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

家畜进化过程中野生种群和家养种群之间基因流动的后果

• 批准号: NE/S00078X/1
• 负责人: Greger Larson
• 金额: $ 81.75万
• 依托单位: University of Oxford
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2019
• 资助国家: 英国
• 起止时间: 2019 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FS00078X%2F1
• 关键词: Consequences; Gene; Flow; between; Wild

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.

一般而言，现代家族物种被积极阻止与野生种群杂交。该规则的少数例外是故意生成新型的混合宠物，例如涉及家庭和野猫物种的宠物。自从野生种群引入基因以来，这种将野生物种融入繁殖品种中的实践强烈劝阻，可以降低生产力和杂种中的驯服程度。然而，在最近的过去，畜牧业的限制性得多。最近的民族志和遗传分析表明，实际上，许多家庭和野生物种之间的杂交是规则，也不是罕见的例外。尽管野生种群的基因流量可能有害，但它也可能对牲畜种群产生积极影响。例如，通过降低与近交和引入遗传变异相关的风险，从而快速适应新的环境。因此，自适应基因流在世界各地的传播过程中可能发挥重要作用。猪尤其如此，因为在欧亚大陆地区存在地理和遗传学分化的野猪种群，并适应了各种各样的气候和环境。因此提供了原材料，这些原材料本来可以通过到达的家猪来吸收的。实际上，我们证明了野猪和家养猪之间的基因流动很普遍，并且在将猪从最初被驯化的近东引入欧洲之后就开始了。尽管有这种基因流动，但欧洲的猪通过保留形态和行为独特性来保持其作为家畜的正直，这表明尽管某些野猪基因组变异被纳入了家用股票，但许多野生野猪遗传变异被积极释放。在这里，我们将确定某些野生遗传变异是否优先删除，以及一些优先纳入国内人群。最终，该项目不仅将通过识别迅速纳入的特定基因组区域来揭示驯化的基因组基础，还将揭示家庭猪如何适应新的环境，以及在基因流动过程中抗拒的基因组区域。为此，我们将评估过去10，000年中从东部和西部的1,000多头古猪和野猪的DNA保存，然后对保存最佳标本的整个基因组进行测序。凭借这些数据，我们将建立将野猪基因掺入到国内股票的比例和基因组位置的空间和时间差异。结果不仅将允许对家畜起源的前所未有的理解，还将对危害濒临灭绝的野猪种群的保护以及猪育种者和猪肉消费者产生重要的影响，而猪的真实性至关重要。

项目成果

Zooarchaeology and Ancient DNA, part 2: new substrates and perspectives

动物考古学和古代 DNA，第 2 部分：新的基础和观点

• DOI: 10.24852/pa2021.1.35.196.204
• 发表时间: 2021
• 期刊: Povolzhskaya Arkheologiya (The Volga River Region Archaeology)
• 作者: Lebrasseur O

Genetic swamping of the critically endangered Scottish wildcat was recent and accelerated by disease

极度濒危的苏格兰野猫的基因淹没最近才出现，并因疾病而加速

• DOI: 10.1016/j.cub.2023.10.026
• 发表时间: 2023
• 期刊: Current Biology
• 影响因子: 9.2
• 作者: Howard-McCombe J

HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data.

• DOI: 10.1371/journal.pcbi.1010493
• 发表时间: 2022-09
• 期刊: PLoS computational biology
• 影响因子: 4.3

Adaptation and Cryptic Pseudogenization in Penguin Toll-Like Receptors.

• DOI: 10.1093/molbev/msab354
• 发表时间: 2022-01-07
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Fiddaman SR;Vinkler M;Spiro SG;Levy H;Emerling CA;Boyd AC;Dimopoulos EA;Vianna JA;Cole TL;Pan H;Fang M;Zhang G;Hart T;Frantz LAF;Smith AL
• 通讯作者: Smith AL

Animal domestication in the era of ancient genomics

• DOI: 10.1038/s41576-020-0225-0
• 发表时间: 2020-04-07
• 期刊: NATURE REVIEWS GENETICS
• 影响因子: 42.7
• 作者: Frantz, Laurent A. F.;Bradley, Daniel G.;Orlando, Ludovic
• 通讯作者: Orlando, Ludovic