Tarantula phylogenomics: A robust phylogeny of deep theraphosid clades inferred from transcriptome data sheds light on the prickly issue of urticating setae evolution

A Case Report of Venezuelan Suntiger Tarantula (Psalmopoeus Irminia) Envenomation and Review of Tarantula Exposures

BACKGROUND

Tarantula envenomations are encountered infrequently but may increase with increased exotic animal ownership. This case report presents the first documented toxicity from a Venezuelan suntiger tarantula (VST), Psalmopoeus irminia, and provides a general framework for approaching patients with tarantula exposures.

CASE REPORT

A 35-year-old man presented to an emergency department 4 h after experiencing a bite from his pet VST. He developed erythema, pain, and edema to the bite site on the left thenar eminence that extended proximally. Within 4 h, he developed abdominal pain, nausea, vomiting, throat itching, and tightness. The patient had a blood pressure of 131/105 mm Hg, heart rate of 102 beats/min, 36.6°C, respiratory rate of 20 breaths/min, and SpO2 of 94%. Laboratory evaluations were within normal limits (other than chronically elevated but improved transaminases). The patient received 0.5 mg epinephrine intramuscularly, 50 mg diphenhydramine IV, 20 mg famotidine IV, 0.4 mg ondansetron IV, and 1 L of normal saline for a suspected anaphylactic reaction. Shortly after epinephrine administration, his gastrointestinal and upper airway symptoms resolved. All symptoms resolved within 1 week. WHY SHOULD AN EMERGENCY PHYSICIAN BE AWARE OF THIS?: Little is known about VST toxicity. Therefore, providers should rely on a general framework for approaching patients with tarantula exposures. Morbidity from tarantula exposures is mediated by mechanical injury, venom effects, and hypersensitivity reactions. Typical clinical findings include local pain, pruritis, edema, erythema, and burning. Muscle cramping, ophthalmia nodosa, and hypersensitivity reactions may occur. Treatment is primarily supportive and includes decontamination, cool compresses, analgesia, treatment of anaphylaxis, and ophthalmology evaluation if ocular exposure.

Sexual selection and predation drive the repeated evolution of stridulation in Heteroptera and other arthropods

Acoustic and substrate-borne vibrations are among the most widely used signalling modalities in animals. Arthropods display a staggering diversity of vibroacoustic organs generating acoustic sound and/or substrate-borne vibrations, and are fundamental to our broader understanding of the evolution of animal signalling. The primary mechanism that arthropods use to generate vibroacoustic signals is stridulation, which involves the rubbing together of opposing body parts. Although stridulation is common, its behavioural context and evolutionary drivers are often hard to pinpoint, owing to limited synthesis of empirical observations on stridulatory species. This is exacerbated by the diversity of mechanisms involved and the sparsity of their description in the literature, which renders their documentation a challenging task. Here, we present the most comprehensive review to date on the systematic distribution and behavioural context of stridulation. We use the megadiverse heteropteran insects as a model, together with multiple arthropod outgroups (arachnids, myriapods, and selected pancrustaceans). We find that stridulatory vibroacoustic signalling has evolved independently at least 84 times and is present in roughly 20% of Heteroptera, representing a remarkable case of convergent evolution. By studying the behavioural context of stridulation across Heteroptera and 189 outgroup lineages, we find that predation pressure and sexual selection are the main behaviours associated with stridulation across arthropods, adding further evidence for their role as drivers of large-scale signalling and morphological innovation in animals. Remarkably, the absence of tympanal ears in most Heteroptera suggests that they typically cannot detect the acoustic component of their stridulatory signals. This demonstrates that the adoption of new signalling modalities is not always correlated with the ability to perceive those signals, especially when these signals are directed towards interspecific receivers in defensive contexts. Furthermore, by mapping their morphology and systematic distribution, we show that stridulatory organs tend to evolve in specific body parts, likely originating from cleaning motions and pre-copulatory displays that are common to most arthropods. By synthesising our understanding of stridulation and stridulatory organs across major arthropod groups, we create the necessary framework for future studies to explore their systematic and behavioural significance, their potential role in sensory evolution and innovation, and the biomechanics of this mode of signalling.

