Disconnecting trapdoors: Phylogenomic analyses reveal evolutionary contrasts in trapdoor spiders with intercontinental distribution (Idiopidae, Idiopinae).

Among Mygalomorphae spiders, the family Idiopidae is the second most diverse, consisting exclusively of trapdoor spiders and is divided into three subfamilies: Arbanitinae, Genysinae, and Idiopinae. The subfamily Idiopinae, distinguished mainly by anterior lateral eyes that project forward, includes 153 species across seven genera, distributed throughout South America, Africa, and parts of Asia. Within this subfamily, the genus Idiops includes the greatest diversity and is the only genus recorded in both the New and Old Worlds.

Phylogeographic and genetic insights into Sinonychia martensi: an endemic cave-dwelling harvestman in Beijing.

Caves are one of the most exciting environments on earth, often considered an evolutionary laboratory due to the suite of convergent adaptive traits (troglomorphisms) of organisms inhabiting them. Sinonychia martensi Zhang & Derkarabetian, 2021, is the first and only Travunioidea species recorded in China and is endemic to Beijing, being known from multiple caves. However, nothing is known regarding its phylogeographic or evolutionary history.

Systematic revision of the South American "" (Opiliones, Laniatores, Triaenonychidae).

The genus has long been the most speciose within the Opiliones family Triaenonychidae, comprising 63 species and subspecies distributed across New Zealand and South America. Recent molecular studies utilizing Sanger sequencing and ultraconserved elements (UCEs) have indicated that this genus is not monophyletic, and true are actually confined to New Zealand. Here, the morphology of all South American triaenonychids is re-examined and DNA sequence data compiled from three markers (18S rRNA, 28S rRNA and cytochrome oxidase subunit I) for a large number of triaenonychid species, including specimens from all areas with species currently and formerly classified in to reassess their phylogenetic position.

Infrequent Long-Range Dispersal and Evolution of a Top Terrestrial Arthropod Predator in the Sub-Antarctic.

AbstractThe sub-Antarctic terrestrial ecosystems survive on isolated oceanic islands in the path of circumpolar currents and winds that have raged for more than 30 million years and are shaped by climatic cycles that surpass the tolerance limits of many species. Surprisingly little is known about how these ecosystems assembled their native terrestrial fauna and how such processes have changed over time. Here, we demonstrate the patterns and timing of colonization and speciation in the largest and dominant arthropod predators in the eastern sub-Antarctic: spiders of the genus .

Reassessing the phylogeny of Cyphophthalmi with phylogenomics: A UCE-based phylogeny of mite harvesters (Opiliones).

Cyphophthalmi (the mite harvesters) are a group of Opiliones with broad interest due to their species being classic examples of short-range endemics and displaying model biogeographical patterns for poor dispersers. Cyphophthalmi phylogeny has received attention using morphology, Sanger-based sequencing data, or transcriptomics. Here we turn to a new type of data, ultraconserved elements (UCEs) and provide a first phylogeny for the entire suborder Cyphophthalmi using such data and including representatives from 36 of the 46 currently recognized genera.

An ultraconserved element probe set for velvet worms (Onychophora).

Onychophora are cryptic, soil-dwelling invertebrates known for their biogeographic affinities, diversity of reproductive modes, close phylogenetic relationship to arthropods, and peculiar prey capture mechanism. The 216 valid species of Onychophora are grouped into two families - Peripatopsidae and Peripatidae - and apart from a few relationships among major lineages within these two families, a stable phylogenetic backbone for the phylum has yet to be resolved. This has hindered our understanding of onychophoran biogeographic patterns, evolutionary history, and systematics.

Under the hood: Phylogenomics of hooded tick spiders (Arachnida, Ricinulei) uncovers discordance between morphology and molecules.

Ricinulei or hooded tick-spiders are a cryptic and ancient group of arachnids. The order consists of around 100 highly endemic extant species restricted to the Afrotropics and the Neotropics along with 22 fossil species. Their antiquity and low vagility make them an excellent group with which to interrogate biogeographic questions.

