Data from: A critical appraisal of the placement of Xiphosura (Chelicerata) with account of known sources of phylogenetic error

Horseshoe crabs (Xiphosura) are traditionally regarded as sister to the
clade of terrestrial chelicerates (Arachnida). This hypothesis has been
challenged by recent phylogenomic analyses, but the non-monophyly of
Arachnida has consistently been disregarded as artifactual. We reevaluated
the placement of Xiphosura among chelicerates using the most complete
phylogenetic dataset to date, expanding outgroup sampling and including
data from whole genome sequencing projects. In spite of uncertainty in
theplacement of some arachnid clades, all analyses show Xiphosura
consistently nested within Arachnida as the sister group to Ricinulei
(hooded tick spiders). It is apparent that the radiation of Arachnids is
an old one and occurred over a brief period of time, resulting in several
consecutive short internodes, and thus is a potential case for the
confounding effects of incomplete lineage sorting (ILS). We simulated
coalescent gene trees to explore the effects of increasing levels of ILS
on the placement of horseshoe crabs. In addition, common sources of
systematic error were evaluated, as well as the effects of fast evolving
partitions and the dynamics of problematic long branch orders. Our results
indicated that the placement of horseshoe crabs can not be explained by
missing data, compositional biases, saturation, or incomplete lineage
sorting. Interrogation of the phylogenetic signal showed that the majority
of loci favor the derived placement of Xiphosura over a monophyletic
Arachnida. Our analyses support the inference that horseshoe crabs
represent a group of aquatic arachnids comparable to aquatic mites,
breaking a long standing paradigm in chelicerate evolution and altering
previous interpretations of the ancestral transition to the terrestrial
habitat. Future studies testing chelicerate relationships should approach
the task with a sampling strategy where the monophyly of Arachnida is not
held as the premise.