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

猪是世界上最早和目前最重要的家养动物之一，在中国发挥着特别重要的作用。事实上，在2018年，全球超过一半的猪都是在中国发现的。与此同时，几项研究表明，中国是大约1万年前开始独立驯养猪的地方之一。更重要的是，有充分的证据表明，猪在中国不同的地方被驯化了好几次，其中包括黄河地区、湄公河流域和长江地区。然而，由于贸易和人类的扩散，猪在不同地区之间的迁移，以及驯化猪种群与当地野猪的渗入，猪驯化的原始信号已经变得模糊。因此，为了充分了解猪的驯化历史，对最早的驯化猪、后来的文化和地方品种的猪遗骸进行古代DNA分析是必不可少的。直到几年前，这样的项目还不可能实现，因为古基因组测序非常昂贵。然而，测序成本的降低以及古代DNA研究分析方法的进步使得从许多古代遗骸中获得基因组数据成为可能，新的生物信息学方法也允许对低覆盖率基因组进行透视，并从这些数据揭示物种的进化史。该项目旨在利用大规模平行测序技术，从中国最古老的猪遗骸和大量利用猪的各种较年轻的文化遗址中获得基因组数据。此外，我们还将获得中国本地猪品种的基因组数据，这些数据尚未完全获得。我们将对这些数据进行综合分析，以解决一系列问题，包括与野生祖先和来自中国和其他地区的现代猪种群相比，第一批驯化猪的功能和中性遗传多样性，以及这些最古老的猪种群与来自中国较年轻考古文化的猪的关系。此外，我们将利用这些数据调查人类贸易传播和文化变化对中国不同地区猪的遗传多样性和传播的影响。总之，这些数据将为中国最重要的驯化动物物种的驯化历史提供信息，并为驯化物种与人类相互作用的进化路线提供新的见解。

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.