Phylotranscriptomics interrogation uncovers a complex evolutionary history for the planarian genus Dugesia (Platyhelminthes, Tricladida) in the Western Mediterranean

The Mediterranean is one of the most biodiverse areas of the Paleartic region. Here, basing on large data sets of single copy orthologs obtained from transcriptomic data, we investigated the evolutionary history of the genus Dugesia in the Western Mediterranean area. The results corroborated that the complex paleogeological history of the region was an important driver of diversification for the genus, speciating as microplates and islands were forming. These processes led to the differentiation of three main biogeographic clades: Iberia-Apennines-Alps, Corsica-Sardinia, and Iberia-Africa. The internal relationships of these major clades were analysed with several representative samples per species. The use of large data sets regarding the number of loci and samples, as well as state-of-the-art phylogenomic inference methods allowed us to answer different unresolved questions about the evolution of particular groups, such as the diversification path of D. subtentaculata in the Iberian Peninsula and its colonization of Africa. Additionally, our results support the differentiation of D. benazzii in two lineages which could represent two species. Finally, we analysed here for the first time a comprehensive number of samples from several asexual Iberian populations whose assignment at the species level has been an enigma through the years. The phylogenies obtained with different inference methods showed a branching topology of asexual individuals at the base of sexual clades. We hypothesize that this unexpected topology is related to long-term asexuality. This work represents the first phylotranscriptomic analysis of Tricladida, laying the first stone of the genomic era in phylogenetic studies on this taxonomic group.

Improving the Annotation of the Venom Gland Transcriptome of Pamphobeteus verdolaga, Prospecting Novel Bioactive Peptides

Spider venoms constitute a trove of novel peptides with biotechnological interest. Paucity of next-generation-sequencing (NGS) data generation has led to a description of less than 1% of these peptides. Increasing evidence supports the underestimation of the assembled genes a single transcriptome assembler can predict. Here, the transcriptome of the venom gland of the spider Pamphobeteus verdolaga was re-assembled, using three free access algorithms, Trinity, SOAPdenovo-Trans, and SPAdes, to obtain a more complete annotation. Assembler's performance was evaluated by contig number, N50, read representation on the assembly, and BUSCO's terms retrieval against the arthropod dataset. Out of all the assembled sequences with all software, 39.26% were common between the three assemblers, and 27.88% were uniquely assembled by Trinity, while 27.65% were uniquely assembled by SPAdes. The non-redundant merging of all three assemblies' output permitted the annotation of 9232 sequences, which was 23% more when compared to each software and 28% more when compared to the previous P. verdolaga annotation; moreover, the description of 65 novel theraphotoxins was possible. In the generation of data for non-model organisms, as well as in the search for novel peptides with biotechnological interest, it is highly recommended to employ at least two different transcriptome assemblers.

Two new species of the genus Chilobrachys (Araneae, Theraphosidae) from China

Two new species of the genus Chilobrachys Karsh, 1892 are described from China: Chilobrachysdominus Lin & Li, sp. nov. from Yunnan and C.jinchengi Lin & Li, sp. nov. from Tibet. Photos and a morphological description of the new species are given. The type specimens of the new species are deposited in the Institute of Zoology, Chinese Academy (IZCAS) in Beijing.

