From forests to deserts: Sequencing of the giant forest hog completes the genomic history of the African suids

Abstract

The giant forest hog (GFH; Hylochoerus meinertzhageni), the largest and most elusive wild pig, is found in a disjunct range across tropical Africa, from Guinea to the Ethiopian highlands. The GFH has three morphologically defined subspecies. Here, we present the first whole-genome data for nine samples from Guinea and Uganda, its two most geographically distant subspecies. We identify the GFH as sister to warthogs among African suids, diverging around 4.6 Mya, with the two GFH populations splitting between 1.7 and 0.5 Mya and following distinct demographic trajectories. The deep evolutionary split is confirmed by species-level genetic differentiation and the lowest heterozygosity level in the Guinean population compared with all the African suids, likely reflecting long-term low effective population size and isolation. Our findings have implications for understanding the habitat-change consequences in African rainforests and reveal a deep evolutionary divergence within the GFH with potential conservation relevance.