Exon probe sets and bioinformatics pipelines for all levels of fish phylogenomics

We present seven new probe sets for modern target-capture phylogenomic protocols that capture ~1,100 exons explicitly filtered for paralogs using gene trees and span the diversity of teleost fishes. By integrating new exon-capture data into an existing matrix of 1,100 exons and 300 ray-finned fish species, we show that 56 newly-generated sequences fall out in their expected phylogenetic placements.

本研究开发了7套全新的探针组，适配现代目标捕获（target-capture）系统发育基因组学（phylogenomic）实验方案，该方案可捕获约1100个经基因树（gene tree）明确筛选旁系同源基因（paralog）的外显子（exon），且覆盖真骨鱼类（teleost fishes）的物种多样性。我们将新生成的外显子捕获（exon-capture）数据整合至一套包含1100个外显子与300种辐鳍鱼类的已有特征矩阵中，分析结果表明56条新生成序列均位于其预期的系统发育位置（phylogenetic placement）。