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

Spider's Silk as a Potential Source of Antibiotics: An Integrative Review

Spiders produce webs, which are still a largely unexplored source of antibacterial compounds, although the reports of its application in the medical field. Therefore, this study aims to present an integrative review of the antibacterial activity of spider webs. The research was conducted using Google Scholar, Scielo, Web of Science, PubMed, ScienceDirect, Medline EBSCO, LILACS, and Embase. The inclusion criteria were original articles written in English that studied the antibiotic properties of the web or isolated compounds tested. The studies were compared according to the spider species studied, the type of web, treatment of the sample, type of antimicrobial test, and the results obtained. Nine hundred and seventy-three publications were found, and after applying the inclusion and exclusion criteria, sixteen articles were selected. Bacterial inhibition was found in seven studies against various species of bacteria such as Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Salmonella Typhi, Bacillus megaterium, Listeria monocytogenes, Acinetobacter baumannii, Streptococcus pneumoniae, Pasteurella multocida, and Bacillus subtilis. Additionally, there was no apparent relationship between the proximity of the spider species evaluated in the studies and the presence or absence of activity. Methodological problems detected may affected the reproducibility and reliability of the results in some studies, such as the lack of description of the web or microorganism strain, as well as the absence of adequate controls and treatments to sterilize the sample. Spider webs can be a valuable source of antibiotics; however, more studies are needed to confirm the real activity of the web or components involved.

Nephila spider male aggregation: preference for optimal female size and web clustering

Sexual size dimorphism theory predicts biased operational sex ratios (OSRs) and an uneven distribution of males among certain females. We studied this phenomenon through a field census of the giant wood spider Nephila pilipes (family Nephilidae) in Singapore, a species where females are, on average, 6.9 times larger than males. Specifically, we tested two hypotheses concerning male distribution, given their tendency to aggregate in certain female webs. The optimal female size hypothesis predicts that males would predominantly occupy webs of intermediate-sized females. The web clustering hypothesis posits that more males would be found in webs closer together compared to those farther apart. Our snapshot census revealed a female-biased OSR (females: males = 1.85) with an uneven distribution of males in female webs. Most males were found in webs of intermediate-sized females aligning with the optimal female size hypothesis. Proximity among female webs was indicative of male presence, lending support to the web clustering hypothesis. While our study's limited sample size warrants caution, we conclude that in N. pilipes, male occupation of female webs is facilitated by the clustering of webs, and males prefer to cohabit with optimally sized, receptive females.

Microstructure of the silk fibroin-based hydrogel scaffolds derived from the orb-web spider Trichonephila clavata

Due to the unique properties of the silk fibroin (SF) made from silkworm, SF-based hydrogels have recently received significant attention for various biomedical applications. However, research on the SF-based hydrogels isolated from spider silks has been rtricted due to the limited collection and preparation of naïve silk materials. Therefore, this study focused on the microstructural characteristics of hydrogel scaffolds derived from two types of woven silk glands: the major ampullate gland (MAG) and the tubuliform gland (TG), in the orb-web spider Trichonephila clavate. We compared these spider glands with those of the silk fibroin (SF) hydrogel scaffold extracted from the cocoon of the insect silkworm Bombyx mori. Our FESEM analysis revealed that the SF hydrogel has high porosity, translucency, and a loose upper structure, with attached SF fibers providing stability. The MAG hydrogel displayed even higher porosity, as well as elongated fibrous structures, and improved mechanical properties: while the TG hydrogel showed increased porosity, ridge-like or wall-like structures, and stable biocapacity formed by physical crosslinking. Due to their powerful and versatile microstructural characteristics, the MAG and TG hydrogels can become tailored substrates, very effective for tissue engineering and regenerative medicine applications.

Physiochemical and biological characteristics of fouling on landfill leachate treatment systems surface

Fouling of landfill leachate, a biofilm formation process on the surface of the collection system, migration pipeline and treatment system causes low efficiency of leachate transportation and treatment and increases cost for maintenance of those facilities. In addition, landfill leachate fouling might accumulate pathogens and antibiotic resistance genes (ARGs), posing threats to the environment. Characterization of the landfill leachate fouling and its associated environmental behavior is essential for the management of fouling. In this study, physicochemical and biological properties of landfill leachate fouling and the possible accumulation capacity of pathogens and ARGs were investigated in nitrification (aerobic condition) and denitrification (anaerobic condition) process during landfill leachate biological treatment, respectively. Results show that microbial (bacterial, archaeal, eukaryotic, and viral) community structure and function (carbon fixation, methanogenesis, nitrification and denitrification) differed in fouling under aerobic and anaerobic conditions, driven by the supplemental leachate water quality. Aerobic fouling had a higher abundance of nitrification and denitrification functional genes, while anaerobic fouling harbored a higher abundance of carbon fixation and methanogenesis genes. Both forms of leachate fouling had a higher abundance of pathogens and ARGs than the associated leachate, suggesting the accumulation capacity of fouling on biotic pollutants. Specifically, aerobic fouling harbored three orders of magnitude higher multidrug resistance genes mexD than its associated leachate. This finding provides fundamental knowledge on the biological properties of leachate fouling and suggests that leachate fouling might harbor significant pathogens and ARGs.