The biology and evolution of spider venoms

Spiders are diverse, predatory arthropods that have inhabited Earth for around 400 million years. They are well known for their complex venom systems that are used to overpower their prey. Spider venoms contain many proteins and peptides with highly specific and potent activities suitable for biomedical or agrochemical applications, but the key role of venoms as an evolutionary innovation is often overlooked, even though this has enabled spiders to emerge as one of the most successful animal lineages. In this review, we discuss these neglected biological aspects of spider venoms. We focus on the morphology of spider venom systems, their major components, biochemical and chemical plasticity, as well as ecological and evolutionary trends. We argue that the effectiveness of spider venoms is due to their unprecedented complexity, with diverse components working synergistically to increase the overall potency. The analysis of spider venoms is difficult to standardize because they are dynamic systems, fine-tuned and modified by factors such as sex, life-history stage and biological role. Finally, we summarize the mechanisms that drive spider venom evolution and highlight the need for genome-based studies to reconstruct the evolutionary history and physiological networks of spider venom compounds with more certainty.

Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci

Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.

Phylogenomic Subsampling and the Search for Phylogenetically Reliable Loci

Phylogenomic subsampling is a procedure by which small sets of loci are selected from large genome-scale data sets and used for phylogenetic inference. This step is often motivated by either computational limitations associated with the use of complex inference methods or as a means of testing the robustness of phylogenetic results by discarding loci that are deemed potentially misleading. Although many alternative methods of phylogenomic subsampling have been proposed, little effort has gone into comparing their behavior across different data sets. Here, I calculate multiple gene properties for a range of phylogenomic data sets spanning animal, fungal, and plant clades, uncovering a remarkable predictability in their patterns of covariance. I also show how these patterns provide a means for ordering loci by both their rate of evolution and their relative phylogenetic usefulness. This method of retrieving phylogenetically useful loci is found to be among the top performing when compared with alternative subsampling protocols. Relatively common approaches such as minimizing potential sources of systematic bias or increasing the clock-likeness of the data are found to fare worse than selecting loci at random. Likewise, the general utility of rate-based subsampling is found to be limited: loci evolving at both low and high rates are among the least effective, and even those evolving at optimal rates can still widely differ in usefulness. This study shows that many common subsampling approaches introduce unintended effects in off-target gene properties and proposes an alternative multivariate method that simultaneously optimizes phylogenetic signal while controlling for known sources of bias.

Phylogenomic analyses reveal a Gondwanan origin and repeated out of India colonizations into Asia by tarantulas (Araneae: Theraphosidae)

The study of biogeography seeks taxa that share a key set of characteristics, such as timescale of diversification, dispersal ability, and ecological lability. Tarantulas are ideal organisms for studying evolution over continental-scale biogeography given their time period of diversification, their mostly long-lived sedentary lives, low dispersal rate, and their nevertheless wide circumtropical distribution. In tandem with a time-calibrated transcriptome-based phylogeny generated by PhyloBayes, we estimate the ancestral ranges of ancient tarantulas using two methods, DEC+j and BBM, in the context of their evolution. We recover two ecologically distinct tarantula lineages that evolved on the Indian Plate before it collided with Asia, emphasizing the evolutionary significance of the region, and show that both lineages diversified across Asia at different times. The most ancestral tarantulas emerge on the Americas and Africa 120 Ma-105.5 Ma. We provide support for a dual colonization of Asia by two different tarantula lineages that occur at least 20 million years apart, as well as a Gondwanan origin for the group. We determine that their current distributions are attributable to a combination of Gondwanan vicariance, continental rafting, and geographic radiation. We also discuss emergent patterns in tarantula habitat preferences through time.

Muscle spasms - A common symptom following theraphosid spider bites?

Despite the popularity of theraphosids, detailed reports on bite symptoms are still limited to few geographic regions and subfamilies. We therefore examined 363 published bite reports and noticed muscles cramps caused by theraphosids from nearly all continents and subfamilies. Symptoms are mostly locally restricted and mild, but 12.7% of victims experience pronounced cramps with highest incidence rates by Poecilotheriinae, Harpactirinae and Stromatopelminae subfamilies. We discuss how variations in venom quantity correlate with muscle cramp prevalence.

