The Consequences of Gene Flow between Wild and Domestic Populations during Livestock Evolution

一般来说，现代家养物种被积极地阻止与野生种群杂交。这一规则的少数例外涉及故意产生新的杂交宠物，如那些涉及家养和野生猫物种。这种将野生物种纳入育种系的做法在牲畜物种中是强烈反对的，因为从野生种群引入基因会降低杂交种的生产力和驯服程度。然而，在最近的过去，畜牧业的做法远没有那么严格。最近的人种学和遗传学分析表明，许多家养物种和野生物种之间的杂交实际上是一种规则，而不是一个罕见的例外。虽然来自野生种群的基因流动可能是有害的，但它也可能对牲畜种群产生积极的影响。例如，通过减少与近亲繁殖相关的风险，以及通过引入允许快速适应新环境的遗传变异。因此，适应性基因流动在家畜在世界各地的传播过程中可能发挥了重要作用。猪尤其如此，因为野猪的地理和遗传差异种群遍布欧亚大陆，并适应各种气候和环境;因此提供了可能被到达的家猪吸收的原材料。事实上，我们证明了野猪和家猪之间的基因流动是很常见的，而且在猪从近东引入欧洲之后就立即开始了，在那里它们最初被驯化。尽管有这种基因流动，欧洲的猪通过保留其形态和行为的独特性，保持了它们作为家畜的完整性，这表明尽管一些野猪基因组变异被纳入了家畜种群，但许多野猪遗传变异被积极地删除了。在这里，我们将确定一些野生遗传变异是否被优先删除，以及一些是否被优先纳入国内人口。最终，该项目不仅将揭示驯化的基因组基础，还将揭示家猪如何适应新的环境，通过识别快速整合的特定基因组区域，以及哪些基因组区域在基因流动过程中受到抵制。为此，我们将评估过去10,000年来欧亚大陆东部和西部1,000多只古代猪和野猪的DNA保存情况，然后对保存最好的标本的整个基因组进行测序。有了这些数据，我们将建立野猪基因纳入国内股票的比例和基因组位置的空间和时间差异。这些结果不仅将使人们对家畜的起源有前所未有的了解，而且还将对濒危野猪种群的保护以及对猪育种者和猪肉消费者产生重要影响，对他们来说，家畜和野生肉的真实性至关重要。

Generally speaking, modern domestic species are actively prevented from interbreeding with wild populations. The few exceptions to this rule involve the deliberate generation of novel hybrid pets such as those involving domestic and wild cat species. This practice of incorporating wild species in breeding lines is strongly discouraged amongst livestock species since the introduction of genes from wild populations reduces productivity and the degree of tameness in the hybrids. In the recent past, however, husbandry practices were far less restrictive. Recent ethnographic and genetic analyses have revealed that interbreeding between numerous species of domestic and wild species was, in fact, the rule and not a rare exception.While gene flow from wild populations can be detrimental, it can also have a positive impact on livestock populations. For example, by decreasing the risks associated with inbreeding and by introducing genetic variation that allowed for rapid adaptation to novel environments. Adaptive gene flow therefore potentially played an important role during the spread of domestic animals across the world. This is especially true of pigs since geographically and genetically differentiated populations of wild boar are present across Eurasia and adapted to a wide variety of climates and environments; thus providing raw material that could have been absorbed by arriving domestic pigs. In fact, we demonstrated that gene flow between wild and domestic pigs was common and that it began immediately following the introduction of pigs to Europe from the Near East where they were initially domesticated. Despite this gene flow, pigs in Europe maintained their integrity as domestic animals by retaining their morphological and behavioural distinctiveness, suggesting that though some wild boar genomic variation was incorporated into domestic stocks, many wild boar genetic variants were actively expunged. Here, we will determine whether some wild genetic variants were preferentially expunged and whether some were preferentially incorporated into domestic populations. Ultimately, this project will reveal not only the genomic basis for domestication, but also how domestic pigs adapted to novel environments, by identifying specific genomic regions that were rapidly incorporated, and which ones were resisted during gene flow. To do so, we will assess the DNA preservation of more than 1,000 ancient pigs and wild boar from Eastern and Western Eurasia over the past 10,000 years, and then sequence the entire genomes of the best preserved specimens. Armed with this data, we will establish the spatial and temporal differences in the proportion and genomic location of the incorporation of wild boar genes into domestic stocks. The results will allow not only an unprecedented understanding of the origins of domestic animals, they will also have important ramifications for the conservation of endangered wild boar populations and for pig breeders and consumers of pork for whom the authenticity of domestic and wild meat is crucial.