Physical Properties of the Second Type of Aciniform Spidroin (AcSp2) from Neoscona theisi Reveal a pH-Dependent Self-Assembly Repetitive Domain

Orb-weaving spiders can use an array of specialized silks with diverse mechanical properties and functions for daily survival. Of all spider silk types, aciniform silk is the toughest silk fiber that combines high strength and elasticity. Although aciniform spidroins (AcSp) are the main protein in aciniform silks, their complete genes have rarely been characterized until now. Moreover, the structural and physical properties of AcSp variant proteins within the species are also unclear. Here, we present three full-length AcSp genes (named AcSp1A, AcSp1B, and AcSp2) from the orb-weaving spider Neoscona theisi and investigate the structural and mechanical features of these three AcSp repetitive domains. We demonstrate that all three AcSp proteins have mainly α-helical structural features in neutral solution and high thermal stability. Significantly, the AcSp2 repetitive domain shows a pH-dependent structural transition from α to β conformations and can self-assemble into amyloid fibrils under acidic conditions, which is the first reported AcSp repetitive domain with pH-dependent self-assembly capacity. Compared with the other two AcSp spidroins, AcSp2 demonstrated the lowest expression level in the aciniform gland but had the highest strength for its silk fiber. Collectively, our findings provide new insight into the physical properties of each component of aciniform silk and expand the repertoire of known spidroin sequences for the synthesis of artificial silk materials.

Attachment discs of the diving bell spider Argyroneta aquatica

To adhere their silk threads for the construction of webs and to fix the dragline, spiders produce attachment discs of piriform silk. Uniquely, the aquatic spider Argyroneta aquatica spends its entire life cycle underwater. Therefore, it has to glue its attachment discs to substrates underwater. Here we show that Argyroneta aquatica applies its thread anchors within an air layer around the spinnerets maintained by superhydrophobic setae. During spinning, symmetric movements of the spinnerets ensure retaining air in the contact area. The flat structure of the attachment discs is thought to facilitate fast curing of the piriform adhesive cement and improves the resistance against drag forces. Pull-off tests on draglines connected with attachment discs on different hydrophilic substrates point to dragline rupture as the failure mode. The Young´s modulus of the dragline (8.3 GPa) is within the range as in terrestrial spiders. The shown structural and behavioral adaptations can be the model for new artificial underwater gluing devices.

Dynamic evolution of size and colour in the highly specialized Zodarion ant-eating spiders

Ecological specialists constitute relevant case studies for understanding the mechanisms, potential and limitations of evolution. The species-rich and strictly myrmecophagous spiders of the genus Zodarion show diversified defence mechanisms, including myrmecomorphy of different ant species and nocturnality. Through Hybridization Capture Using RAD Probes (hyRAD), a phylogenomic technique designed for sequencing poorly preserved specimens, we reconstructed a phylogeny of Zodarion using 52 (approx. a third of the nominal) species that cover its phylogenetic and distributional diversity. We then estimated the evolution of body size and colour, traits that have diversified noticeably and are linked to defence mechanisms, across the group. Our genomic matrix of 300 loci led to a well-supported phylogenetic hypothesis that uncovered two main clades inside Zodarion. Ancestral state estimation revealed the highly dynamic evolution of body size and colour across the group, with multiple transitions and convergences in both traits, which we propose is likely indicative of multiple transitions in ant specialization across the genus. Our study will allow the informed targeted selection of Zodarion taxa of special interest for research into the group's remarkable adaptations to ant specialization. It also exemplifies the utility of hyRAD for phylogenetic studies using museum material.

