrees or older genetic estimates," says first author Annika Freudiger from Leipzig University and the Max Planck Institute for Evolutionary Anthropology.

In addition, the researchers found discrepancies where actual genetic inheritance exceeded predicted levels based on pedigrees. These discrepancies indicate an underestimation of shared ancestry due to incomplete knowledge of familial relationships through the pedigree. They also identified a significant difference in genetic recombination rates between the sexes, which could reveal the sex of unknown ancestors and thus indicate whether pairs of individuals are related through the maternal or paternal line.

Discover the latest in science, tech, and space with over 100,000 subscribers who rely on Phys.org for daily insights. Sign up for our free newsletter and get updates on breakthroughs, innovations, and research that matter—daily or weekly.

Subscribe

Cayo Santiago: Collecting data since 1956

The research was conducted on Cayo Santiago, a small island off the coast of Puerto Rico managed by the Caribbean Primate Research Center. Consistent collection of demographic and genetic data since 1956 allowed the researchers to test this new method in a free-ranging population with extensive pedigree data available over several decades.

This has provided new insights into this study population. Despite the prolonged genetic isolation of the rhesus macaque population, the levels of inbreeding are surprisingly low, likely due to sex-biased dispersal and/or effective kin recognition.

"With this innovative tool, we're able to accurately measure the continuous distribution of relatedness in animal populations, even from relatively low-quality sequencing data. This could lead to a significant change in our understanding of ecological and evolutionary patterns in social animals," concludes senior author Anja Widdig from Leipzig University and the Max Planck Institute for Evolutionary Anthropology.

This research underscores the potential of using advanced methodologies to further our understanding of biological relatedness across species and populations. This will lead to new insights into previously largely ambiguous family structures and preferential behaviors.

More information: Annika Freudiger et al, Estimating realized relatedness in free-ranging macaques by inferring identity-by-descent segments, Proceedings of the National Academy of Sciences (2025). DOI: 10.1073/pnas.2401106122

Journal information: Proceedings of the National Academy of Sciences

Provided by Max Planck Society