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Within the arachnids, chromosome-level genome assemblies have greatly accelerated the understanding of gene family evolution and developmental genomics in key groups, such as spiders (Araneae), mites and ticks (Acariformes and Parasitiformes). Among other poorly studied arachnid orders that lack genome assemblies altogether are the clade Pedipalpi, which is comprised of three orders that form the sister group of spiders, which diverged over 400 Mya. We close this gap by generating the first chromosome-level assembly from a single specimen of the vinegaroon Mastigoproctus giganteus (Uropygi). We show that this highly complete genome retains plesiomorphic conditions for many gene families that have undergone lineage-specific derivations within the more diverse spiders. Consistent with the phylogenetic position of Uropygi, macrosynteny in the M. giganteus genome substantiates the signature of an ancient whole genome duplication. 

The systematics of the arachnid order Solifugae have been an enigma, owing to challenges in interpreting morphology, a paucity of molecular phylogenetic studies sampling across the group, and a dearth of taxonomic attention for many lineages. Recent work has suggested that solifuge families largely exhibit contiguous distributions and reflect patterns of vicariance, with the exception of three families: Melanoblossidae, Daesiidae and Gylippidae. Morphological studies have cast doubt on their existing circumscriptions and the present composition of these taxa renders their distributions as disjunct. We leveraged ultraconserved elements (UCEs) to test the phylogenetic placement of three key lineages of Solifugae that cause these anomalous distributions: Dinorhax rostrumpsittaci (putative melanoblossid), Namibesia (putative daesiid), and Trichotoma (putative gylippid). Phylogenetic placement of these three genera based on UCEs rendered the families that harbor them as para- or polyphyletic, recovering instead relationships that better accord with a biogeographic history driven by vicariance. Toward a stable and phylogenetically informed classification of Solifugae, we establish three new families, Dinorhaxidae new rank, Namibesiidae new rank and Lipophagidae new rank. 

Asymmetrical rates of cladogenesis and extinction abound in the tree of life, resulting in numerous minute clades that are dwarfed by larger sister groups. Such taxa are commonly regarded as phylogenetic relicts or “living fossils” when they exhibit an ancient first appearance in the fossil record and prolonged external morphological stasis, particularly in comparison to their more diversified sister groups. Due to their special status, various phylogenetic relicts tend to be well-studied and prioritized for conservation. A notable exception to this trend is found within Amblypygi (“whip spiders”), a visually striking order of functionally hexapodous arachnids that are notable for their antenniform first walking leg pair (the eponymous “whips”). Paleoamblypygi, the putative sister group to the remaining Amblypygi, is known from Late Carboniferous and Eocene deposits but is survived by a single living species, Paracharon caecusHansen (1921), that was last collected in 1899. Due to the absence of genomic sequence-grade tissue for this vital taxon, there is no global molecular phylogeny for Amblypygi to date, nor a fossil-calibrated estimation of divergences within the group. Here, we report a previously unknown species of Paleoamblypygi from a cave site in Colombia. Capitalizing upon this discovery, we generated the first molecular phylogeny of Amblypygi, integrating ultraconserved element sequencing with legacy Sanger datasets and including described extant genera. To quantify the impact of sampling Paleoamblypygi on divergence time estimation, we performed in silico experiments with pruning of Paracharon. We demonstrate that the omission of relicts has a significant impact on the accuracy of node dating approaches that outweighs the impact of excluding ingroup fossils, which bears upon the ancestral range reconstruction for the group. Our results underscore the imperative for biodiversity discovery efforts in elucidating the phylogenetic relationships of “dark taxa,” and especially phylogenetic relicts in tropical and subtropical habitats. The lack of reciprocal monophyly for Charontidae and Charinidae leads us to subsume them into one family, Charontidae, new synonymy. 

