Evolutionary analyses of pig paleogenomes to reveal origin and domestication of the pig

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Pigs are among both the earliest and currently the most important domesticated animals in the world and play an especially important role in China. In fact, in 2018, more than half of all pigs worldwide were found in China. At the same time, several lines of research have suggested that China was one of the places, where pigs were independently domesticated starting about 10,000 years ago. Even more, there is good evidence that pigs were domesticated several times in different places within China, including, among others, the Yellow River region, the Mekong basin and the Yangtze River region. However, the original signals of pig domestication have been blurred by translocation of pigs between regions due to trade and human dispersal as well as by introgression of domesticated pig populations with local wild boars. Therefore, for a full understanding of pig domestication history, ancient DNA analyses from the earliest domesticated pigs, pig remains from later cultures and local breeds are indispensable. Until a few years ago, such a project would not have been possible since sequencing paleogenomes was extremely expensive. However, reductions in sequencing costs as well as progress in analytical approaches in ancient DNA research have made it possible to obtain genomic data from many ancient remains and new bioinformatic approaches allow putting also low coverage genomes into perspective and revealing the evolutionary history of a species from such data. This project aims at obtaining genomic data using massively parallel sequencing technologies from both the oldest pig remains from China and a variety of younger cultural sites with intensive pig utilization. In addition, we will obtain genomic data from local Chinese pig breeds for which these data are not completely available. We will analyze these data together in order to address a number of questions, including the functional and neutral genetic diversity of the first domesticated pigs in comparison to both their wild ancestors and modern pig populations from China and other regions and the relationships of these oldest pig populations to pigs from younger archaeological cultures within China. In addition, we will use the data to investigate the effects of human trade dispersal and cultural change on the genetic diversity and dispersal of pigs in various regions of China. Together, these data will inform on the domestication history of China's most important domesticated animal species and provide new insights into the evolutionary routes of domesticated species in their interplay with humans.