Genomic insights into Hippopotamus amphibius through museomics

Ancient DNA studies and museomics are reshaping the value of museum collections, revealing their potential to bridge cultural heritage and genomics. By extracting genetic information from preserved specimens, these approaches facilitate significant advancements, including the reconstruction of phylogenetic relationships, the mapping of genetic erosion, and the monitoring of species biodiversity. This study focuses on Hippopotamus amphibius, a species which is still underrepresented in genomic research. Five subspecies have been proposed based on morphology, but their validity remains controversial due to limited molecular characterization, which has been confined to partial fragments of the mitochondrial DNA and few nuclear markers. To address this issue, we sequenced the genomes of historical museum specimens from the last few centuries and integrated them with data from contemporary individuals. We applied population genetics methods to: (i) comprehensively characterize the genomic history of H. amphibius, (ii) clarify intraspecific diversity and subspecies classification, (iii) explore the demographic history of the species, including the potential impact of human activities since the XX century, and (iv) investigate the evolutionary history of the Hippopotamidae family, by also comparing it with Choeropsis liberiensis, for which a few specimens were also sequenced. Our findings highlight the role of museum collections as significant archives of biodiversity and their evolution over time. By integrating these findings into exhibits and educational programs, we aim to foster public engagement with conservation and biodiversity and emphasize the importance of genomic data in enhancing the invaluable natural heritage preserved in museums.