Increasing Information Content and Diagnosability in Family-Level Classifications

Higher-level classifications often must account for monotypic taxa representing depauperate evolutionary lineages and lacking synapomorphies of their better-known, well-defined sister clades. In a ranked (Linnean) or unranked (phylogenetic) classification system, discovering such a depauperate taxon does not necessarily invalidate the rank classification of sister clades. Named higher taxa must be monophyletic to be phylogenetically valid. Ranked taxa above the species level should also maximize information content, diagnosability, and utility (e.g., in biodiversity conservation). In spider classification, families are the highest rank that is systematically catalogued, and incertae sedis is not allowed. Consequently, it is important that family-level taxa be well defined and informative. We revisit the classification problem of Orbipurae, an unranked suprafamilial clade containing the spider families Nephilidae, Phonognathidae, and Araneidae sensu stricto. We argue that, to maximize diagnosability, information content, conservation utility, and practical taxonomic considerations, this "splitting" scheme is superior to its recently proposed alternative, which lumps these families together as Araneidae sensu lato. We propose to redefine Araneidae and recognize a monogeneric spider family, Paraplectanoididae fam. nov. to accommodate the depauperate lineage Paraplectanoides. We present new subgenomic data to stabilize Orbipurae topology which also supports our proposed family-level classification. Our example from spiders demonstrates why classifications must be able to accommodate depauperate evolutionary lineages, for example, Paraplectanoides. Finally, although clade age should not be a criterion to determine rank, other things being equal, comparable ages of similarly ranked taxa do benefit comparative biology. [Classification, family rank, phylogenomics, systematics, monophyly, spider phylogeny.].

Molecular timetrees using relaxed clocks and uncertain phylogenies

A common practice in molecular systematics is to infer phylogeny and then scale it to time by using a relaxed clock method and calibrations. This sequential analysis practice ignores the effect of phylogenetic uncertainty on divergence time estimates and their confidence/credibility intervals. An alternative is to infer phylogeny and times jointly to incorporate phylogenetic errors into molecular dating. We compared the performance of these two alternatives in reconstructing evolutionary timetrees using computer-simulated and empirical datasets. We found sequential and joint analyses to produce similar divergence times and phylogenetic relationships, except for some nodes in particular cases. The joint inference performed better when the phylogeny was not well resolved, situations in which the joint inference should be preferred. However, joint inference can be infeasible for large datasets because available Bayesian methods are computationally burdensome. We present an alternative approach for joint inference that combines the bag of little bootstraps, maximum likelihood, and RelTime approaches for simultaneously inferring evolutionary relationships, divergence times, and confidence intervals, incorporating phylogeny uncertainty. The new method alleviates the high computational burden imposed by Bayesian methods while achieving a similar result.

Fine structural characteristics of the chorionic microspheres on the egg surface of the orb web spider Trichonephila clavata

The eggs laid by the orb web spider Trichonephila clavata must overwinter in bitterly freezing and dry conditions before hatching, but there does not seem to be any protection like a compact silk case covering the entire eggmass. Instead, the surface of the eggmass is completely coated with a milky coating called chorionic microspheres (CM). Therefore, we investigated the fine structural characteristics of CM to demonstrate their ecological importance. Although the diameter of CM in outer eggmass exhibits a significant variation, the chorionic surface is coated with a single layer of CM, characterized by a consistent diameter of approximately 2.3 µm. The surface structure of aggregated CM shows short papillary projections demonstrating segmental adhesion of mucous components. CM is insoluble in water but partially soluble in anhydrous ethanol, and its spherical structure is completely decomposed by hexafluoroisopropanol (HFIP), a strong organic solvent. Since our fine structural observations clearly show that CM is not derived from vitellogenic or choriogenetic processes, the CM adhesive coatings during ovipositional process appears to be equivalent to cocoon silk for various protective functions in silken eggcase.

Complete mitochondrial genome of a golden orb-web spider Trichonephila clavata (Chelicerata, Arachnida) from South Korea

The mitochondrial genome of a golden orb-web spider Trichonephila clavata (L. Koch, 1878) from South Korea is determined and characterized in detail, which is the second mitochondrial genome reported from this species: the first was published from the Chinese sample by Pan et al. (2016). It was 14,436 bp in length being composed of 13 protein-coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and one control region (CR). It has a base composition of 35.99% for 'A,' 14.88% for 'G,' 9.09% for 'C,' and 40.04% for 'T.' Comparing the South Korean and Chinese mitochondrial genomes, we observed 8% nucleotide sequence differences between their CRs, caused by the different numbers and sorts of possessed tandem repeats, suggesting a promising molecular marker to distinguish South Korean individuals from Chinese ones. The phylogenetic trees using the maximum likelihood (ML) method were reconstructed with nucleotides (without 3rd codon position) and amino acids from 13 PCGs, respectively, which consistently confirmed that T. clavata (Subfamily Nephilinae) from South Korea and China are clustered together, distinctly separated from the other subfamily Araneinae in the monophyletic family Araneidae.

