Members of the New Zealand Enantiobuninae constitute some of the most charismatic soil arthropods of the archipelago, and a striking example of sexual dimorphism, with nondescript females but colourful males boasting exaggerated chelicerae many times longer than their bodies. The genera Forsteropsalis and Pantopsalis recently underwent revision, but many questions remained about the validity of species designations owing to historical issues of characters of dubious taxonomic value, female specimens designated as holotypes despite the males holding all the diagnostic characters, and the suspected presence of more than one male form within some species. We present the first phylogeny based on molecular data for the New Zealand species in the genera Forsteropsalis, Pantopsalis and Mangatangi, and comment on the taxonomic implications of our results, including the diagnostic viability of important morphological characters. Our analyses reject the monophyly of Neopilionidae and Forsteropsalis, but support the monophyly of Pantopsalis. Finally, we comment on the taxonomic implications of the results, including the diagnostic validity of morphological characters traditionally used on the groups.

Chelicerata represents one of the oldest groups of arthropods, with a fossil record extending to the Cambrian, and is sister to the remaining extant arthropods, the mandibulates. Attempts to resolve the internal phylogeny of chelicerates have achieved little consensus, due to marked discord in both morphological and molecular hypotheses of chelicerate phylogeny. The monophyly of Arachnida, the terrestrial chelicerates, is generally accepted, but has garnered little support from molecular data, which have been limited either in breadth of taxonomic sampling or depth of sequencing. To address the internal phylogeny of this group, we employed a phylogenomic approach, generating transcriptomic data for 17 species in combination with existing data, including two complete genomes. We analyzed multiple datasets containing up to 1,235,912 sites across 3,644 loci, using alternative approaches to optimization of matrix composition. Here we show that phylogenetic signal for the monophyly of Arachnida is restricted to the 500 slowest-evolving genes in the dataset. Accelerated evolutionary rates in the orders Acariformes, Pseudoscorpiones, and Parasitiformes potentially engender long-branch attraction artifacts, yielding non-monophyly of Arachnida with increasing support upon incrementing the number of concatenated genes. Mutually exclusive hypotheses are supported by locus groups of variable evolutionary rate, revealing significant conflicts in phylogenetic signal. Analyses of gene-tree discordance indicate marked incongruence in relationships among chelicerate orders, whereas derived relationships are demonstrably robust. Consistently recovered and supported relationships include the monophyly of Chelicerata, Euchelicerata, Tetrapulmonata, and all orders represented by multiple terminals. Relationships supported by subsets of slow-evolving genes include Ricinulei + Solifugae; a clade comprised of Ricinulei, Opiliones, and Solifugae; and a clade comprised of Tetrapulmonata, Scorpiones, and Pseudoscorpiones. We demonstrate that outgroup selection without regard for branch length distribution exacerbates long branch attraction artifacts and does not mitigate gene-tree discordance, regardless of high gene representation for outgroups that are model organisms. Arachnopulmonata (new name) is proposed for the clade comprising Scorpiones + Tetrapulmonata (previously named Pulmonata).

Sipunculans (also known as peanut worms) are an ancient group of exclusively marine worms with a global distribution and a fossil record that dates back to the Early Cambrian. The systematics of sipunculans, now considered a distinct subclade of Annelida, has been studied for decades using morphological and molecular characters, and has reached the limits of Sanger-based approaches. Here, we reevaluate their family-level phylogeny by comparative transcriptomic analysis of eight species representing all known families within Sipuncula. Two data matrices with alternative gene occupancy levels (large matrix with 675 genes and 62% missing data; reduced matrix with 141 genes and 23% missing data) were analysed using concatenation and gene-tree methods, yielding congruent results and resolving each internal node with maximum support. We thus corroborate prior phylogenetic work based on molecular data, resolve outstanding issues with respect to the familial relationships of Aspidosiphonidae, Antillesomatidae and Phascolosomatidae, and highlight the next area of focus for sipunculan systematics.

In Opiliones, one of the largest orders within the class Arachnida, with more than 6000 described species, sexual dimorphism can be widespread and exaggerated. This great variety of forms of gender-based dimorphism suggests that sexual selection may play an important role in the diversification of some lineages. It also impacts species identification, assignment of females to described species and biodiversity assessments. Here we use DNA-sequence-based species discovery methods (the Poisson Tree Processes model with Bayesian support values, bPTP, and the Generalized Mixed Yule–Coalescent approach, GMYC, accounting for phylogenetic uncertainty) to shed light on the morphological disparity displayed in several species of neopilionid harvestmen from New Zealand. Both species delimitation analyses recovered many clades that coincide with our prior assignment of morphospecies, based solely on males, and allowed us to assign females and juveniles to these species as well as to identify putative new species and to assign some unidentified species to genera. Several genetic species, particularly Forsteropsalis inconstans and Pantopsalis cheliceroides-listeri, showed complex morphological disparity in the size and shape of the male chelicerae, but also in the general size and coloration patterns of the males. The systematic implications of our results and a possible ecological explanation for the exaggerated traits are discussed. Following our findings, the following taxonomic action is taken: Forsteropsalis nigra is considered a junior synonym of F. inconstans (new synonymy).

Spiders constitute one of the most successful clades of terrestrial predators [1]. Their extraordinary diversity, paralleled only by some insects and mites [2], is often attributed to the use of silk, and, in one of the largest lineages, to stereotyped behaviors for building foraging webs of remarkable biomechanical properties [1]. However, our understanding of higher-level spider relationships is poor and is largely based on morphology [2-4]. Prior molecular efforts have focused on a handful of genes [5, 6] but have provided little resolution to key questions such as the origin of the orb weavers [1]. We apply a next-generation sequencing approach to resolve spider phylogeny, examining the relationships among its major lineages. We further explore possible pitfalls in phylogenomic reconstruction, including missing data, unequal rates of evolution, and others. Analyses of multiple data sets all agree on the basic structure of the spider tree and all reject the long-accepted monophyly of Orbiculariae, by placing the cribellate orb weavers (Deinopoidea) with other groups and not with the ecribellate orb weavers (Araneoidea). These results imply independent origins for the two types of orb webs (cribellate and ecribellate) or a much more ancestral origin of the orb web with subsequent loss in the so-called RTA clade. Either alternative demands a major reevaluation of our current understanding of the spider evolutionary chronicle.