Caligid sea lice represent a significant threat to salmonid aquaculture worldwide. Population genetic analyses have consistently shown minimal population genetic structure in North Atlantic Lepeophtheirus salmonis, frustrating efforts to track louse populations and improve targeted control measures. The aim of this study was to test the power of reduced representation library sequencing (IIb-RAD sequencing) coupled with random forest machine learning algorithms to define markers for fine-scale discrimination of louse populations. We identified 1286 robustly supported SNPs among four L. salmonis populations from Ireland, Scotland and Northern Norway. Only weak global structure was observed based on the full SNP dataset. The application of a random forest machine-learning algorithm identified 98 discriminatory SNPs that dramatically improved population assignment, increased global genetic structure and resulted in significant genetic population differentiation. A large proportion of SNPs found to be under directional selection were also identified to be highly discriminatory. Our data suggest that it is possible to discriminate between nearby L. salmonis populations given suitable marker selection approaches, and that such differences might have an adaptive basis. We discuss these data in light of sea lice adaption to anthropogenic and environmental pressures as well as novel approaches to track and predict sea louse dispersal.

中文翻译：

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使用随机森林分类方法对东北大西洋鲑鱼虱（Lepeophtheirus鲑鱼）种群进行遗传指纹分析。

哈里吉斯海虱对全世界鲑鱼养殖业构成了重大威胁。种群遗传学分析一致地表明，北大西洋鲑鱼Leopophtheirus鲑鱼的遗传结构最少，这对追踪虱子种群和改进有针对性的控制措施的努力令人沮丧。这项研究的目的是测试简化表示库测序（IIb-RAD测序）与随机森林机器学习算法相结合的功能，以定义对虱子种群进行细微区分的标记。我们在爱尔兰，苏格兰和挪威北部的四个沙门氏菌种群中鉴定了1286个有力支持的SNP。基于完整的SNP数据集，仅观察到了较弱的全局结构。随机森林机器学习算法的应用确定了98个具有歧视性的SNP，这些SNP显着改善了种群分配，增加了全球遗传结构，并导致了显着的遗传种群分化。还发现大部分定向选择的SNP具有很高的歧视性。我们的数据表明，使用合适的标记选择方法可以区分附近的鲑鱼L.鲑鱼种群，并且这种差异可能具有适应性基础。我们根据海虱对人为和环境压力的适应性以及跟踪和预测海虱扩散的新方法来讨论这些数据。还发现大部分定向选择的SNP具有很高的歧视性。我们的数据表明，使用合适的标记选择方法可以区分附近的沙门氏菌种群，并且这种差异可能具有适应性基础。我们根据海虱对人为和环境压力的适应性以及跟踪和预测海虱扩散的新方法来讨论这些数据。还发现大部分定向选择的SNP具有很高的歧视性。我们的数据表明，使用合适的标记选择方法可以区分附近的鲑鱼L.鲑鱼种群，并且这种差异可能具有适应性基础。我们根据海虱对人为和环境压力的适应性以及跟踪和预测海虱扩散的新方法来讨论这些数据。