A molecular phylogeny of the European nesticid spiders (Nesticidae, Araneae): Implications for their systematics and biogeography

Nesticidae is a small family of spiders with a worldwide distribution that includes 15 genera and 272 described species. Seven genera and 56 species are known from Europe, distributed from the Iberian Peninsula to the Caucasus and the Ural Mountains. Most of these European species are cave dwellers and many of them are troglobites. In this study we present the first molecular phylogeny of the family Nesticidae in Europe with a wide geographical sampling across the continent. In our analysis the European nesticid fauna is well represented, including six genera and 40 of the 56 currently accepted species including the type species of all sampled genera. We have included in the analysis representatives of the North American and Asian fauna to test the monophyly of the European species and the phylogenetic relationships of European lineages. Phylogenetic relationships were reconstructed using maximum likelihood and Bayesian inference. As part of our Bayesian analyses, we also dated the phylogeny using two approaches, one based only on fossil calibrations and one that included an additional biogeographical constraint. Our results show paraphyly of the European nesticids with respect to the Asian and North American taxa. We recover four main lineages within Europe. These four European lineages and all European genera have 100% bootstrap support and high posterior probability support in the BEAST2 analysis. The Typhlonesticus lineage is the earliest branching clade present in Europe and includes seven species, the five currently accepted species plus T. parvus from Bosnia and Herzegovina and T. silvestrii from western North America. The Eastern lineage includes the genus Aituaria and is the sister group of the Asian genera Nesticella and Wraios. The Domitius lineage is likely the sister group of the Central European lineage and spreads over the Iberian and Italian peninsulas. Finally, the Central European lineage includes three genera: Kryptonesticus, distributed from the karstic massifs of the Balkan Peninsula to Turkey, Nesticus with a single synanthropic species N. cellulanus and Carpathonesticus, exclusive to the Carpathian Mountains. With the exception of the genus Typhlonesticus, all European genera show an allopatric distribution (except for the two European synanthropic species). The results obtained in this study together with the revision of the original descriptions, redescriptions, and illustrations, lead us to propose 11 nomenclatural changes (new combinations) concerning the genera Typhlonesticus, Nesticus and Carpathonesticus.

Fine structural aspects on the web glue production in the golden orb-web spider Trichonephila clavata

The water-soluble glue substance of the capture threads in Trichonephila clavata is solely produced from two pairs of aggregate silk glands. During the web glue production, secretory vesicles were synthesized via the extensive rough endoplasmic reticulum of epithelial cells. Unlike the clearly described fibrous web production in spiders, the process of aqueous web glue production appears to involve either a condensing or a packaging step by the Golgi complex. In particular, the fine structure of secretory vesicles varies from cell to cell and may represent the secretory cycle. The electron-dense multivesicular bodies were clearly visible as discrete droplets, and the mature secretory product in the glandular epithelium appeared as a spherical vacuole grown by fusion with surrounding small vesicles. Our fine structural observation reveals that the secretion occurs when the release of secreted material involves the loss of part of the cytoplasm. The bleb along the luminal surface of the secretory cells and membrane-bound extracellular vesicles which pinched off from the cell suggests that the secretory product is released by the mechanism of apocrine secretion.

Assessing the relative performance of fast molecular dating methods for phylogenomic data

Advances in genome sequencing techniques produced a significant growth of phylogenomic datasets. This massive amount of data represents a computational challenge for molecular dating with Bayesian approaches. Rapid molecular dating methods have been proposed over the last few decades to overcome these issues. However, a comparative evaluation of their relative performance on empirical data sets is lacking. We analyzed 23 empirical phylogenomic datasets to investigate the performance of two commonly employed fast dating methodologies: penalized likelihood (PL), implemented in treePL, and the relative rate framework (RRF), implemented in RelTime. They were compared to Bayesian analyses using the closest possible substitution models and calibration settings. We found that RRF was computationally faster and generally provided node age estimates statistically equivalent to Bayesian divergence times. PL time estimates consistently exhibited low levels of uncertainty. Overall, to approximate Bayesian approaches, RelTime is an efficient method with significantly lower computational demand, being more than 100 times faster than treePL. Thus, to alleviate the computational burden of Bayesian divergence time inference in the era of massive genomic data, molecular dating can be facilitated using the RRF, allowing evolutionary hypotheses to be tested more quickly and efficiently.

The Jorō spider (Trichonephila clavata) in the southeastern U.S.: an opportunity for research and a call for reasonable journalism

