SG: Selection in Bottlenecked Populations

这项研究将使用前哥伦布时代到现代的样本来检查海獭种群的基因变化。许多稀有或濒危物种的数量急剧下降，被称为人口“瓶颈”。这些瓶颈可能产生有害的遗传影响，类似于近亲繁殖，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。海獭是经历过人口瓶颈的物种的典型例子。在18 -19世纪的毛皮贸易中，它的数量下降了99%，几乎被猎杀到灭绝。20世纪，在严密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，研究人员将努力确定毛皮贸易的下降是否对现存种群中观察到的海獭基因组产生了持久的影响。研究人员将比较整个地理范围内生活在皮毛贸易之前的海獭和今天生活的海獭的基因组。可以追溯到前哥伦布时代的美洲原住民垃圾沉积物，即所谓的垃圾堆，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，并预测它们对个体和群体的影响。研究结果将为这些种群的未来管理计划提供参考，并为珍稀濒危物种的研究提供新的先例。研究人员还将与蒙特利湾水族馆和史密森尼保护生物学研究所合作，举办展览，展示基因组测序如何有助于保护工作，并为一种在维持沿海海带森林生态系统中发挥重要作用的有魅力的物种提供新的基因组见解。该项目将利用来自6个现代和3个古代瓶颈海獭种群的低覆盖率和高覆盖率基因组测序，重建人口统计历史，量化有害变异模式，作为遗传负荷的代理。将开发一个新的分析框架，利用遗传变异数据跨多个时间点来研究小群体规模和有害突变模式之间的关系。使用前向时间模拟，将开发遗传漂变如何作用于不同基因组元素的零期望，以便与经验基因组数据集进行比较，并且将量化自然选择在保存和清除有害变异方面的重要性。净化、放松和平衡选择的作用将通过检测跨基因区域的有害变异的富集来检验。这项研究将提供一个框架来区分中度和强烈有害突变，并在分子水平上评估瓶颈对自然选择的影响，这可以适用于其他系统。由于这项研究的结果，将检测和量化具有复杂人口统计历史的物种中最近发生的各种人口统计事件，将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，将评估小种群规模对净化和平衡选择的影响方式。最近在海獭种群中发生的极端人口统计事件的复制，以及前哥伦布时期中部大量的皮毛贸易前海獭样本，为隔离瓶颈对有害变异和遗传负荷的影响提供了前所未有的机会。本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。

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.