Love bites - Do venomous arachnids make safe pets?

With a global estimate of tens of thousands of arachnid enthusiasts, spiders and scorpions are gaining increasing popularity as pets in industrialised countries in Europe, Northern America and Asia. As most spiders and all scorpions are venomous and due to their mostly negative image in the public media, several governments are already considering introducing legislation to regulate the domestic care of potentially dangerous captive animals. We aimed to investigate the circumstances and effects of exposure to arachnids kept in captivity. Thus, we collected and analysed data from 354 self-reported bites and stings attributed to pet arachnids. Our data revealed that on average there were less than 20 recorded envenomations per year with ~90% preventable by due care. We also categorized the severity of the resulting symptoms and found that the vast majority of symptoms were either local (60.7%) or minor (32.8%), 5.4% were asymptomatic, only 1.1% were severe and no fatalities were recorded. Based on our database of bite and sting reports, we performed a risk assessment for arachnid pet ownership and concluded that, with the proper care, arachnids can be safely kept as pets and pose a lower risk than many other recreational activities.

Another stripe on the tiger makes no difference? Unexpected diversity in the widespread tiger tarantula Davus pentaloris (Araneae: Theraphosidae: Theraphosinae)

Integrative taxonomy is relevant for the discovery and delimitation of cryptic species by incorporating different sources of evidence to construct rigorous species hypotheses. The genus Davus was recently revised and it was found that Davus pentaloris presents high morphological variation across its widespread distribution. However, tarantulas usually present low dispersal capabilities that occasionally result in local endemism. In order to evaluate species boundaries within this taxon, we examine the morphological variation and, additionally, employ four strategies based on mtDNA data (COI): two distance-based [automatic barcode gap discovery (ABGD) and Neighbor-Joining (NJ)] and two tree-based methods [general mixed Yule coalescent (GMYC) and Bayesian Poisson tree process (bPTP)]. Available morphological evidence recovers 13 putative morphospecies, but the different methods based on molecular data recover a variable number of candidate species (16–18). Based on the congruence across all analyses and the available morphological data, we recognize 13 clearly diagnosable species, 12 of them new to science. We conclude that the underestimation of the diversity in D. pentaloris was mainly caused by deficient practices in taxonomy, rather than by the presence of cryptic diversity. Although COI is a functional barcoding marker and it gives reliable results in our study, we recommend combining multiple sources of evidence and strategies to construct better species delimitation hypotheses.

The evolution of coloration and opsins in tarantulas

Tarantulas paradoxically exhibit a diverse palette of vivid coloration despite their crepuscular to nocturnal habits. The evolutionary origin and maintenance of these colours remains mysterious. In this study, we reconstructed the ancestral states of both blue and green coloration in tarantula setae, and tested how these colours correlate with presence of stridulation, urtication and arboreality. Green coloration has probably evolved at least eight times, and blue coloration is probably an ancestral condition that appears to be lost more frequently than gained. While our results indicate that neither colour correlates with the presence of stridulation or urtication, the evolution of green coloration appears to depend upon the presence of arboreality, suggesting that it ptobably originated for and functions in crypsis through substrate matching among leaves. We also constructed a network of opsin homologues across tarantula transcriptomes. Despite their crepuscular tendencies, tarantulas express a considerable diversity of opsin genes-a finding that contradicts current consensus that tarantulas have poor colour vision on the basis of low opsin diversity. Overall, our findings raise the possibility that blue coloration could have ultimately evolved via sexual selection and perhaps proximately be used in mate choice or predation avoidance due to possible sex differences in mate-searching.

