Revisiting Aurochs Haplogroup C: Paleogenomic Perspectives from Northeastern China

Aurochs (Bos primigenius), one of the earliest and largest herbivores domesticated by humans, were widely distributed in Eurasia and North Africa during the Pleistocene and Holocene. Studies of aurochs in China have focused mainly on the Northeastern region. Previous studies have suggested that haplogroup C is a haplogroup unique to China, but recent studies have shown that this is not the case. We have compiled all data on haplogroup C to revisit the classification of the aurochs haplogroup C.

In this study, we obtained 13 nearly complete mitochondrial genomes from Late Pleistocene to early Holocene bovine samples from Northeastern China through fossil sample collection, ancient DNA extraction, library construction, and high-throughput sequencing. Based on the acquired ancient DNA data and in combination with previously published bovine data, the phylogenetic status, lineage divergence time, and population dynamics of aurochs in Northeastern China were analyzed.

Phylogenetic analyses and divergence time estimations suggest that the current definition of haplogroup C is overly inclusive, necessitating a refined reclassification of this haplogroup. We also estimated the population dynamics of aurochs in Northeastern China using Bayesian skyline plots found that the maternal effective population size of the aurochs increased significantly during Marine Isotope Stage 5 (MIS5), but began to decrease in the second half of MIS3 before they eventually became extinct.

Our results provide new molecular evidence on the phylogenetic status, divergence time, and population dynamics of aurochs in Northeastern China.