Human influences on animals from an ancient DNA perspective : case studies on Chinese domestic cats (Felis catus), Chinese leopard cats (Prionailurus bengalensis), fallow deer (Dama dama), and Chinese domestic pigs (Sus scrofa)

Human-animal interactions since the late Pleistocene have exerted long-lasting and significant influences on animals. With the advance of ancient DNA techniques, the availability of genomic data from ancient samples has profoundly increased, and now with great possibilities we are able to investigate the past and gain knowledge of the phased genetic changes in history. Applying predominantly ancient genomic methods, I have conducted case studies on four different species under the states of domestication, semi-domestication, and commensalism respectively to explore how the anthropogenic exercises have affected the evolutionary trajectories of animals. The first case involves Chinese domestic cats (Felis silvestris catus) by examining 4 nuclear genomes and 22 mitochondrial genomes from 22 ancient Chinese samples spanning 5,500 years. Chinese domestic cats are descended from African wild cats (Felis silvestris lybica) and were likely brought to China via the Silk Road during the 7th and 9th centuries AD. Leopard cats (Prionailurus bengalensis) might have been enjoying a commensal relationship alongside humans in the Late Neolithic before domestic cats arrived in China (6,000-5,500 BP). However, this commensal link did not survive the Han Dynasty (202 BC - 220 AD). Small felids and humans did not cohabit again until the Tang Dynasty (618-907 AD) when domestic cats were imported. Since then, domestic cats have not mixed with any Chinese native wild cat species, including the Chinese mountain cat (Felis silvestries bieti) and Asiatic wild cat (Felis silvestries ornata). The second case involves the Chinese leopard cat (Prionailurus bengalensis), who were in a commensal relationship with humans since the Chinese Neolithic period (5,500 BP). This study collected seven ancient leopard cats from the Middle Reach of the Yellow River Basin. Ancient genome study shows that the leopard cats from the Middle Reach of the Yellow River Basin and Far East Russia were closely related, albeit the former was receiving introgression with Indochina leopard cats. According to archaeological, chronological, and literary analysis, leopard cats and humans ceased their commensal connection when the Han Dynasty (202 BC - 220 AD) fell, and never recovered. Domestic cats replaced leopard cats in the human niche, when they were introduced around the Tang Dynasty (618-907 AD). The third case involves the Persian and European fallow deer (Dama dama mesopotamica and Dama dama dama). The post-glacial dispersal of the fallow deer was nearly entirely mediated by people. We generated and analysed 29 partial or mitochondrial genomes of ancient fallow deer to gain insights into their evolution and range changing. Ancient DNA analysis indicates that the two fallow deer subspecies diverged 0.57 million years ago and might have interbred in Southwestern Anatolia. An ancient maritime commercial route brought Persian fallow deer from the Levant to Cyprus and westward to the Mediterranean, while European fallow deer from Anatolia were dispersed to continental Europe. The fourth case involves the Chinese domestic pigs (Sus domesticus). The Middle Reach of the Yellow River Basin was one of the domestication hubs of pigs. We have conducted ancient genomic investigation of five nuclear and nine mitochondrial genomes of ancient domestic pigs from two archaeological sites in the Middle Reach of the Yellow River Basin spanning at least 3,000 years, and zooarchaeological analysis on 1,400 pieces faunal remains excavated from the Zheng-Han City (2,500 BP). I suggest that the populations represented by the ancient domestic pigs from the Middle Reach of the Yellow River Basin had contributed to the formation of modern Chinese breeds and issued new hypothesis of the origin of the Chinese domestic pigs. Zooarchaeological approaches showed a reduction in pigs' prominence in archaeological sites and potential intensified pig husbandry in the MYR from the late Neolithic to the Iron Age. Combining the results of the four case studies, we have addressed the importance of anthropogenic forces in altering the evolutionary trajectories of animals: 1) The human-mediated dispersal can dramatically change the range of the species, even for the animals who had lost most of their genetic diversities, accompanying the migration of human, they were still able to be spread globally. 2) By establishing affinities or cultural connections with human, the population dynamics of animals would closely correlate with the development of human societies. 3) Importing new species would lead to the admixtures between exotic animals and its related local counterparts. Such admixtures could in one hand introduce new genetic diversities, while in another hand, offset the adaptability of the native species to local environment.