Genomics approaches to the management of mixed stock fisheries in Canada: developing tools for promotingfishery stability and the protection of biodiversity

物种通常由多个种群组成，每个种群都与特定的环境有关，并且通常具有对当地环境或特定生态环境的适应性。以多种种群为目标的渔业可以从这种适应性多样性中受益，因为它们的生产力更高、更稳定、更能适应环境变化，而且关闭的次数更少，这一系列好处被称为组合效应。然而，为了从组合效应中获益，混合种群渔业必须以控制的方式针对个别种群；这反过来又需要能够识别这些种群的工具。遗传方法长期以来一直用于这一目的，但传统方法往往不能解决种群和适应多样性的关键单位。最近，检测数百万个DNA碱基和数千个基因的“下一代”（NGS） DNA测序技术已被证明能够精确地分辨当地人群及其遗传特征。迄今为止，这些方法的新颖性和它们产生的数据的复杂性限制了它们在渔业管理中的应用。我们将开发DNA和软件工具，以识别重要种群，使混合种群渔业管理和保护具有重要经济和文化意义的鱼类物种的生物多样性成为可能。我们将利用NGS在梅尔维尔湖和拉布拉多海岸的大西洋鲑鱼以及纽芬兰和拉布拉多海岸的大西洋鳕鱼中实现这些目标。这些物种支持混合种群收获，遭受了重大损失，并面临着失去重要多样性的风险。鲑鱼对土著食物渔业很重要，可能会受到计划中的水电站大坝的影响。我们还将开发一个软件包，以简化NGS数据的分析和DNA变异与环境或表型特征之间关联的测试，从而使未经生物信息学培训的科学家能够更容易地访问NGS数据的力量。通过广泛的基因组分析，我们将确定可能特别适合支持稳定渔业的菌株或种群，并生产可用于保护各种适应性组合的工具，包括供其他科学家追求类似目标的软件工具。

Species usually consist of multiple populations, each associated with a particular environment, and often harbouring adaptations to the local environment or a particular ecological context. Fisheries that target multiple populations can benefit from this adaptive diversity by being more productive, stable, resilient to environmental change, and subject to fewer closures, a set of benefits known as the portfolio effect. However, to benefit from the portfolio effect, mixed stock fisheries must target individual populations in a controlled fashion; this in turn requires tools that enable identification of those populations. Genetic methods have long been used for this purpose, but traditional approaches often fail to resolve stocks and critical units of adaptive diversity. Recently, ('next generation', NGS) DNA sequencing technologies that examine millions of DNA bases and thousands of genes have proven capable of fine-scale resolution of local populations and their genetic traits. The novelty of these methods and the complexity of the data they produce have so far limited their application in fisheries management. We will develop DNA and software tools to identify important populations, enable management of mixed-stock fisheries and conservation of biodiversity within economically and culturally important fish species. We will use NGS to address these objectives in Atlantic salmon in Lake Melville and coastal Labrador, and Atlantic cod along Newfoundland and Labrador's coast. These species support mixed stock harvests, have suffered major declines, and risk losing important diversity. Salmon are important for aboriginal food fisheries, and may be affected by a planned hydroelectric dam. We will also develop a software package to ease analysis of NGS data and testing for associations between DNA variations and environmental or phenotypic features, thus enabling scientists without bioinformatic training to more easily access the power of NGS data. Using extensive genomic analyses, we will identify strains or populations that may be especially well suited to support stable fisheries, and produce tools that that can be used to conserve diverse adaptive portfolios, including software tools for other scientists to pursue similar objectives.