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.

一般来说，现代家养物种被积极地阻止与野生种群杂交。这条规则的少数例外涉及故意产生新的杂交宠物，如那些涉及家猫和野猫物种。在家畜品种中，强烈不鼓励将野生物种纳入育种系的做法，因为从野生种群引入基因会降低生产力和杂交品种的驯服程度。然而，在最近的过去，畜牧业实践的限制要少得多。最近的人种学和遗传分析表明，许多家养物种和野生物种之间的杂交实际上是一种规律，而不是罕见的例外。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影响。例如，通过降低与近亲繁殖有关的风险，以及通过引入允许快速适应新环境的遗传变异。因此，适应性基因流在家畜在世界范围内的传播过程中可能发挥了重要作用。猪的情况尤其如此，因为野猪在地理上和遗传上存在差异，并且适应各种各样的气候和环境；这样就提供了可以被到达的家猪吸收的原料。事实上，我们证明了野猪和家猪之间的基因流动是普遍的，而且这种流动是在猪最初被驯化的地方从近东被引入欧洲之后立即开始的。尽管有这种基因流动，欧洲的猪通过保持形态和行为的独特性来保持其作为家畜的完整性，这表明尽管一些野猪基因组变异被纳入了国内种群，但许多野猪遗传变异被积极地消除了。在这里，我们将确定是否有一些野生遗传变异被优先清除，是否有一些被优先纳入国内种群。最终，该项目不仅将揭示驯化的基因组基础，还将通过识别快速整合的特定基因组区域以及在基因流动中被抵制的特定基因组区域，揭示家猪如何适应新环境。为此，我们将评估过去1万年来来自欧亚大陆东部和西部的1000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。利用这些数据，我们将建立野猪基因纳入国内种群的比例和基因组位置的时空差异。研究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、养猪者和猪肉消费者产生重要影响，对他们来说，家猪肉和野肉的真实性至关重要。

项目成果

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

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

Grey wolf genomic history reveals a dual ancestry of dogs.

• DOI: 10.1038/s41586-022-04824-9
• 发表时间: 2022-07
• 期刊: Nature
• 影响因子: 64.8