Genomic insights into the persistence of Nubian giraffe (Giraffa camelopardalis camelopardalis) in conflict-affected South Sudan

Abstract Armed conflicts can severely disrupt wildlife conservation and management, yet their long-term genomic consequences remain poorly understood. South Sudan has experienced decades of conflict that have limited conservation efforts and prevented genomic assessment of its fauna, including the endangered subspecies of Nubian giraffe ( Giraffa camelopardalis camelopardalis ). Due to long-standing logistical and political challenges, populations from South Sudan have remained largely unsampled. The Nubian giraffe represents a critical conservation unit and new sampling efforts provide an opportunity to investigate its genomic diversity and potential genetic isolation by the White Nile River, a hypothesized gene flow barrier. Here, we present genomic data from 30 individuals sampled in Boma and Badingilo National Parks in eastern South Sudan. Adding these sequences to existing genomic data reveals genetically distinct groups within the Nubian giraffe according to three regions: Ethiopia-South Sudan, Kenya, Uganda. Despite limited wildlife management due to economic and political constraints in South Sudan, the Nubian giraffe populations have maintained high heterozygosity (He ≈ 0.14%) and minimal evidence of inbreeding (mean F ROH ≈ 0.15) compared to Kenya’s Nubian giraffe populations. Contrary to expectations, our results reveal measurable gene flow across the White Nile between Nubian giraffe and Kordofan giraffe ( G. c. antiquorum ). These findings highlight South Sudanese Nubian giraffe as a population that retained genetic diversity and conservation efforts should be enhanced where feasible to ensure this stronghold long-term.