Phylogeny of a cosmopolitan family of morphologically conserved trapdoor spiders (Mygalomorphae, Ctenizidae) using Anchored Hybrid Enrichment, with a description of the family, Halonoproctidae Pocock 1901

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. Utilizing a taxon set from the Neotropical and Afrotropical regions, with specimens collected from 1947 to 2021, our study provides the first phylogenomic analysis of the family based on Ultraconserved Elements (UCEs). To assess the monophyly of Idiopinae and Idiops, as well as the relationships among genera within the subfamily, we conducted phylogenetic analyses employing maximum likelihood, Bayesian inference, and coalescent-based methods. The phylogenetic trees reveal that Idiopinae forms a monophyletic lineage, split into two geographically distinct groups: one with African species and the other with Neotropical species. We did not recover monophyly of the genus Idiops; Neotropical Idiops form a monophyletic lineage, while African Idiops species group with Titanidiops, forming a sister lineage to the remaining African Idiopinae. The relationship between the phylogenetic results obtained and the main morphological differences observed among the genera is discussed. Finally, our study challenges the monophyly of Idiopidae by including Neocteniza, which is found to be an independent lineage sister to Ctenizidae and the rest of Idiopidae.

Description of five new species from southern China, with note on the type species of Latouchia Pocock, 1901 (Araneae, Halonoproctidae)

Background

The genus Latouchia Pocock, 1901 previously included 25 known species and one subspecies from Asia, 12 species and one subspecies were reported in China.

New information

Five new species of Latouchia Pocock, 1901 from southern China are described: L.calcicola sp. nov. (♂♀) from Hainan, L.jinyun sp. nov. (♂♀) from Chongqing, L.linmufu sp. nov. (♂♀) from Hunan, L.wenchuan sp. nov. (♂) from Sichuan and L.yaoi sp. nov. (♂♀) from south part of Shaanxi. DNA barcodes of the new species described herein are provided. The potential error in the previous illustrations of the alleged male of L.fossoria Pocock, 1901 (type species of the genus) is pointed out.

Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)

The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.

The phylogenetic structure and coalescent species delimitation of an endemic trapdoor spider genus, Stasimopus (Araneae, Mygalomorphae, Stasimopidae) in the Karoo region of South Africa

The Karoo region of South Africa is a unique and sensitive ecosystem which is facing pressure for development due to economic incentives such as mining, farming and shale gas exploration. The species diversity of many taxa in the area is largely unknown. A phylogenetic analysis of the cork-lid trapdoor spider genus, Stasimopus (Stasimopidae) was undertaken in order to gain insight into the relationships between the species that may be present in the area. The species within Stasimopus are challenging to identify and define using traditional morphological methods due to a high degree of morphological conservatism within the genus. For this reason, multiple coalescent based species delimitation methods were used to attempt to determine the species present for Stasimopus in the region which was tested against the morphological identifications and genetic clades (based on CO1, 16S and EF-1ɣ). We tested single-locus methods Automatic Barcode Gap Discovery (ABGD), Bayesian implementation of Poisson Tree Processes (bPTP) and General Mixed Yule- Coalescent (GMYC), as well as multi-locus Brownie. The phylogenetic analysis of Stasimopus in the Karoo showed that there is a high degree of genetic diversity within the genus. The species delimitation results proved unfruitful for the genus, as they appear to delimit population structure rather than species for most methods. Alternative methods should be investigated to aid in the identification of the species in order truly understand the species diversity of the genus.