High-throughput sequencing for community analysis: the promise of DNA barcoding to uncover diversity, relatedness, abundances and interactions in spider communities

Large-scale studies on community ecology are highly desirable but often difficult to accomplish due to the considerable investment of time, labor and, money required to characterize richness, abundance, relatedness, and interactions. Nonetheless, such large-scale perspectives are necessary for understanding the composition, dynamics, and resilience of biological communities. Small invertebrates play a central role in ecosystems, occupying critical positions in the food web and performing a broad variety of ecological functions. However, it has been particularly difficult to adequately characterize communities of these animals because of their exceptionally high diversity and abundance. Spiders in particular fulfill key roles as both predator and prey in terrestrial food webs and are hence an important focus of ecological studies. In recent years, large-scale community analyses have benefitted tremendously from advances in DNA barcoding technology. High-throughput sequencing (HTS), particularly DNA metabarcoding, enables community-wide analyses of diversity and interactions at unprecedented scales and at a fraction of the cost that was previously possible. Here, we review the current state of the application of these technologies to the analysis of spider communities. We discuss amplicon-based DNA barcoding and metabarcoding for the analysis of community diversity and molecular gut content analysis for assessing predator-prey relationships. We also highlight applications of the third generation sequencing technology for long read and portable DNA barcoding. We then address the development of theoretical frameworks for community-level studies, and finally highlight critical gaps and future directions for DNA analysis of spider communities.

First phylogenetic assessment and taxonomic synopsis of the open-holed trapdoor spider genus Namea (Mygalomorphae: Anamidae): a highly diverse mygalomorph lineage from Australia’s tropical eastern rainforests

The tropical and subtropical rainforests of Australia’s eastern mesic zone have given rise to a complex and highly diverse biota. Numerous old endemic, niche-conserved groups persist in the montane rainforests south of Cooktown, where concepts of serial allopatric speciation resulting from the formation of xeric interzones have largely driven our biogeographic understanding of the region. Among invertebrate taxa, studies on less vagile arachnid lineages now complement extensive research on vertebrate taxa, and phylogenetic studies on mygalomorph spiders in particular are revealing significant insights about the biogeographic history of the Australian continent since the Eocene. One mygalomorph lineage entirely endemic to Australia’s tropical and subtropical eastern rainforests is the open-holed trapdoor spider genus Namea Raven, 1984 (family Anamidae). We explore, for the first time, the phylogenetic diversity and systematics of this group of spiders, with the aims of understanding patterns of rainforest diversity in Namea, of exploring the relative roles of lineage overlap versus in situ speciation in driving predicted high levels of congeneric sympatry, and of broadly reconciling morphology with evolutionary history. Original and legacy sequences were obtained for three mtDNA and four nuDNA markers from 151 specimens, including 82 specimens of Namea. We recovered a monophyletic genus Namea sister to the genus Teyl Main, 1975, and monophyletic species clades corresponding to 30 morphospecies OTUs, including 22 OTUs nested within three main species-complex lineages. Remarkable levels of sympatry for a single genus of mygalomorph spiders were revealed in rainforest habitats, with upland subtropical rainforests in south-eastern Queensland often home to multiple (up to six) congeners of usually disparate phylogenetic affinity living in direct sympatry or close parapatry, likely the result of simultaneous allopatric speciation in already co-occurring lineages, and more recent dispersal in a minority of taxa. In situ speciation, in contrast, appears to have played a relatively minor role in generating sympatric diversity within rainforest ‘islands’. At the population level, changes in the shape and spination of the male first leg relative to evolutionary history reveal subtle but consistent interspecific morphological shifts in the context of otherwise intraspecific variation, and understanding this morphological variance provides a useful framework for future taxonomic monography. Based on the phylogenetic results, we further provide a detailed taxonomic synopsis of the genus Namea, formally diagnosing three main species-complexes (the brisbanensis-complex, the dahmsi-complex and the jimna-complex), re-illustrating males of all 15 described species, and providing images of live spiders and burrows where available. In doing so, we reveal a huge undescribed diversity of Namea species from tropical and subtropical rainforest habitats, and an old endemic fauna that is beginning to shed light on more complex patterns of rainforest biogeography.

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.