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

猪是世界上最早也是现在最重要的家养动物之一，在中国身上扮演着特别重要的角色。事实上，2018年，全球一半以上的生猪都是在中国身上发现的。与此同时，多项研究表明，中国是大约1万年前开始独立驯养猪的地方之一。此外，有很好的证据表明，猪在中国内部的不同地方被驯养了几次，其中包括黄河地区、湄公河流域和长江地区。然而，由于贸易和人类扩散导致的猪在地区之间的转移，以及驯化的猪种群与当地野猪的相互渗透，最初的猪驯化信号已经变得模糊。因此，为了全面了解猪的驯化历史，来自最早的驯化猪的古代DNA分析、后来文化中的猪遗骸和地方品种是必不可少的。直到几年前，这样的项目是不可能的，因为对古基因组进行测序极其昂贵。然而，测序成本的降低以及古代DNA研究中分析方法的进步使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使人们能够透视低覆盖率的基因组，并从这些数据中揭示物种的进化史。该项目旨在使用大规模并行测序技术从中国最老的猪遗骸和各种集约化利用猪的年轻养殖场获得基因组数据。此外，我们还将获得中国本地猪品种的基因组数据，而这些数据并不是完全可用的。我们将一起分析这些数据，以解决一些问题，包括第一批驯化猪与它们的野生祖先和来自中国等地区的现代猪群体相比的功能性和中性遗传多样性，以及这些最古老的猪群体与中国境内较年轻考古文化中的猪的关系。此外，我们还将利用这些数据来调查人类贸易传播和文化变迁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家养动物物种的驯化历史提供信息，并为家养物种与人类互动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.