Phylogenomic analysis, reclassification, and evolution of South American nemesioid burrowing mygalomorph spiders

The family Nemesiidae was once among the most species-rich of mygalomorph spider families. However, over the past few decades both morphological and molecular studies focusing on mygalomorph phylogeny have recovered the group as paraphyletic. Hence, the systematics of the family Nemesiidae has more recently been controversial, with numerous changes at the family-group level and the recognition of the supra-familial clade Nemesioidina. Indeed, in a recent study by Opatova and collaborators, six nemesiid genera were transferred to the newly re-established family Pycnothelidae. Despite these changes, 12 South American nemesiid genera remained unplaced, and classified as incertae sedis due to shortcomings in taxon sampling. Accordingly, we evaluate the phylogenetic relationships of South American nemesioid species and genera with the principle aim of resolving their family level placement. Our work represents the most exhaustive phylogenomic sampling for South American Nemesiidae by including nine of the 12 genera described for the continent. Phylogenetic relationships were reconstructed using 457 loci obtained using the spider Anchored Hybrid Enrichment probe set. Based on these results Nemesiidae, Pycnothelidae, Microstigmatidae and Cyrtaucheniidae are not considered monophyletic. Our study also indicates that the lineage including the genus Fufius requires elevation to the family level (Rhytidicolidae Simon, 1903 (NEW RANK)). In Pycnothelidae, we recognize/delimit five subfamilies (Diplothelopsinae, Pionothelinae NEW SUBFAMILY, Prorachiinae NEW SUBFAMILY, Pselligminae NEW RANK, Pycnothelinae). We also transfer all the 12 South American nemesiid genera to Pycnothelidae: Chaco, Chilelopsis, Diplothelopsis, Flamencopsis, Hermachura, Longistylus, Lycinus, Neostothis, Prorachias, Psalistopoides, Pselligmus, Rachias. Additionally, we transferred the microstigmatid genus Xenonemesia to Pycnothelidae, and we propose the following generic synonymies and species transfers: Neostothis and Bayana are junior synonyms of Pycnothele (NEW SYNONYMY), as P. gigas and P. labordai, respectively (NEW COMBINATIONS); Hermachura is a junior synonym of Stenoterommata (NEW SYNONYMY), as S. luederwaldti (NEW COMBINATION); Flamencopsis is a junior synonym of Chilelopsis (NEW SYNONYMY), as C. minima (NEW COMBINATION); and Diplothelopsis is a junior synonym of Lycinus (NEW SYNONYMY), as L. ornatus and L. bonariensis (NEW COMBINATIONS). Considering the transferred genera and synonymies, Pycnothelidae now includes 15 described genera and 137 species. Finally, these results provide a robust phylogenetic framework that includes enhanced taxonomic sampling, for further resolving the biogeography and evolutionary time scale for the family Pycnothelidae.

Two new species of the genus Latouchia Pocock, 1901 from southeast China (Araneae: Mygalomorphae: Halonoproctidae)

Background

The genus Latouchia Pocock, 1901 (Araneae: Mygalomorphae: Halonoproctidae: Ummidiinae) includes 21 species and 1 subspecies occurring in southeast Eurasia. Just like other trapdoor spiders, the specimens of Latouchia are rare in collections, unless from targeted collecting.

New information

Two new species of mygalomorph spiders, Latouchiarufa sp. n. from Guangdong, China and L.yejiei sp. n. from Hainan, China, are described and illustrated from both sexes. Diagnostic characters of the two species are provided.

Descriptions of four new trapdoor spider species in the subfamily Ummidiinae from Thailand (Araneae, Mygalomorphae, Halonoproctidae)

Males and females of four mygalomorph spider species (family Halonoproctidae, subfamily Ummidiinae) are newly described from Thailand, and the taxonomy of Ummidiinae is discussed. This is the first time that trapdoor spider species in this subfamily are described from Thailand. Two of these new species belong to the genus Conothele, the other two species are placed in the genus Latouchia. Conothele martensi spec. nov. was found in the north of the country (Chiang Mai Province), C. isan spec. nov. and Latouchia incerta spec. nov. were collected in northeastern Thailand (Buri Ram Province, Surin Province and Roi Et Province), and L. maculosa spec. nov. was found in the southern coastal province of Prachuap Khiri Khan.

