Ancient mitogenomes reveal the genetic relationship among extinct and extant water buffaloes

Water buffaloes (Bubalus spp.), currently confined to South and Southeast Asia, were once widespread across Eurasia during the Pleistocene. While multiple fossil species have been morphologically defined, their phylogenetic relationships remained unclear due to the absence of molecular evidence. This study obtained 32 mitochondrial genomes of Bubalus mephistopheles, the hypothesized wild progenitor of domestic water buffaloes that persisted in temperate Eurasia until the Holocene, and B. wangsjoki, a presumed cold-adapted Late Pleistocene species from Northeast Asia. Phylogenetic reconstruction revealed that these morphologically and spatiotemporally distinct animals are actually conspecific with high phenotypic and ecological plasticity. This extinct lineage was a sister taxon with Indonesian anoas, despite their disjunct geographical distributions, rather than linking directly to domestic water buffaloes. Our findings demonstrate that the widespread species survived Pleistocene climatic oscillations before a mid-Holocene extinction, potentially driven by intensified human activities. This study provides insights into water buffalo evolution, and highlights the importance of palaeogenomic data for accurately classifying extinct species.