Abstract Biodiversity catalogs are an invaluable resource for biological research. Efforts to scientifically document biodiversity have not been evenly applied, either because of charisma or because of ease of study. Spiders are among the most precisely cataloged and diverse invertebrates, having surpassed 50,000 described species globally. The World Spider Catalog presents a unique opportunity to assess the disproportionate documentation of spider diversity. In the present article, we develop a taxonomic ratio relating new species descriptions to other taxonomic activity as a proxy for taxonomic effort, using spiders as a case study. We use this taxonomic effort metric to examine biases along multiple axes: phylogeny, zoogeography, and socioeconomics. We also use this metric to estimate the number of species that remain to be described. This work informs arachnologists in identifying high-priority taxa and regions for species discovery and highlights the benefits of maintaining open-access taxonomic databases—a necessary step in overcoming bias and documenting the world's biodiversity. 

We complement and expand the existing descriptions of the Australian araneid spider Paraplectanoides crassipes Keyserling, 1886, and provide the first detailed analysis of the male palpal homologies to include examination of the expanded organ and scanning electron micrographs of the palpal sclerites. We study the placement of Paraplectanoides and the classification of the family Araneidae by combining ultraconserved elements with Sanger markers. We also added Sanger sequences of the Australian araneid genus Venomius to the molecular dataset of Scharff et al. (2020) to explore the phylogenetic placement and implications for classification of the family. We evaluate a recent proposal on the classification of the family Araneidae by Kuntner et al. (2023) in which a new family is erected for P. crassipes. Paraplectanoides is monotypic. Examination of the type material shows that Paraplectanoides kochi O. Pickard-Cambridge, 1877 is misplaced in the genus and the name is a senior synonym of the araneid Isoxya penizoides Simon, 1887 (new synonymy) that results in the new combination Isoxya kochi (O. Pickard-Cambridge, 1877). The classification of Araneidae is revised and the following nomenclatural acts are introduced: Paraplectanoididae Kuntner, Coddington, Agnarsson and Bond, 2023 is a junior synonym of Araneidae Clerck, 1757 new synonymy; phonognathines and nephilines are subfamilies of Araneidae (Subfamily Phonognathinae Simon, 1894 rank resurrected; and Subfamily Nephilinae Simon, 1894 rank resurrected). The results of our analyses corroborate the sister group relationship between Paraplectanoides and the araneid subfamily Nephilinae. Venomius is sister to the Nephilinae + Paraplectanoides clade. The placement of the oarcine araneids and Venomius renders the family Araneidae non-monophyletic if this were to be circumscribed as in Kuntner et al. (2023). In light of the paucity of data that the latter study presents, and in absence of a robust, stable and more densely sampled phylogenetic analysis of Araneidae, the changes and definitions introduced by that classification are premature and could lead to a large number of new families for what once were araneid species if the maximum-crown-clade family definitions were to be used. Consequently, we argue for restoring the familial and subfamilial classification of Araneidae of Dimitrov et al. (2017), Scharff et al. (2020) and Kallal et al. (2020). 

Advanced sequencing technologies have expedited resolution of higher-level arthropod relationships. Yet, dark branches persist, principally among groups occurring in cryptic habitats. Among chelicerates, Solifugae ("camel spiders") is the last order lacking a higher-level phylogeny and have thus been historically characterized as "neglected [arachnid] cousins". Though renowned for aggression, remarkable running speed, and xeric adaptation, inferring solifuge relationships has been hindered by inaccessibility of diagnostic morphological characters, whereas molecular investigations have been limited to one of 12 recognized families. Our phylogenomic dataset via capture of ultraconserved elements sampling all extant families recovered a well-resolved phylogeny, with two distinct groups of New World taxa nested within a broader Paleotropical radiation. Divergence times using fossil calibrations inferred that Solifugae radiated by the Permian, and most families diverged prior to the Paleogene-Cretaceous extinction, likely driven by continental breakup. We establish Boreosolifugae new suborder uniting five Laurasian families, and Australosolifugae new suborder uniting seven Gondwanan families using morphological and biogeographic signal. 

