Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach.
Genetic fingerprinting of salmon louse (Lepeophtheirus salmonis) populations in the North-East Atlantic using a random forest classification approach.
复制标题
鲑鱼虱（Lepeophtheirus salmonis）种群在东北大西洋的遗传指纹使用随机的森林分类方法。
DOI：
10.1038/s41598-018-19323-z
复制
发表时间：
2018-01-19
影响因子：
4.6
通讯作者：
Llewellyn MS
中科院分区：
文献类型：
--
作者：
Jacobs A;De Noia M;Praebel K;Kanstad-Hanssen Ø;Paterno M;Jackson D;McGinnity P;Sturm A;Elmer KR;Llewellyn MS
卡利体海虱对全世界鲑科水产养殖构成重大威胁。种群遗传分析一直显示北大西洋Lepeophtheirus salmonis最小的种群遗传结构，使追踪虱子种群和改进有针对性的控制措施的努力受挫。本研究的目的是测试减少表征库测序（IIb-RAD测序）与随机森林机器学习算法相结合的能力，以定义虱子种群的精细区分标记。我们从来自爱尔兰、苏格兰和挪威北部的四个L.鲑科菌种群中鉴定出1286个强有力支持的snp。基于完整的SNP数据集，只观察到弱的全局结构。随机森林机器学习算法的应用鉴定了98个歧视性snp，这些snp显著改善了群体分配，增加了整体遗传结构，并导致了显著的遗传群体分化。在定向选择下发现的大部分snp也被确定为高度歧视性的。我们的数据表明，在适当的标记选择方法下，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以及跟踪和预测海虱扩散的新方法来讨论这些数据。
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.
登录
查看更多内容
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
4.9
作者：
Laporte，M.;Pavey，S. A.;Bernatchez，L.
通讯作者：
Bernatchez，L.
影响因子：
4.5
作者：
Jackson, D.;O'Donohoe, P.;Nolan, G.
通讯作者：
Nolan, G.
影响因子：
3.3
作者：
Foll, Matthieu;Gaggiotti, Oscar
通讯作者：
Gaggiotti, Oscar
影响因子：
5.8
作者：
Jombart, Thibaut;Ahmed, Ismail
通讯作者：
Ahmed, Ismail