Trichonephila clavata, also known as the Jorō spider, was first discovered in Georgia, USA in 2014. Its arrival from Asia and subsequent range expansion across the southeastern U.S. has received much media coverage, spanning from factual to sensational. Here, we describe T. clavata's invasion potential and known invasive range, and review its biology, dispersal abilities, potential impacts, and management strategies. As of October 2022, T. clavata's range spans at least 120,000 km2, occurring across Georgia, South Carolina, North Carolina, and Tennessee, with additional reports in Alabama, Maryland, Oklahoma, and West Virginia. Its pattern of spread suggests it is primarily driven by natural dispersal mechanisms, such as ballooning, though human-mediated transport cannot be discounted. Like other large-bodied orb-weavers, T. clavata captures and feeds on flying insects and potentially other small animals, and we suggest thirteen co-occurring spider species that should be monitored for competition with T. clavata for resources and web-building sites. Since T. clavata is spreading across both natural and urban habitats, management options are limited. Overall, very little is known about this species in its new North American range, especially its impacts within this novel ecosystem. Thus, we advise journalists and experts alike against exaggerating its potential environmental impact or uncritical acceptance of the spider as ecologically harmless. Instead, T. clavata's rapid spread should be carefully monitored, and we should take a cautious, evidence-based approach when determining next steps.

The new Australian leaf-curling orb-weaving spider genus Leviana (Araneae, Araneidae)

The new Australian orb-weaving spider genus Levianagen. nov. is described to include five species, all known from both sexes: Leviana dimidiata (L. Koch, 1871) comb. nov. (type species) (= Epeira sylvicola Rainbow, 1897 syn. nov.), L. cincinnatasp. nov., L. foliumsp. nov., L. minimasp. nov. and L. mulieraria (Keyserling, 1887) comb. nov. Male pedipalp morphology, specifically the presence of a single patella spine and the median apophysis forming an arch over the radix, place Levianagen. nov. in the informal Australian ‘backobourkiine’ clade; however, the genus differs from all other genera of this group by the presence of a spine inside the basal median apophysis arch of the male pedipalp, an epigyne that is wider than long with a scape that is approximately as long as the epigyne (but often broken off) and a lack of humeral humps on the elongate ovoid abdomen. In addition, unlike any other backobourkiine, Levianagen. nov. incorporate a rolled leaf as retreat into the periphery of their web. Levianagen. nov. species exhibit only a moderate sexual size dimorphism with female to male ratios between 1.3 and 1.7. Levianagen. nov. occurs in eastern Australia from northern Queensland in the north to Victoria in the south, with a single tropical species, L. mulierariacomb. nov., spreading into northern Western Australia.

Characterization of the genome and silk-gland transcriptomes of Darwin's bark spider (Caerostris darwini)

Natural silks crafted by spiders comprise some of the most versatile materials known. Artificial silks-based on the sequences of their natural brethren-replicate some desirable biophysical properties and are increasingly utilized in commercial and medical applications today. To characterize the repertoire of protein sequences giving silks their biophysical properties and to determine the set of expressed genes across each unique silk gland contributing to the formation of natural silks, we report here draft genomic and transcriptomic assemblies of Darwin's bark spider, Caerostris darwini, an orb-weaving spider whose dragline is one of the toughest known biomaterials on Earth. We identify at least 31 putative spidroin genes, with expansion of multiple spidroin gene classes relative to the golden orb-weaver, Trichonephila clavipes. We observed substantial sharing of spidroin repetitive sequence motifs between species as well as new motifs unique to C. darwini. Comparative gene expression analyses across six silk gland isolates in females plus a composite isolate of all silk glands in males demonstrated gland and sex-specific expression of spidroins, facilitating putative assignment of novel spidroin genes to classes. Broad expression of spidroins across silk gland types suggests that silks emanating from a given gland represent composite materials to a greater extent than previously appreciated. We hypothesize that the extraordinary toughness of C. darwini major ampullate dragline silk may relate to the unique protein composition of major ampullate spidroins, combined with the relatively high expression of stretchy flagelliform spidroins whose union into a single fiber may be aided by novel motifs and cassettes that act as molecule-binding helices. Our assemblies extend the catalog of sequences and sets of expressed genes that confer the unique biophysical properties observed in natural silks.

Male mating strategies to counter sexual conflict in spiders

When sexual conflict selects for reproductive strategies that only benefit one of the sexes, evolutionary arms races may ensue. Female sexual cannibalism is an extreme manifestation of sexual conflict. Here we test two male mating strategies aiming at countering sexual cannibalism in spiders. The "better charged palp" hypothesis predicts male selected use of the paired sexual organ (palp) containing more sperm for their first copulation. The "fast sperm transfer" hypothesis predicts accelerated insemination when cannibalism is high. Our comparative tests on five orbweb spider species with varying levels of female sexual cannibalism and sexual size dimorphism (SSD) reveal that males choose the palp with more sperm for the first copulation with cannibalistic females and that males transfer significantly more sperm if females are cannibalistic or when SSD is biased. By supporting the two hypotheses, these results provide credibility for male mating syndrome. They, however, open new questions, namely, how does a male differentiate sperm quantities between his palps? How does he perform palp choice after assessing his cannibalistic partner? By conducting follow-up experiments on Nephilengys malabarensis, we reveal that it is sperm volume detection, rather than left-right palp dominance, that plays prominently in male palp choice.

