SG: Selection in Bottlenecked Populations

SG：瓶颈种群的选择

• 批准号: 1556705
• 负责人: Robert Wayne
• 金额: $ 14.99万
• 依托单位: University of California-Los Angeles
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-04-01 至 2020-03-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1556705&HistoricalAwards=false
• 关键词: SG; Selection; Bottlenecked; Populations

This study will examine genetic changes in sea otter populations using samples from Pre-Columbian to Modern times. Many rare or endangered species have experienced sharp population declines known as population "bottlenecks". These bottlenecks can have deleterious genetic impacts similar to inbreeding and affect the probability of species recovery. Understanding and quantifying these effects in populations allows for more effective management and better prediction of survival outcomes. A model example of a species that has experienced population bottlenecks is the sea otter. It was hunted almost to extinction, with numerical declines of 99% during the course of the 18th -19th century fur trade. The small number of surviving otters increased over the 20th century under careful monitoring and enhanced protection. In this project, the researchers will endeavor to determine whether the fur trade decline had lasting impacts on the sea otter genome that can be observed in extant populations. The researchers will compare genomes of sea otters that lived before the fur trade to those living today across the entire geographic range. Native American rubbish deposits, known as middens, dating back to Pre-Columbian times will supply the prehistoric and historical samples. The researchers will use cutting-edge gene sequencing technology to identify deleterious genes and predict their effect on individuals and populations. The results will inform future management plans for these populations and provide a new precedent for research on rare and endangered species. Researchers also will work with the Monterey Bay Aquarium and Smithsonian Conservation Biology Institute to create exhibits demonstrating how genome sequencing can aid conservation efforts and provide new genomic insights into a charismatic species that has an essential role in maintaining coastal kelp forest ecosystems.This project will utilize low and high coverage genome sequencing of individuals from six modern and three ancient pre-bottlenecked sea otter populations to reconstruct demographic history and quantify patterns of deleterious variation as a proxy for genetic load. A novel analytical framework will be developed using genetic variation data across multiple time points to study the relationship between small population size and patterns of deleterious mutations. Using forward-in-time simulations, null expectations of how genetic drift should act on different genomic elements will be developed for comparison to the empirical genomic dataset, and the importance of natural selection in preserving and purging deleterious variation will be quantified. The roles of purifying, relaxed and balancing selection will be examined by testing for enrichment of deleterious variation across genic regions. This research will provide a framework for distinguishing between moderately and strongly deleterious mutations and for evaluating the effects of bottlenecks on natural selection at the molecular level that can be applicable to other systems. As a result of this research, a variety of recent demographic events in a species with a complex demographic history will be detected and quantified, patterns of deleterious mutations across multiple time points will be compared, and patterns of genetic load will be predicted. Finally, the ways in which purifying and balancing selection are affected by small population sizes will be evaluated. The replication of recent extreme demographic events across sea otter populations and the abundance of pre-fur trade otter samples in Pre-Columbian middens provide unprecedented opportunities to isolate the effects of a bottleneck on deleterious variation and genetic load. The results and methods developed in this study will be broadly applicable to understanding the biology of small populations, especially those that are endangered.

这项研究将使用前哥伦布时期到现代的样本来研究海獭种群的遗传变化。许多稀有或濒危物种都经历了人口急剧下降，称为人口“瓶颈”。 这些瓶颈可能会产生类似于近亲繁殖的有害遗传影响，并影响物种恢复的可能性。了解和量化人群中的这些影响可以更有效地管理和更好地预测生存结果。海獭是一个经历过种群瓶颈的典型物种。牠们几乎被猎杀至灭绝，在世纪的毛皮贸易中，牠们的数量减少了99%。在世纪，在仔细的监测和加强的保护下，幸存的水獭数量有所增加。在这个项目中，研究人员将奋进确定毛皮贸易的下降是否对现存种群中可以观察到的海獭基因组产生了持久的影响。研究人员将比较生活在毛皮贸易之前的海獭的基因组与生活在整个地理范围内的海獭的基因组。美洲原住民的垃圾沉积物，被称为垃圾堆，可以追溯到前哥伦布时代，将提供史前和历史样本。 研究人员将使用尖端的基因测序技术来识别有害基因，并预测它们对个人和群体的影响。研究结果将为这些种群的未来管理计划提供信息，并为稀有和濒危物种的研究提供新的先例。研究人员还将与蒙特雷湾水族馆和史密森尼保护生物学研究所合作，创建展览，展示基因组测序如何帮助保护工作，并提供新的基因组见解，以了解一种在维持沿海海带森林生态系统方面发挥重要作用的魅力物种。海獭种群重建人口统计学的历史和量化模式的有害变化作为遗传负荷的代理。将使用多个时间点的遗传变异数据开发一种新的分析框架，以研究小群体大小与有害突变模式之间的关系。使用向前的时间模拟，零期望的遗传漂变应如何作用于不同的基因组元素将被开发用于与经验基因组数据集进行比较，并将量化自然选择在保存和清除有害变异中的重要性。纯化，放松和平衡选择的作用将通过检测基因区域之间有害变异的富集来检查。这项研究将提供一个框架，用于区分中度和强烈有害的突变，并在分子水平上评估瓶颈对自然选择的影响，可适用于其他系统。作为这项研究的结果，将检测和量化具有复杂人口统计学历史的物种中的各种最近的人口统计学事件，比较多个时间点的有害突变模式，并预测遗传负荷模式。最后，纯化和平衡选择的方式受到影响的小人口规模将进行评估。复制最近的极端人口事件在整个海獭种群和丰富的前毛皮贸易水獭样本在前哥伦布贝登斯提供了前所未有的机会，隔离的影响，一个瓶颈的有害变化和遗传负荷。这项研究的结果和方法将广泛适用于了解小种群的生物学，特别是那些濒临灭绝的种群。