Based on a media release by the Max Planck Institute for Evolutionary Anthropology
Researchers from the Max Planck Institute for Evolutionary Anthropology (MPI EVA), Leipzig University (UL), the German Centre for Integrative Biodiversity Research (iDiv), and the Freie Universität Berlin (FU) have developed a transformative approach that identifies stretches of DNA that two individuals inherited from a common ancestor. The team successfully applied their new tool in a free-ranging population of rhesus macaques in Puerto Rico.
The results show that even with low-quality sequencing data, this method can accurately determine relatedness among pairs of individuals, without needing 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 behaviour, 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.
Identity-by-descent: A powerful new genetic tool identifies pairs of relatives
The international team of researchers developed a bioinformatics pipeline that breaks new ground in estimating genetic relatedness in animal populations. The software analyses 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”, says one of the senior authors, Harald Ringbauer of the MPI EVA.
“These so-called identity-by-descent (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”, he adds.
Higher genetic relatedness than predicted in 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 other methods: While conventional methods estimate relatedness in categories, this method is able to precisely represent the continuous nature of relatedness.
The team also 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 UL and the MPI EVA.
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.
Nearly 70 years of data collected on Cayo Santiago
The research was conducted on Cayo Santiago, a small island off the coast of Puerto Rico managed by the Caribbean Primate Research Centre. 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 are 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[KK1] and iDiv member Anja Widdig from UL and the MPI EVA. 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 behaviours.
Original publication
(iDiv researchers bolded)
Freudiger, A., Jovanovic, V. M., Huang, Y., Snyder-Mackler, N., Conrad, D. F., Miller, B., … & Widdig, A. (2025). Estimating realized relatedness in free-ranging macaques by inferring identity-by-descent segments. Proceedings of the National Academy of Sciences of the United States of America, 122(3), e2401106122. 10.1073/pnas.2401106122
Contact
Dr Anja Widdig
Leipzig University
Max Planck Institute for Evolutionary Anthropology
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig
email: anja.widdig@idiv.de
Christine Coester
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig
Media and Communications
email: christine.coester@idiv.de
Please note: Use of the pictures provided by iDiv is permitted for reports related to this media release only, and under the condition that credit is given to the picture originator