We address the phylogenetic relationships of pimoid spiders (Pimoidae) using a standard target-gene approach with an extensive taxonomic sample, which includes representatives of the four currently recognized pimoid genera, 26 linyphiid genera, a sample of Physoglenidae, Cyatholipidae and one Tetragnathidae species. We test the monophyly of Pimoidae and Linyphiidae and explore the biogeographic history of the group. Nanoa Hormiga, Buckle and Scharff, 2005 and Pimoa Chamberlin & Ivie, 1943 form a clade which is the sister group of a lineage that includes all Linyphiidae, Weintrauboa Hormiga, 2003 and Putaoa Hormiga and Tu, 2008. Weintrauboa, Putaoa, Pecado and Stemonyphantes form a clade (Stemonyphantinae) sister to all remaining linyphiids. We use the resulting optimal molecular phylogenetic tree to assess hypotheses on the male palp sclerite homologies of pimoids and linyphiids. Pimoidae is redelimited to only include Pimoa and Nanoa. We formalize the transfer from Pimoidae of the genera Weintrauboa and Putaoa to Linyphiidae, re-circumscribe the linyphiid subfamily Stemonyphantinae, and offer revised morphological diagnoses for Pimoidae and Linyphiidae. 

Hickmania troglodytes is an emblematic cave spider representing a monotypic cribellate spider genus. This is the only Australian lineage of Austrochilidae while the other members of the family are found in southern South America. In addition to being the largest spider in Tasmania, Hickmania is an oddity in Austrochilidae because this is the only lineage in the family bearing posterior book lungs, tarsal spines and an embolar process on male pedipalps. Six-gene Sanger sequences and genome scale data such as ultraconserved elements (UCEs) and transcriptomes have suggested that Hickmania troglodytes is not nested with the family of current classification, Austrochilidae. We studied the phylogenetic placement of Hickmania troglodytes using an increased taxon sample by combining publicly available UCE and UCEs recovered from transcriptomic data in a parsimony and maximum likelihood framework. Based on our phylogenetic results we formally transfer Hickmania troglodytes from Austrochilidae to the family Gradungulidae. The cladistic placement of Hickmania in the family Gradungulidae fits the geographic distribution of both gradungulids (restricted to Australia and New Zealand) and austrochilids (restricted to southern South America) more appropriately. 

Abstract In the last decade and a half, advances in genetic sequencing technologies have revolutionized systematics, transforming the field from studying morphological characters or a few genetic markers, to genomic datasets in the phylogenomic era. A plethora of molecular phylogenetic studies on many taxonomic groups have come about, converging on, or refuting prevailing morphology or legacy‐marker‐based hypotheses about evolutionary affinities. Spider systematics has been no exception to this transformation and the inter‐relationships of several groups have now been studied using genomic data. About 51 500 extant spider species have been described, all with a conservative body plan, but innumerable morphological and behavioural peculiarities. Inferring the spider tree of life using morphological data has been a challenging task. Molecular data have corroborated many hypotheses of higher‐level relationships, but also resulted in new groups that refute previous hypotheses. In this review, we discuss recent advances in the reconstruction of the spider tree of life and highlight areas where additional effort is needed with potential solutions. We base this review on the most comprehensive spider phylogeny to date, representing 131 of the 132 spider families. To achieve this sampling, we combined six Sanger‐based markers with newly generated and publicly available genome‐scale datasets. We find that some inferred relationships between major lineages of spiders (such as Austrochiloidea, Palpimanoidea and Synspermiata) are robust across different classes of data. However, several new hypotheses have emerged with different classes of molecular data. We identify and discuss the robust and controversial hypotheses and compile this blueprint to design future studies targeting systematic revisions of these problematic groups. We offer an evolutionary framework to explore comparative questions such as evolution of venoms, silk, webs, morphological traits and reproductive strategies.