Progress on ancient DNA investigation of Late Quaternary mammals in China

It has been more than 40 years since the beginning of exploring the genetic composition of ancient organisms from the perspective of ancient DNA. In the recent 20 years, with the development and application of high-throughput sequencing technology platforms and the improved efficiency of retrieving highly fragmented DNA molecules, ancient DNA research moved forward to a brand-new era of deep-time paleogenomics. It not only solved many controversial phylogenetic problems, enriched the migration and evolution details of various organisms including humans, but also launched exploration of the molecular responses to climate changes in terms of "whole genomic-big data-multi-species" level. Moreover, it expanded the sample age from no more than 100,000 years to the Early Pleistocene, ~2 million years ago. Recently, Chinese scientists have made many influential breakthroughs in evolution and migration integration of East Asian populations and thus filled an important gap in the evolutionary process of modern human. Compared to the situation in human paleogenomic studies, less attention has been paid to the study of ancient DNA from vertebrates remains. In this review, we introduce a series of advances in ancient DNA investigations of large mammals in Late Quaternary in China, summarize the research breakthroughs in revealing the systematic evolutionary relationship between ancient and extant groups, gene flow, and molecular responses of mammalian populations to climate change, and explore the opportunities and key challenges in the field of mammalian paleogenomics.