Ancient mitogenomes reveal unexpected diversity in Madagascar's extinct hippopotamuses

Madagascar's extinct hippopotamuses were a distinctive component of the island's recently lost megafauna, yet their origins, diversification history, and taxonomy have remained unresolved. Here, we recover the first ancient mitochondrial genomes from Malagasy hippopotamuses, obtaining phylogenetic data from 37 subfossil specimens across seven localities and all three named species, and integrate these data with morphology and total-evidence phylogenetic analyses. The 35 endemic specimens form a single clade most closely related to Hippopotamus amphibius, supporting a single colonization of Madagascar. Within this radiation, five deeply divergent and geographically structured mitochondrial lineages diversified across most regions of Madagascar during the Pleistocene. Tip-dating estimates a remarkably young crown age of ~1.41 Ma, following divergence from mainland Hippopotamus at ~3.24 Ma. These lineages do not map cleanly onto traditional taxonomy: material assigned to H. lemerleispans several divergent clades, while H. laloumena and H. madagascariensis are nested within this broader diversity. Morphology supports some lineage assignments but also points to previously unrecognized diversity, while ancestral-state reconstruction supports early body-size reduction followed by a secondary increase in H. laloumena. Malagasy hippopotamuses therefore represent an exceptionally recent radiation of large-bodied island mammals (and the youngest in Madagascar), showing that Madagascar continued to generate endemic mammalian diversity well into the Pleistocene. Their late-Holocene extinction erased the product of more than a million years of rapid insular diversification, the drivers of which remain enigmatic.