CBER Seminar - Harrison Ostridge, UCL

Abstract: Chimpanzees, along with bonobos, are our closest living relatives. They are separated into four subspecies: central, eastern, Nigeria-Cameroon and western, all of which are endangered. They inhabit a diversity of habitats in sub-Saharan Africa, from cool wet rainforest to hot dry woodland-savannah, which provides the opportunity for local genetic adaptations. Understanding such adaptations would provide fundamental insights into chimpanzee evolution and essential information to aid conservation efforts. However, studies of fine-scale adaptation in chimpanzees have been hindered by the difficulties associated with accessing genetic samples from endangered wild populations. Our work analyses a new dataset of unprecedented scale and resolution. We sequence the functional coding regions of the genome (exomes) from 828 faecal samples of wild chimpanzees from across the distribution of all four subspecies representing a range of habitat types. We investigate signatures of local genetic adaptation by combining this genomic data with newly collected environmental data in a genotype-environment association (GEA) analysis revealing genome-wide evidence of local adaptation to habitat type. Genetic variants inferred to be beneficial in woodland-savannah habitats are enriched for physiological functions, while variants inferred to be beneficial in forest habitats are enriched for pathogen-related genes. We find particularly strong evidence for adaptation to malaria in lowland forests with selection targeting the same genes that underly adaptation in humans. Our work demonstrates the power of genomic analysis of non-invasive samples to reveal fine-scale local adaptation in endangered wild populations of large mammals.