Mitochondrial genetic diversity and evolutionary history of Late Pleistocene woolly mammoths in Northeast China

As one of the representatives of extinct mammals in Late Quaternary, Mammuthus primigenius was widely distributed across middle-to-high latitude regions of Eurasia and North America. In China, it was mainly distributed in the northeast and represented not only the core member of the Mammuthus-Coelodonta fauna in Northern China during the Late Pleistocene, but also a key component of this hot spot species from mid-latitude region in Asia. Compared to the comprehensive paleogenomic exploration of its counterparts from Europe, Siberia, and North America, M. primigenius remains in Northeastern China have only been molecularly investigated using short mitochondrial fragments and thus the genomic level is inadequate. Therefore, the phylogenetic relationship of the woolly mammoth in China to Eurasian and North American individuals remains an open question. Moreover, paleontologists have suggested classifying the woolly mammoth from Northeastern China as a separate species based on its morphological characters. Here, we performed ancient DNA extraction, sequencing library construction and next-generation sequencing (NGS) on woolly mammoth fossils collected in Northern and Northeastern China. By data filtering and mapping to reference genome, we obtained high-quality complete mitochondrial genomes or partial mitochondrial sequences from 16 individuals. We carried out radiocarbon isotope dating for three out of these 16 samples and obtained dates for the rest either from the literature or by molecular dating. We ran mapDamage to authenticate our data as ancient and confirm substitution characteristics typical of ancient DNA sequences. Phylogenetic analyses based on our newly obtained mitochondrial sequences and published mitogenomic data showed that all three known mitochondrial clades of M. primigenius are present in the analyzed Chinese woolly mammoths. Specifically, among the 16 individuals, there are nine individuals clustered with M. primigenius from Northern Siberia and central Asia in Clade I; six individuals clustered with samples from Northeastern Asia to form Clade II; one individual belonged to Clade III. The placement in multiple clades suggests that M. primigenius in Northeastern China had relatively high mitochondrial diversity. In a Bayesian phylogenetic using complete mitochondrial genomes of five of our Northeastern Chinese individuals and other published individuals from Asia and North America, the available age information of all individuals and their mitochondrial genetic structure show that Clade I and Clade II+III diverged from each other approximately 1.63 Ma, corresponding to the first migration event of the woolly mammoth from Eurasia to North America. A second migration was detected within Clade I, in which a population in Northeastern China split from the ancestral woolly mammoth population that headed into North America around 0.61 Ma.In addition, it is the first time that individuals belonged to Clade II have been identified from Northeastern China, which indicates that the population represented by Clade II was once widely distributed in Northeast Asia in the Late Pleistocene. Prior to the Last Glacial Maximum (LGM), this population probably experienced habitat contraction and remained as a small population in Northeastern China, since the only individual that dated close to LGM has only be found in this region. Overall, we provide mitogenomic insights into both the phylogenetic positions and genetic diversity of M. primigenius in China, as well as the response of woolly mammoths to the Late Pleistocene climate change.