Hybrid sequencing reveals the full-length Nephila pilipes pyriform spidroin 1 (PySp1)

Araneid spider silk glands can spin seven silk types that have task-specific properties owing to the higher order structure of spider silk proteins. This gives silks superior potential as novel biomaterials. Nephila pilipes, the giant golden orb-weaver, is one of the largest spiders and spins silk with exceptional torsional deformation, toughness, and other properties to support its mass; further investigation relies on a complete amino acid sequence. However, there are no full-length N. pilipes spidroin sequences; in fact, across species, most sequences remain fragmentary because of repetitive region assembly difficulties in short-read sequencing. Here, we develop a hybrid sequencing method that utilizes short-read sequencing to identify seven spidroin terminals in N. pilipes, and long-read sequencing to confirm the full-length pyriform spidroin 1 (PySp1) gene. PySp1 is 11,181 base pairs, with a single exon encoding a 3,726 amino acid protein, the QQ(x)4Qx motif, and lower repeat homogenization, distinct characteristics of genera Nephilinae PySp1. The full-length N. pilipes PySp1 sequences sheds light on spidroin evolution and demonstrates a helpful strategy to find full-length spidroins.

Limitations of phylogenomic data can drive inferred speciation rate shifts

Biodiversity analyses of phylogenomic timetrees have produced many high-profile examples of shifts in the rate of speciation across the tree of life. Temporally correlated events in ecology, climate, and biogeography are frequently invoked to explain these rate shifts. In a re-examination of 15 genomic timetrees and 25 major published studies of the pattern of speciation through time, we observed an unexpected correlation between the timing of reported rate shifts and the information content of sequence alignments. Here, we show that the paucity of sequence variation and insufficient species sampling in phylogenomic datasets are the likely drivers of many inferred speciation rate shifts, rather than the proposed biological explanations. Therefore, data limitations can produce predictable but spurious signals of rate shifts even when speciation rates may be similar across taxa and time. Our results suggest that the reliable detection of speciation rate shifts requires the acquisition and assembly of long phylogenomic alignments with near-complete species sampling and accurate estimates of species richness for the clades of study.

Phylogenetic evidence for an independent origin of extreme sexual size dimorphism in a genus of araneid spiders (Araneae: Araneidae)

Cyphalonotus is a poorly studied Old World araneid spider genus of which the phylogenetic proximity remains unknown due to the paucity of morphological and molecular data. We test the phylogenetic placement and the taxonomic composition of Cyphalonotus and place the male and female size variation of Cyphalonotus and related genera in an evolutionary context. Our collection and field observations from Taiwan and China facilitate description of a new and a known species, and original sequence data enable species delimitation and phylogenetic analyses. The phylogenetic results reject all four classification hypotheses from the literature and instead recover a well-supported clade comprising Cyphalonotus + Poltys. We review the male and female size variation in Cyphalonotus, Poltys and related genera. These data reveal that all known species of Poltys are extremely sexually size dimorphic (eSSD = females over twice the size of males) reaching values exceeding 10-fold differences, whereas Cyphalonotus and other genera in phylogenetic proximity are relatively sexually monomorphic (SSD < 2.0). This confirms an independent origin of eSSD in Poltys, one of multiple convergent evolutionary outcomes in orbweb spiders.

Phylogeny and secondary sexual trait evolution in Schizocosa wolf spiders (Araneae, Lycosidae) shows evidence for multiple gains and losses of ornamentation and species delimitation uncertainty

Members of the Nearctic spider genus Schizocosa Chamberlin, 1904 have garnered much attention in behavioral studies and over many decades, a number of species have developed as model systems for investigating patterns of sexual selection and multimodal communication. Many of these studies have employed a comparative approach using putative, but not rigorously tested, sister species pairs that have distinctive morphological traits and attendant behaviors. Despite past emphasis on the efficacy of these presumably comparative-based studies of closely related species, generating a robust phylogenetic hypothesis for Schizocosa has been an ongoing challenge. Here, we apply a phylogenomic approach using anchored hybrid enrichment to generate a data set comprising over 400 loci representing a comprehensive taxonomic sample of 23 Nearctic Schizocosa. Our sampling also includes numerous outgroup lycosid genera that allow for a robust evaluation of genus monophyly. Based on analyses using concatenation and coalescent-based methods, we recover a well-supported phylogeny that infers the following: 1) The New World Schizocosa do not form a monophyletic group; 2) Previous hypotheses of North American species require reconsideration along with the composition of species groups; 3) Multiple longstanding model species are not genealogically exclusive and thus are not "good" species; 4) This updated phylogenetic framework establishes a new working paradigm for studying the evolution of characters associated with reproductive communication and mating. Ancestral character state reconstructions show a complex pattern of homoplasy that has likely obfuscated previous attempts to reconstruct relationships and delimit species. Important characters presumably related to sexual selection, such as foreleg pigmentation and dense bristle formation, have undergone repeated gain and loss events, many of which have led to increased morphological divergence between sister-species. Evaluation of these traits in a comparative framework illuminates how sexual selection and natural selection influence character evolution and provides a model for future studies of multimodal communication evolution and function.