Dynamic evolution of locomotor performance independent of changes in extended phenotype use in spiders.

Many animals use self-built structures (extended phenotypes) to enhance body functions, such as thermoregulation, prey capture or defence. Yet, it is unclear whether the evolution of animal constructions supplements or substitutes body functions-with disparate feedbacks on trait evolution. Here, using brown spiders (Araneae: marronoid clade), we explored if the evolutionary loss and gain of silken webs as extended prey capture devices correlates with alterations in traits known to play an important role in predatory strikes-locomotor performance (sprint speed) and leg spination (expression of capture spines on front legs).

An Opiliones-specific ultraconserved element probe set with a near-complete family-level phylogeny.

Sequence capture of ultraconserved elements (UCEs) has transformed molecular systematics across many taxa, with arachnids being no exception. The probe set available for Arachnida has been repeatedly used across multiple arachnid lineages and taxonomic levels, however more specific probe sets for spiders have demonstrated that more UCEs can be recovered with higher probe specificity. In this study, we develop an Opiliones-specific UCE probe set targeting 1915 UCEs using a combination of probes designed from genomes and transcriptomes, as well as the most useful probes from the Arachnida probe set.

Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data.

The diversity of biological and ecological characteristics of organisms, and the underlying genetic patterns and processes of speciation, makes the development of universally applicable genetic species delimitation methods challenging. Many approaches, like those incorporating the multispecies coalescent, sometimes delimit populations and overestimate species numbers. This issue is exacerbated in taxa with inherently high population structure due to low dispersal ability, and in cryptic species resulting from nonecological speciation.

First record of Travunioidea (Arachnida: Opiliones: Laniatores) from China, with the description of a new monotypic genus from a cave.

A new genus and species of troglobitic Opiliones, Sinonychia martensi gen. n. sp.

An approach using ddRADseq and machine learning for understanding speciation in Antarctic Antarctophilinidae gastropods.

Sampling impediments and paucity of suitable material for molecular analyses have precluded the study of speciation and radiation of deep-sea species in Antarctica. We analyzed barcodes together with genome-wide single nucleotide polymorphisms obtained from double digestion restriction site-associated DNA sequencing (ddRADseq) for species in the family Antarctophilinidae. We also reevaluated the fossil record associated with this taxon to provide further insights into the origin of the group.

Pleistocene persistence and expansion in tarantulas on the Colorado Plateau and the effects of missing data on phylogeographical inferences from RADseq.

Montane species endemic to the "sky islands" of the North American southwest were significantly impacted by changing climates during the Pleistocene. We combined mitochondrial and genomic data with species distribution modelling to determine whether Aphonopelma marxi, a large tarantula from the nearby Colorado Plateau, was similarly impacted by glacial climates. Genetic analyses revealed that the species comprises three main clades that diverged in the Pleistocene.

Integrative species delimitation reveals cryptic diversity in the southern Appalachian Antrodiaetus unicolor (Araneae: Antrodiaetidae) species complex.

Although species delimitation can be highly contentious, the development of reliable methods to accurately ascertain species boundaries is an imperative step in cataloguing and describing Earth's quickly disappearing biodiversity. Spider species delimitation remains largely based on morphological characters; however, many mygalomorph spider populations are morphologically indistinguishable from each other yet have considerable molecular divergence. The focus of our study, the Antrodiaetus unicolor species complex containing two sympatric species, exhibits this pattern of relative morphological stasis with considerable genetic divergence across its distribution.

Sitticine jumping spiders: phylogeny, classification, and chromosomes (Araneae, Salticidae, Sitticini).

The systematics of sitticine jumping spiders is reviewed, with a focus on the Palearctic and Nearctic regions, in order to revise their generic classification, clarify the species of one region (Canada), and study their chromosomes. A genome-wide molecular phylogeny of 23 sitticine species, using more than 700 loci from the arachnid Ultra-Conserved Element (UCE) probeset, confirms the Neotropical origins of sitticines, whose basal divergence separates the Aillutticina (a group of five Neotropical genera) from the subtribe Sitticina (five genera of Eurasia and the Americas). The phylogeny shows that most Eurasian sitticines form a relatively recent and rapid radiation, which we unite into the genus Simon, 1868, consisting of the subgenera Simon, 1901 (seven described species), (41 described species), and Prószyński, 2017 (one species).

