Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. Although conflicting hypotheses prevail in morphological and molecular data sets alike, the monophyly of Arachnida is nearly universally accepted, despite historical lack of support in molecular data sets. Some phylotranscriptomic analyses have recovered arachnid monophyly, but these did not sample all living orders, whereas analyses including all orders have failed to recover Arachnida. To understand this conflict, we assembled a data set of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternative algorithmic approaches to species tree inference. Investigation of sources of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the impact of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but merostomates appeared nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.

Scorpions constitute a charismatic lineage of arthropods and comprise more than 2500 described species. Found throughout various tropical and temperate habitats, these predatory arachnids have a long evolutionary history, with a fossil record that began in the Silurian. While all scorpions are venomous, the asymmetrically diverse family Buthidae harbors nearly half the diversity of extant scorpions, and all but one of the 58 species that are medically significant to humans. However, the lack of a densely sampled scorpion phylogeny has hindered broader inferences of the diversification dynamics of scorpion toxins. To redress this gap, we assembled a phylogenomic data set of 100 scorpion venom gland transcriptomes and genomes, emphasizing the sampling of highly toxic buthid genera. To infer divergence times of venom gene families, we applied a phylogenomic node dating approach for the species tree in tandem with phylostratigraphic bracketing to estimate the minimum ages of mammal-specific toxins. Our analyses establish a robustly supported phylogeny of scorpions, particularly with regard to relationships between medically significant taxa. Analysis of venom gene families shows that mammal-active sodium channel toxins (NaTx) have independently evolved in five lineages within Buthidae. Temporal windows of mammal-targeting toxin origins are correlated with the basal diversification of major scorpion mammal predators such as shrews, bats, and rodents. These results suggest an evolutionary model of relatively recent diversification of buthid NaTx homologs in response to the diversification of scorpion predators. [Adaptation; arachnids; phylogenomic dating; phylostratigraphy; venom.]

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.

The tetragnathid genus Leucauge includes some of the most common orb-weaving spiders in the tropics. Although some species in this genus have attained relevance as model systems for several aspects of spider biology, our understanding of the generic diversity and evolutionary relationships among the species is poor. In this study we present the first attempt to determine the phylogenetic structure within Leucauge and the relationship of this genus with other genera of Leucauginae. This is based on DNA sequences from the five loci commonly used and Histone H4, used for the first time in spider phylogenetics. We also assess the informativeness of the standard markers and test for base composition biases in the dataset. Our results suggest that Leucauge is not monophyletic since species of the genera Opas, Opadometa, Mecynometa and Alcimosphenus are included within the current circumscription of the genus. Based on a phylogenetic re-circumscription of the genus to fulfil the requirement for monophyly of taxa, Leucauge White, 1841 is deemed to be a senior synonym of the genera Opas Pickard-Cambridge, 1896 revalidated synonymy, Mecynometa Simon, 1894 revalidated synonymy, Opadometa Archer, 1951 new synonymy and Alcimosphenus Simon, 1895 new synonymy. We identify groups of taxa critical for resolving relationships within Leucauginae and describe the limitations of the standard loci for accomplishing these resolutions.

Considerable progress has been achieved in resolving higher-level relationships of Arthropoda in the past two decades, largely precipitated by advances in sequencing technology. Yet, dark branches persist in the arthropod tree of life, principally among groups that are difficult to collect, occur in cryptic habitats, or are characterized by minute body size. Among chelicerates, the mesodiverse order Solifugae (commonly called camel spiders or sun spiders) is one of the last orders of Arachnida that lacks a higher-level phylogeny altogether and has long been characterized as one of the “neglected cousins”, a lineage of arachnid orders that are comparatively poorly studied with respect to evolutionary relationships. Though renowned for their aggression, remarkable running speed, and adaptation to arid habitats, inferring solifuge relationships has been hindered by inaccessibility of diagnostic characters in most ontogenetic stages for morphological datasets, whereas molecular investigations to date have been limited to one of the 12 recognized families. In this study we generated a phylogenomic dataset via capture of ultraconserved elements (UCEs) and sampled all extant families. We recovered a well-resolved phylogeny of solifuge families, with two distinct groups of New World taxa nested within a broader Paleotropical radiation. To provide a temporal context to solifuge diversification, we estimated molecular divergence times using fossil calibrations within a least-squares framework. Solifugae were inferred to have radiated by the Permian, with divergences of most families dating to the post Paleogene-Cretaceous extinction. These results accord with a diversification history largely driven by vicariance as a result of continental breakup.