High resolution genome changes during evolution in a classic fisheries experiment

对海洋物种的最大影响之一是捕鱼导致的种群数量减少。即使对于没有被过度捕捞的物种，收获也会占据最大和最快生长个体的很大一部分。因此，渔业对鱼类种群施加了很强的自然选择，选择了生长缓慢的小个体。人工捕捞实验表明，实验室种群的生长速度、成熟大小和其他特征进化迅速。十年前的经典Conover-Munsch实验展示了捕鱼产生快速进化的力量。然而，还没有对在这种受控条件下捕鱼的遗传影响进行分析，也没有试图调查整个基因组对强劲的渔业进化的反应方式。幸运的是，来自他们经典实验中使用的鱼的Conover-Munsch样本得到了保存，现在可以使用现代基因组技术来分析渔业诱导的进化如何塑造这些种群的遗传多样性和基因组结构。众所周知，在其他系统中，强选择会在基因组中留下有害变化的遗产。这项研究的结果将是了解捕捞的长期影响的重要组成部分，因为它们将首次使人们能够机械地理解自然选择如何对鱼类种群产生作用。该项目还将比较捕捞压力放松后发生的变化，以估计是否存在鱼类物种有害基因组变化的后遗症，阻碍它们的恢复。这项研究的数据将展示捕鱼如何在选择的座位上产生变化，以及这种强烈的选择如何由于遗传搭便车和近亲繁殖而产生其他非适应性的变化。研究人员将使用下一代DNA测序来对Conover-Munsch鱼类样本的蛋白质编码区进行测序。他们将发现、记录和比较基因组中大尺寸品系、小尺寸品系和原始种群中的遗传变异，以便在基因组水平上绘制捕鱼造成的进化变化图。他们将使用离群值分析来精确定位强势选择改变等位基因频率的基因座。他们将把这些变化与放松捕捞后鱼类种群的变化进行比较，以区分容易逆转的进化变化与不可逆的进化变化。此外，他们还将比较捕鱼引起的基因变化与美国东海岸环境梯度上自然发生的基因变化。初步数据表明，在渔业实验中选择的许多遗传变异是旧的变异--根据连锁不平衡的模式估计--已经存在于原始种群中。研究自然梯度的遗传学将表明这些变异中的哪些是被自然环境中的进化力量选择的，并随后受到捕鱼这种新的进化压力的青睐。

One of the strongest impacts there is on ocean species is reduction in population size due to fishing. Even for species that are not overfished, harvest takes a large fraction of the biggest and fastest growing individuals. As a result, fishing exerts strong natural selection on fish population, selecting for slow growing, small individuals. Experiments in artificial fishing have shown rapid evolution of growth rates, maturation size and other traits for lab populations. The classic Conover-Munsch experiments ten years ago showed the power of fishing to generate rapid evolution. However, no analysis of the genetic impact of fishing under such controlled conditions has been done, and no investigation of the way whole genomes respond to strong fisheries evolution has been attempted. Luckily, the Conover-Munsch samples - from the fish used in their classic experiment - have been preserved, and modern genomic techniques are now available that can analyze the way fisheries-induced evolution shaped the genetic diversity and genome architecture of these populations. Strong selection is known in other systems to leave a legacy of deleterious changes in the genome. The results of this study will be important components of understanding the long-term effects of fishing because they will for the first time allow a mechanistic understanding of how natural selection works on fish populations. The project will also compare the changes that occur after the relaxation of fishing pressure to estimate if there is a legacy of deleterious genome changes in fished species that impedes their recovery. The data from this study will show how fishing creates change at loci under selection, and also how this strong selection generates other, non-adaptive shifts because of genetic hitchhiking and inbreeding.The investigators will use next generation DNA sequencing to sequence the protein coding regions of the Conover-Munsch fish samples. They will discover, document and compare genetic variants across the genome in lines selected for large size, in lines selected for small size, and in the original populations in order to chart evolutionary changes at the genomic level imposed by fishing. They will use outlier analyses to pinpoint loci at which strong selection has acted to change allele frequencies. They will compare these changes to changes in fish populations after the relaxation of fishing in order to distinguish evolutionary changes that are easily reversible from those that are not. In addition, they will also compare genetic changes induced by fishing to those that occur naturally along an environmental gradient on the US east coast. Preliminary data indicate that many of the genetic variants selected for in the fisheries experiment are old variants - estimated by patterns of linkage disequilibrium - already present in the original population. Working on the genetics of the natural gradient will show which of these variants have been selected by evolutionary forces in the native environment, and subsequently been favored by the novel evolutionary pressure of fishing.