Taxonomic revision of the New World members of the trapdoor spider genus Ummidia Thorell (Araneae, Mygalomorphae, Halonoproctidae)

This study documents a comprehensive taxonomic treatment of the New World Ummidia species. At the onset of this work the genus comprised 27 species and one subspecies with a cosmopolitan distribution that includes North America, South America, Asia, northern Africa, and Europe; of these species the majority of the nominal diversity can be attributed to the New World where 20 species have been previously described. Ummidiaoaxacana (Chamberlin, 1925) is considered a nomen dubium; U.tuobita (Chamberlin, 1917) and U.absoluta (Gertsch and Mulaik, 1940) are both considered junior synonyms of U.audouini (Lucas, 1835); the subspecies U.carabivoraemarginata (Atkinson, 1886) is considered a junior synonym of U.carabivora (Atkinson, 1886); U.pygmaea (Chamberlin and Ivie, 1945) is considered a junior synonym of U.beatula (Gertsch and Mulaik, 1940); U.celsa (Gertsch and Mulaik, 1940) is considered a junior synonym of U.funerea (Gertsch, 1936); Hebestatislanthanus (Valerio, 1987) is considered a junior synonym of U.rugosa (Karsch, 1880). Thirty-three new species are described: U.neilgaimani, U.gingoteague, U.rongodwini, U.okefenokee, U.richmond, U.macarthuri, U.colemanae, U.rosillos, U.mercedesburnsae, U.paulacushingae, U.waunekaae, U.gertschi, U.timcotai, U.gabrieli, U.pesiou, U.rodeo, U.huascazaloya, U.anaya, U.cuicatec, U.brandicarlileae, U.riverai, U.frankellerae, U.hondurena, U.yojoa, U.matagalpa, U.carlosviquezi, U.varablanca, U.quepoa, U.cerrohoya, U.quijichacaca, U.tibacuy, U.neblina, U.tunapuna.

Trapped indoors? Long-distance dispersal in mygalomorph spiders and its effect on species ranges

The Mygalomorphae includes tarantulas, trapdoor, funnel-web, purse-web and sheet-web spiders, species known for poor dispersal abilities. Here, we attempted to compile all the information available on their long-distance dispersal mechanisms from observations that are often spread throughout the taxonomic literature. Mygalomorphs can disperse terrestrially, and in some tarantulas, for example, spiderlings walk together in single files away from their maternal burrow, a mechanism limited in distance covered. Conversely, at least eight species disperse aerially, via dropping on drag lines from elevated positions and being passively blown off ('suspended ballooning'). The first record of this behaviour is 135 years old, but we still know very little about it. Phylogeographic studies suggest several occurrences of transcontinental dispersal in the evolutionary history of mygalomorphs, but these might result from contingent rafting events, rather than regular dispersal mechanisms. We use occurrence data to show that suspended ballooning increases the species ranges in Australian mygalomorph families where this behaviour has been recorded. We also identified Anamidae, Idiopidae, and especially Atracidae, as families that might employ suspended ballooning or another efficient but undiscovered dispersal mechanism. Finally, we suggest that molecular studies with mitochondrial genes will help disentangle behavioural limitations of dispersal from ecological or physical ones.

Phylogenetic Systematics and Evolution of the Spider Infraorder Mygalomorphae Using Genomic Scale Data

The infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3000 nominal species. This ancient group has a worldwide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel-web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae) have been identified as non-monophyletic. However, these data were unable to sufficiently resolve the higher-level (intra- and interfamilial) relationships such that the necessary changes in classification could be made with confidence. Here, we present a comprehensive phylogenomic treatment of the spider infraorder Mygalomorphae. We employ 472 loci obtained through anchored hybrid enrichment to reconstruct relationships among all the mygalomorph spider families and estimate the timeframe of their diversification. We sampled nearly all currently recognized families, which has allowed us to assess their status, and as a result, propose a new classification scheme. Our generic-level sampling has also provided an evolutionary framework for revisiting questions regarding silk use in mygalomorph spiders. The first such analysis for the group within a strict phylogenetic framework shows that a sheet web is likely the plesiomorphic condition for mygalomorphs, as well as providing insights to the ancestral foraging behavior for all spiders. Our divergence time estimates, concomitant with detailed biogeographic analysis, suggest that both ancient continental-level vicariance and more recent dispersal events have played an important role in shaping modern day distributional patterns. Based on our results, we relimit the generic composition of the Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae. We also elevate five subfamilies to family rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). Three families Entypesidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae (NEW FAMILY), and one subfamily Australothelinae (NEW SUBFAMILY) are newly proposed. Such a major rearrangement in classification, recognizing nine newly established family-level rank taxa, is the largest the group has seen in over three decades. [Biogeography; molecular clocks; phylogenomics; spider web foraging; taxonomy.].

