Grasping biological connections is crucial for 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 introduced a revolutionary technique that pinpoints DNA segments shared by individuals from a common ancestor. This team effectively used their innovative tool on a wild population of rhesus macaques, demonstrating that even with low-quality sequence data, it can accurately assess the relatedness between individuals, without needing prior knowledge of family trees in the population. This advancement uncovers previously unidentified relatives and offers valuable insights into wild population structure.
Measuring genetic share among individuals from common ancestors is vital in multiple scientific fields, such as animal behavior, conservation biology, and genetic evolution. Initially, scientists utilized family trees (pedigrees) to clarify these relationships, but their limitations led to the need for more precise methods.
Recent technological advancements have hastened this search significantly. Genetic testing, along with the analysis of single nucleotide polymorphisms (SNPs)—which highlight individual genetic variations—allows researchers to derive biological relatedness directly.
A groundbreaking genetic tool identifies relative pairs
Researchers from around the world have crafted a bioinformatics pipeline, paving the way for a fresh approach in assessing genetic relatedness in animal populations. The software processes whole-genome sequencing data competently, even when the data quality is low. “Our computational tool has unlocked new pathways for a deeper understanding of genetic relationships in the fields of ecology and evolution. It accurately pinpoints matching DNA fragments in pairs that come from a shared ancestor. These identity-by-descent (IBD) segments are extremely effective for uncovering and quantifying biological ties, previously achievable only in high-quality human data—now applicable to animal genomes too,” states Harald Ringbauer, a senior author from the Max Planck Institute for Evolutionary Anthropology.
Differences in actual relatedness within a macaque population
During the development and testing of this tool, the team conducted computational studies on a naturally occurring rhesus macaque population from Cayo Santiago, Puerto Rico. Their new approach garnered significantly better insights than traditional techniques: while older methods typically classify relatedness into categories, the new tool offers a precise representation of its continuum. Furthermore, the researchers uncovered a higher degree of shared genetic inheritance than anticipated, implying that previously unrecognized relatives exist within this population. “By applying our IBD method in a free-ranging primate group, we illustrated its ability to yield more nuanced insights into relatedness than traditional family trees or outdated genetic assessments,” comments Annika Freudiger, the first author from Leipzig University and the Max Planck Institute for Evolutionary Anthropology.
Additionally, discrepancies were found where actual genetic inheritance was greater than what pedigrees predicted, revealing an underrepresentation of shared ancestry due to incomplete familial relationship knowledge in the pedigree. The team also found notable differences in genetic recombination rates according to sex, which might help identify the sex of unknown ancestors and indicate whether individuals share maternal or paternal lineage.
Cayo Santiago: Data collection since 1956
This study took place on Cayo Santiago, a small island near Puerto Rico, overseen by the Caribbean Primate Research Center. The continuous gathering of demographic and genetic data since 1956 allowed researchers to apply this new approach to a wild population with extensive pedigree records spanning decades, yielding fresh insights into this study population. Despite the long-term genetic isolation of the rhesus macaques, inbreeding levels are surprisingly low, possibly due to sex-biased dispersal and/or effective kin recognition.
“Thanks to this innovative tool, we’re able to precisely measure the ongoing spectrum of relatedness in animal populations, even from relatively low-quality sequencing data. This could substantially reshape our understanding of ecological and evolutionary trends in social animals,” concludes Anja Widdig, a senior author from Leipzig University and the Max Planck Institute for Evolutionary Anthropology. This research highlights how advanced methodologies can deepen our understanding of biological relatedness across different species and populations, leading to fresh insight into previously unclear family structures and behavioral preferences.