Phylogenomics and loci dropout patterns of deeply diverged Zodarion ant-eating spiders suggest a high potential of RAD-seq for genus-level spider phylogenetics

RAD sequencing yields large amounts of genome-wide data at a relatively low cost and without requiring previous taxon-specific information, making it ideal for evolutionary studies of highly diversified and neglected organisms. However, concerns about information decay with phylogenetic distance have discouraged its use for assessing supraspecific relationships. Here, using Double Digest Restriction Associated DNA (ddRAD) data, we perform the first deep-level approach to the phylogeny of Zodarion, a highly diversified spider genus. We explore the impact of loci and taxon filtering across concatenated and multispecies coalescent reconstruction methods and investigate the patterns of information dropout in reference to both the time of divergence and the mitochondrial divergence between taxa. We found that relaxed loci-filtering and nested taxon-filtering strategies maximized the amount of molecular information and improved phylogenetic inference. As expected, there was a clear pattern of allele dropout towards deeper time and mitochondrial divergences, but the phylogenetic signal remained strong throughout the phylogeny. Therefore, we inferred topologies that were almost fully resolved, highly supported, and noticeably congruent between setups and inference methods, which highlights overall inconsistency in the taxonomy of Zodarion. Because Zodarion appears to be among the oldest and most mitochondrially diversified spider genera, our results suggest that ddRAD data show high potential for inferring intra-generic relationships across spiders and probably also in other taxonomic groups.

The complete mitochondrial genome of Trichonephila clavipes (Araneae: Araneidae)

Trichonephila clavipes (Linnaeus, 1767) is known as a golden silk orb-weaver and belongs to the family Araneidae. T. clavipes is one of the few spider species whose genome has been reported and model organism for a molecular biology. Here, we present the complete mitochondrial genome sequence (mtDNA) of T. clavipes. The sequence was obtained using a long-read Nanopore technology and corrected with an Illumina technology. The circular genome is 14,902 bp in length, and the AT content was 77.21%. The T. clavipes mitochondrial genome contains 13 protein-coding genes (PCGs), 22 tRNA genes, and 2 rRNA genes. The majority of PCGs were found on the heavy strain.

Converging on the orb: denser taxon sampling elucidates spider phylogeny and new analytical methods support repeated evolution of the orb web

High throughput sequencing and phylogenomic analyses focusing on relationships among spiders have both reinforced and upturned long-standing hypotheses. Likewise, the evolution of spider webs-perhaps their most emblematic attribute-is being understood in new ways. With a matrix including 272 spider species and close arachnid relatives, we analyze and evaluate the relationships among these lineages using a variety of orthology assessment methods, occupancy thresholds, tree inference methods and support metrics. Our analyses include families not previously sampled in transcriptomic analyses, such as Symphytognathidae, the only araneoid family absent in such prior works. We find support for the major established spider lineages, including Mygalomorphae, Araneomorphae, Synspermiata, Palpimanoidea, Araneoidea and the Retrolateral Tibial Apophysis Clade, as well as the uloborids, deinopids, oecobiids and hersiliids Grade. Resulting trees are evaluated using bootstrapping, Shimodaira-Hasegawa approximate likelihood ratio test, local posterior probabilities and concordance factors. Using structured Markov models to assess the evolution of spider webs while accounting for hierarchically nested traits, we find multiple convergent occurrences of the orb web across the spider tree-of-life. Overall, we provide the most comprehensive spider tree-of-life to date using transcriptomic data and use new methods to explore controversial issues of web evolution, including the origins and multiple losses of the orb web.

Fast and accurate bootstrap confidence limits on genome-scale phylogenies using little bootstraps

Felsenstein's bootstrap approach is widely used to assess confidence in species relationships inferred from multiple sequence alignments. It resamples sites randomly with replacement to build alignment replicates of the same size as the original alignment and infers a phylogeny from each replicate dataset. The proportion of phylogenies recovering the same grouping of species is its bootstrap confidence limit. But, standard bootstrap imposes a high computational burden in applications involving long sequence alignments. Here, we introduce the bag of little bootstraps approach to phylogenetics, bootstrapping only a few little samples, each containing a small subset of sites. We report that the median bagging of bootstrap confidence limits from little samples produces confidence in inferred species relationships similar to standard bootstrap but in a fraction of computational time and memory. Therefore, the little bootstraps approach can potentially enhance the rigor, efficiency, and parallelization of big data phylogenomic analyses.