Spider-specific probe set for ultraconserved elements offers new perspectives on the evolutionary history of spiders (Arachnida, Araneae)

Phylogenomic methods have proven useful for resolving deep nodes and recalcitrant groups in the spider tree of life. Across arachnids, transcriptomic approaches may generate thousands of loci, and target-capture methods, using the previously designed arachnid-specific probe set, can target a maximum of about 1,000 loci. Here, we develop a specialized target-capture probe set for spiders that contains over 2,000 ultraconserved elements (UCEs) and then demonstrate the utility of this probe set through sequencing and phylogenetic analysis. We designed the 'spider-specific' probe set using three spider genomes (Loxosceles, Parasteatoda and Stegodyphus) and ensured that the newly designed probe set includes UCEs from the previously designed Arachnida probe set. The new 'spider-specific' probes were used to sequence UCE loci in 51 specimens. The remaining samples included five spider genomes and taxa that were enriched using Arachnida probe set. The 'spider-specific' probes were also used to gather loci from a total of 84 representative taxa across Araneae. On mapping these 84 taxa to the Arachnida probe set, we captured at most 710 UCE loci, while the spider-specific probe set captured up to 1,547 UCE loci from the same taxon sample. Phylogenetic analyses using maximum likelihood and coalescent methods corroborate most nodes resolved by recent transcriptomic analyses, but not all (e.g. UCE data suggest monophyly of 'symphytognathoids'). Our preferred hypothesis based on topology tests, suggests monophyly of the 'symphytognathoids' (the miniature orb weavers), which in previous studies has only been supported by a combination of morphological and behavioural characters.

Phylogeny-Guided Selection of Priority Groups for Venom Bioprospecting: Harvesting Toxin Sequences in Tarantulas as a Case Study

Animal venoms are promising sources of novel drug leads, but their translational potential is hampered by the low success rate of earlier biodiscovery programs, in part reflecting the narrow selection of targets for investigation. To increase the number of lead candidates, here we discuss a phylogeny-guided approach for the rational selection of venomous taxa, using tarantulas (family Theraphosidae) as a case study. We found that previous biodiscovery programs have prioritized the three subfamilies Ornithoctoninae, Selenocosmiinae, and Theraphosinae, which provide almost all of the toxin sequences currently available in public databases. The remaining subfamilies are poorly represented, if at all. These overlooked subfamilies include several that form entire clades of the theraphosid life tree, such as the subfamilies Eumenophorinae, Harpactirinae, and Stromatopelminae, indicating that biodiversity space has not been covered effectively for venom biodiscovery in Theraphosidae. Focusing on these underrepresented taxa will increase the likelihood that promising candidates with novel structures and mechanisms of action can be identified in future bioprospecting programs.

