Over the course of the project, we established an internationally leading research program in primate genomics, delivering major scientific, methodological, and societal advances. The work created a global framework for understanding genome diversity, evolutionary history, and conservation of great apes and other primates. By integrating large-scale genomic data, methodological innovation, and translational applications, the project significantly advanced evolutionary genomics and conservation science.
A central achievement was the generation and analysis of a comprehensive global genome diversity panel for great apes. We expanded datasets to include more than 2,000 individuals across chimpanzees, gorillas, bonobos, and orangutans, enabling a unified framework for population structure, demographic history, and gene flow. Genome-wide analyses of gorillas and bonobos were completed and integrated with chimpanzee data, while ~700 orangutan genomes extended the framework to Asian lineages. These datasets represent the most extensive catalogue of great ape genomic diversity to date and provide a lasting resource for research and conservation.
The project also advanced a broader comparative understanding of primate evolution through analyses of more than 200 species, contributing to a coordinated Science Special Issue (2023). These efforts produced a global catalogue of primate genomic diversity and frameworks to characterize tolerated genetic variation. By leveraging deep evolutionary information, we identified functionally constrained genomic regions and established a foundation for AI-based prediction of deleterious mutations, linking evolutionary genomics and medical applications.
A second major achievement was the integration of historical museum specimens. We developed protocols for sequencing degraded DNA and generated genome-wide data from museum collections, incorporated into analyses of gorilla and bonobo populations. This enabled direct temporal comparisons between historical and contemporary populations, revealing recent demographic changes and shifts in genetic diversity. This represents the first catalogue capturing both present-day and historical genomic variation in great apes.
The project further extended genomic analyses into deep time through fossil specimens. By combining genomic and proteomic approaches, we analysed fossil primates, including orangutan-related lineages. This overcomes key technical barriers and marks a major advance in primate palaeogenomics, enabling robust taxonomic identification and evolutionary interpretation.
We also developed methodological innovations to analyse complex evolutionary processes. New frameworks were established to detect ancestral introgression and ghost admixture, revealing previously unrecognized gene flow among great ape lineages and improving understanding of reticulate evolution.
A key enabling technology was the large-scale application of chromosome capture optimized for non-invasive and low-quality samples. This enabled sequencing of more than 2,000 genomes from fecal, museum, and fossil material, expanding accessible biological material.
Importantly, the project translated these advances into tools with direct societal impact. A high-resolution geolocalization framework infers the geographic origin of individual great apes with high precision and underpins the Atlas of Sources of Illegal Trafficking, supporting forensics, law enforcement, and conservation across Africa.
A second achievement is a targeted SNP-amplicon sequencing technology for individual identification, enabling scalable population monitoring and genetic management, and advancing through an ERC Proof of Concept.
Finally, the project had a transformative impact on the research environment, enabling a multidisciplinary team and positioning the group as an internationally recognized leader in primate genomics.
In summary, the project delivered an integrative framework for studying primate genomic diversity across spatial and temporal scales, advancing both fundamental knowledge and conservation applications.
