A comprehensive examination of Chelicerate genomes reveals no evidence for a whole genome duplication among spiders and scorpions

Whole genome duplications (WGDs) can be a key event in evolution, playing a role in both adaptation and speciation. While WGDs are common throughout the history of plants, only a few examples have been proposed in metazoans. Among these, recent proposals of WGD events in Chelicerates, the group of Arthropods that includes horseshoe crabs, ticks, scorpions, and spiders, include several rounds in the history of horseshoe crabs, with an additional WGD proposed in the ancestor of spiders and scorpions. However, many of these inferences are based on evidence from only a small portion of the genome (in particular, the Hox gene cluster); therefore, genome-wide inferences with broader species sampling may give a clearer picture of WGDs in this clade. Here, we investigate signals of WGD in Chelicerates using whole genomes from 17 species. We employ multiple methods to look for these signals, including gene tree analysis of thousands of gene families, comparisons of synteny, and signals of divergence among within-species paralogs. We test several scenarios of WGD in Chelicerates using multiple species trees as a backbone for all hypotheses. While we do find support for at least one WGD in the ancestral horseshoe crab lineage, we find no evidence for a WGD in the history of spiders and scorpions using any genome-scale method. This study not only sheds light on genome evolution and phylogenetics within Chelicerates, but also demonstrates how a combination of comparative methods can be used to investigate signals of ancient WGDs.