Sequence capture phylogenomics of historical ethanol-preserved museum specimens: Unlocking the rest of the vault.

Natural history collections play a crucial role in biodiversity research, and museum specimens are increasingly being incorporated into modern genetics-based studies. Sequence capture methods have proven incredibly useful for phylogenomics, providing the additional ability to sequence historical museum specimens with highly degraded DNA, which until recently have been deemed less valuable for genetic work. The successful sequencing of ultraconserved elements (UCEs) from historical museum specimens has been demonstrated on multiple tissue types including dried bird skins, formalin-fixed squamates and pinned insects.

A demonstration of unsupervised machine learning in species delimitation.

One major challenge to delimiting species with genetic data is successfully differentiating population structure from species-level divergence, an issue exacerbated in taxa inhabiting naturally fragmented habitats. Many fields of science are now using machine learning, and in evolutionary biology supervised machine learning has recently been used to infer species boundaries. These supervised methods require training data with associated labels.

Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci.

The atypoid mygalomorphs include spiders from three described families that build a diverse array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors, turrets and silken collars. Molecular phylogenetic analyses have generally supported the monophyly of Atypoidea, but prior studies have not sampled all relevant taxa. Here we generated a dataset of ultraconserved element loci for all described atypoid genera, including taxa ( and key to understanding familial monophyly, divergence times, and patterns of entrance web evolution.

Sequence capture phylogenomics of eyeless spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae).

Morphological, mitochondrial, and nuclear phylogenomic data were combined to address phylogenetic and species delimitation questions in cave-limited spiders from central Texas. Special effort was focused on specimens and cave locations in the San Antonio region (Bexar County), home to four eyeless species listed as US Federally Endangered. Sequence capture experiments resulted in the recovery of ~200-400 homologous ultra-conserved element (UCE) nuclear loci across taxa, and nearly complete COI mitochondrial DNA sequences from the same set of individuals.

A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements.

Molecular phylogenetics has transitioned into the phylogenomic era, with data derived from next-generation sequencing technologies allowing unprecedented phylogenetic resolution in all animal groups, including understudied invertebrate taxa. Within the most diverse harvestmen suborder, Laniatores, most relationships at all taxonomic levels have yet to be explored from a phylogenomics perspective. Travunioidea is an early-diverging lineage of laniatorean harvestmen with a Laurasian distribution, with species distributed in eastern Asia, eastern and western North America, and south-central Europe.

Phylogenomic reclassification of the world's most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution.

Here we show that the most venomous spiders in the world are phylogenetically misplaced. Australian atracine spiders (family Hexathelidae), including the notorious Sydney funnel-web spider Atrax robustus, produce venom peptides that can kill people. Intriguingly, eastern Australian mouse spiders (family Actinopodidae) are also medically dangerous, possessing venom peptides strikingly similar to Atrax hexatoxins.

Cryptic elevational zonation in trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus janus complex) from the California southern Sierra Nevada.

The relative roles of ecological niche conservatism versus niche divergence in promoting montane speciation remains an important topic in biogeography. Here, our aim was to test whether lineage diversification in a species complex of trapdoor spiders corresponds with riverine barriers or with an ecological gradient associated with elevational tiering. Aliatypus janus was sampled from throughout its range, with emphasis on populations in the southern Sierra Nevada Mountains of California.

High phylogenetic utility of an ultraconserved element probe set designed for Arachnida.

Arachnida is an ancient, diverse and ecologically important animal group that contains a number of species of interest for medical, agricultural and engineering applications. Despite their importance, many aspects of the arachnid tree of life remain unresolved, hindering comparative approaches to arachnid biology. Biologists have made considerable efforts to resolve the arachnid phylogeny; yet, limited and challenging morphological characters, as well as a dearth of genetic resources, have hindered progress.