Golden Orbweavers Ignore Biological Rules: Phylogenomic and Comparative Analyses Unravel a Complex Evolution of Sexual Size Dimorphism

Instances of sexual size dimorphism (SSD) provide the context for rigorous tests of biological rules of size evolution, such as Cope's rule (phyletic size increase), Rensch's rule (allometric patterns of male and female size), as well as male and female body size optima. In certain spider groups, such as the golden orbweavers (Nephilidae), extreme female-biased SSD (eSSD, female:male body length $\ge$2) is the norm. Nephilid genera construct webs of exaggerated proportions, which can be aerial, arboricolous, or intermediate (hybrid). First, we established the backbone phylogeny of Nephilidae using 367 anchored hybrid enrichment markers, then combined these data with classical markers for a reference species-level phylogeny. Second, we used the phylogeny to test Cope and Rensch's rules, sex specific size optima, and the coevolution of web size, type, and features with female and male body size and their ratio, SSD. Male, but not female, size increases significantly over time, and refutes Cope's rule. Allometric analyses reject the converse, Rensch's rule. Male and female body sizes are uncorrelated. Female size evolution is random, but males evolve toward an optimum size (3.2-4.9 mm). Overall, female body size correlates positively with absolute web size. However, intermediate sized females build the largest webs (of the hybrid type), giant female Nephila and Trichonephila build smaller webs (of the aerial type), and the smallest females build the smallest webs (of the arboricolous type). We propose taxonomic changes based on the criteria of clade age, monophyly and exclusivity, classification information content, and diagnosability. Spider families, as currently defined, tend to be between 37 million years old and 98 million years old, and Nephilidae is estimated at 133 Ma (97-146), thus deserving family status. We, therefore, resurrect the family Nephilidae Simon 1894 that contains Clitaetra Simon 1889, the Cretaceous GeratonephilaPoinar and Buckley (2012), Herennia Thorell 1877, IndoetraKuntner 2006, new rank, Nephila Leach 1815, Nephilengys L. Koch 1872, Nephilingis Kuntner 2013, Palaeonephila Wunderlich 2004 from Tertiary Baltic amber, and TrichonephilaDahl 1911, new rank. We propose the new clade Orbipurae to contain Araneidae Clerck 1757, Phonognathidae Simon 1894, new rank, and Nephilidae. Nephilid female gigantism is a phylogenetically ancient phenotype (over 100 Ma), as is eSSD, though their magnitudes vary by lineage.

Four new species of the trapdoor spider genus Conothele Thorell, 1878 (Araneae, Halonoproctidae) from China

Herein four species of the trapdoor spider genus Conothele Thorell, 1878 collected from China are described as new to science based on the female genital morphology: C.baisha sp. n. (Hainan Province), C.baoting sp. n. (Hainan Province), C.linzhi sp. n. (Tibet), and C.jinggangshan sp. n. (Jiangxi Province). For two Hainan species, C.baisha sp. n. and C.baoting sp. n., between which it is difficult to distinguish solely based on female genital morphology, additional diagnoses derived from species-specific nucleotide substitution information and genetic distances using the mitochondrial gene, cytochrome c oxidase subunit I are provided.

Phylogenetic relationships and biogeographic history of the Australian trapdoor spider genus Conothele (Araneae: Mygalomorphae: Halonoproctidae): diversification into arid habitats in an otherwise tropical radiation

In Australia, climate change and continental drift have given rise to a complex biota comprising mesic specialists, arid-adapted lineages, and taxa that have arrived on the continent from Asia. We explore the phylogenetic diversity and biogeographic history of the Australian trapdoor spider genus Conothele Thorell, 1878 that is widespread in Australia’s monsoonal tropics and arid zone. We sequenced three mtDNA and five nuDNA markers from 224 specimens. We reconstructed the phylogenetic relationships among specimens and estimated the number of operational taxonomic units (OTUs) using species delimitation methods. The timing of divergences was estimated and ancestral area reconstructions were conducted. We recovered 61 OTUs, grouped into four major clades; a single clade represented by an arboreal ecomorph, and three fossorial clades. The Australian Conothele had a crown age of ~19 million years, and ancestral area reconstructions showed a complex history with multiple transitions among the monsoonal tropics, central arid zone, south-west and Pilbara bioregion. Conothele arrived on the continent during periods of biotic exchange with Asia. Since then, Conothele has colonised much of the Australian arid and monsoonal zones, during a period of climatic instability. The Pilbara bioregion harbours high lineage diversity, emphasising the role of climate refugia.