Data from: Population structure and gene flow in the global pest, Helicoverpa armigera

Helicoverpa armigera is a major agricultural pest that is distributed across Europe, Asia, Africa and Australasia. This species is hypothesized to have spread to the Americas 1.5 million years ago, founding a population that is at present, a distinct species, Helicoverpa zea. In 2013, H. armigera was confirmed to have re-entered South America via Brazil and subsequently spread. The source of the recent incursion is unknown and population structure in H. armigera is poorly resolved, but a basic understanding would highlight potential biosecurity failures and determine the recent evolutionary history of region-specific lineages. Here, we integrate several end points derived from high-throughput sequencing to assess gene flow in H. armigera and H. zea from populations across six continents. We first assemble mitochondrial genomes to demonstrate the phylogenetic relationship of H. armigera with other Heliothine species and the lack of distinction between populations. We subsequently use de novo genotyping-by-sequencing and whole-genome sequences aligned to bacterial artificial chromosomes, to assess levels of admixture. Primarily, we find that Brazilian H. armigera are derived from diverse source populations, with strong signals of gene flow from European populations, as well as prevalent signals of Asian and African ancestry. We also demonstrate a potential field-caught hybrid between H. armigera and H. zea, and are able to provide genomic support for the presence of the H. armigera conferta subspecies in Australasia. While structure among the bulk of populations remains unresolved, we present distinctions that are pertinent to future investigations as well as to the biosecurity threat posed by H. armigera.棉铃实夜蛾（Helicoverpa armigera）是一种分布于欧洲、亚洲、非洲及澳大拉西亚的重大农业害虫。该物种被推测于150万年前扩散至美洲，进而演化形成了如今的独立物种美洲棉铃虫（Helicoverpa zea）。2013年，研究证实棉铃实夜蛾经巴西重新入侵南美洲并随后扩散。此次近期入侵的来源尚不明确，且棉铃实夜蛾的种群结构仍未得到充分解析，但对其开展基础研究可揭示潜在的生物安全漏洞，并明确区域特异性谱系的近期进化历史。本研究整合了高通量测序（high-throughput sequencing）产生的多类测序数据，以评估六大洲棉铃实夜蛾与美洲棉铃虫种群间的基因交流情况。首先通过组装线粒体基因组（mitochondrial genome），阐明了棉铃实夜蛾与其他实夜蛾亚科物种的系统发育关系，同时证实其种群间并无显著遗传分化。随后采用从头基因型分型测序（de novo genotyping-by-sequencing）及比对至细菌人工染色体（bacterial artificial chromosome）的全基因组序列，评估种群的遗传混合水平。研究主要发现：巴西的棉铃实夜蛾种群源自多样的源种群，存在来自欧洲种群的强烈基因流信号，同时普遍带有亚洲与非洲血统的遗传特征。此外，本研究还发现了一头野外捕获的棉铃实夜蛾与美洲棉铃虫的杂交个体，并为澳大拉西亚地区存在棉铃实夜蛾澳大拉西亚亚种（Helicoverpa armigera conferta）提供了基因组学证据。尽管多数种群的遗传结构仍未得到充分解析，但本研究的相关发现可为后续相关研究以及棉铃实夜蛾所带来的生物安全威胁防控提供重要参考。