Population genomic and phylogenetic analysis of three wireworm (Coleoptera: Elateridae) species

A group of pest species that is resurging as a significant threat to economically important crops worldwide is the larvae of click beetles (Coleoptera: Elateridae), known as wireworms. Here, we produce one of the first wireworm genome assemblies (Limonius californicus), and investigate population genetic structure and phylogenetic relationships of three described species (L. californicus, L. infuscatus, L. canus) across the northwest US and southwest Canada using genome-wide markers (RADseq) and genome skimming. We found two species (L. californicus and L. infuscatus) are comprised of genetically distinct groups that diverged around one million years ago but have no known distinguishing morphological characters, and therefore could be considered cryptic species complexes. Most of the cryptic species have disjunct geographic distributions separated by mountain ranges, but one pair has overlapping distributions, and another pair is separated by no obvious geographic barriers. We also found within-species population structure across relatively short geographic distances (e.g., 25km), but no evidence for distinct populations within a single agricultural field. Genome scans for selection with RADseq data provided evidence for signatures of genomic adaptation associated with changes in pesticide treatment in an experimental agricultural field trial for L. canus. We demonstrate that genomic tools can be a strong asset in the development of effective wireworm control strategies by enabling identification of cryptic species and populations present in a given area, as well as identification of genomic adaptation to pesticide treatment.

一组害虫物种正作为对全球经济作物构成重大威胁而再次崛起，该物种为叩头甲幼虫（鞘翅目：叩头甲科），俗称线虫。在本研究中，我们完成了首个线虫基因组组装（Limonius californicus），并利用全基因组标记（RADseq）和基因组扫描技术，对三个已描述的物种（L. californicus、L. infuscatus、L. canus）在美国西北部和加拿大西南部的种群遗传结构和系统发育关系进行了研究。我们发现，两种物种（L. californicus和L. infuscatus）由遗传上不同的群体组成，这些群体在大约一百万年前分化，但并无已知的区分形态学特征，因此可被视为隐秘物种复合体。大多数隐秘物种具有由山脉分隔的间断地理分布，但有一对物种具有重叠的分布范围，另一对物种则无明显的地理障碍分隔。我们还发现，在相对较短的地域距离内（例如，25公里），存在物种内部的种群结构，但在单个农田内并无证据表明存在不同的种群。利用RADseq数据进行的选择基因组扫描提供了证据，表明在L. canus的实验性农田试验中，与农药处理变化相关的基因组适应性标记。我们证明了基因组工具可以成为开发有效的线虫控制策略的强大工具，它能够识别特定区域内存在的隐秘物种和种群，以及识别对农药处理的基因组适应性。