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造成的种群规模减少。即使是那些没有被过度捕捞的物种，收获量也占了最大和生长最快的个体的很大一部分。因此，捕鱼对鱼类种群施加了强烈的自然选择，选择生长缓慢的小个体。人工捕鱼的实验表明，实验室种群的生长速度、成熟大小和其他性状都在迅速进化。10年前经典的科诺弗-蒙施实验显示了捕鱼产生快速进化的力量。然而，没有人分析在这种受控条件下捕鱼的遗传影响，也没有人试图调查整个基因组对强烈的渔业进化的反应方式。幸运的是，Conover-Munsch的样本--来自他们经典实验中使用的鱼类--已经被保存下来，现在可以使用现代基因组技术来分析鱼类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。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理解捕鱼的长期影响的重要组成部分，因为它们将首次允许对自然选择如何对鱼类种群起作用的机械理解。该项目还将比较捕捞压力放松后发生的变化，以估计捕捞物种中是否存在阻碍其恢复的有害基因组变化。这项研究的数据将显示捕鱼如何在选择的基因座上产生变化，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变化。研究人员将使用下一代DNA测序技术对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的遗传变异，选择大尺寸的品系，选择小尺寸的品系，以及原始种群，以便在基因组水平上绘制捕鱼造成的进化变化。他们将使用离群值分析来精确定位强选择作用改变等位基因频率的位点。他们将把这些变化与放松捕鱼后鱼类种群的变化进行比较，以区分容易逆转的进化变化和不易逆转的进化变化。此外，他们还将比较捕鱼引起的遗传变化与美国东海岸沿着环境梯度自然发生的遗传变化。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-通过连锁不平衡模式估计-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在原生环境中被进化力量选择的，随后又受到捕鱼的新进化压力的青睐。

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.