Gene expression profiling reveals candidate genes for defining spider silk gland types

Molecular studies of the secretory glands involved in spider silk production have revealed candidate genes for silk synthesis and a complicated history of spider silk gene evolution. However, differential gene expression profiles of the multiple silk gland types within an individual orb-web weaving spider are lacking. Each of these gland types produces a functionally distinct silk type. Comparison of gene expression among spider silk gland types would provide insight into the genes that define silk glands generally from non-silk gland tissues, and the genes that define silk glands from each other. Here, we perform 3' tag digital gene expression profiling of the seven silk gland types of the silver garden orb weaver Argiope argentata. Five of these gland types produce silks that are non-adhesive fibers, one silk includes both fibers and glue-like adhesives, and one silk is exclusively glue-like. We identify 1275 highly expressed, significantly upregulated, and tissue specific silk gland specific transcripts (SSTs). These SSTs include seven types of spider silk protein encoding genes known as spidroin genes. We find that the fiber-producing major ampullate and minor ampullate silk glands have more similar expression profiles than any other pair of glands. We also find that a subset of the SSTs is enriched for transmembrane transport and oxidoreductases, and that these transcripts highlight differences and similarities among the major ampullate, minor ampullate, and aggregate silk glands. Furthermore, we show that the wet glue-producing aggregate glands have the most unique SSTs, but still share some SSTs with fiber producing glands. Aciniform glands were the only gland type to share a majority of SSTs with other silk gland types, supporting previous hypotheses that duplication of aciniform glands and subsequent divergence of the duplicates gave rise to the multiple silk gland types within an individual spider.

Giant and dwarf females: how to explain the fourfold variation in body size and fecundity in Trichonephila senegalensis (Aranea: Nephilidae)

Variation in life-history traits within a population is caused by genetic, maternal and environmental factors. We explored the high variability in development time, adult body weight and fecundity in females of the sexually size dimorphic spider Trichonephila senegalensis. Their mothers originated from two habitats—strongly seasonal Namibia and mildly seasonal South Africa—and we reared F1 females under standardized laboratory conditions. We found that a considerable part of the variability in recorded life-history traits is caused by family-specific effects, comprising genetic, maternal and early environmental influences. Furthermore, we show population differences in development time, where females originating from Namibia matured within shorter periods than females from South Africa. Also, the relationship between development time and adult weight differs between the two populations, as a significant correlation is only found in females with Namibian origin. Against common wisdom, there was a weak overall correlation between adult weight and clutch mass. We also found that females make different life-history decisions under increasing rather than under decreasing daylength. Although a considerable part of variability in life-history traits is family-specific, we discuss how the between-population differences in life histories and their trade-offs reflect adaptation to diverse habitats.

Golden orb-weaving spider (Trichonephila clavipes) silk genes with sex-biased expression and atypical architectures

Spider silks are renowned for their high-performance mechanical properties. Contributing to these properties are proteins encoded by the spidroin (spider fibroin) gene family. Spidroins have been discovered mostly through cDNA studies of females based on the presence of conserved terminal regions and a repetitive central region. Recently, genome sequencing of the golden orb-web weaver, Trichonephila clavipes, provided a complete picture of spidroin diversity. Here, we refine the annotation of T. clavipes spidroin genes including the reclassification of some as non-spidroins. We rename these non-spidroins as spidroin-like (SpL) genes because they have repetitive sequences and amino acid compositions like spidroins, but entirely lack the archetypal terminal domains of spidroins. Insight into the function of these spidroin and SpL genes was then examined through tissue- and sex-specific gene expression studies. Using qPCR, we show that some silk genes are upregulated in male silk glands compared to females, despite males producing less silk in general. We also find that an enigmatic spidroin that lacks a spidroin C-terminal domain is highly expressed in silk glands, suggesting that spidroins could assemble into fibers without a canonical terminal region. Further, we show that two SpL genes are expressed in silk glands, with one gene highly evolutionarily conserved across species, providing evidence that particular SpL genes are important to silk production. Together, these findings challenge long-standing paradigms regarding the evolutionary and functional significance of the proteins and conserved motifs essential for producing spider silks.

Correlation between protein secondary structure and mechanical performance for the ultra-tough dragline silk of Darwin's bark spider

The spider major ampullate (MA) silk exhibits high tensile strength and extensibility and is typically a blend of MaSp1 and MaSp2 proteins with the latter comprising glycine-proline-glycine-glycine-X repeating motifs that promote extensibility and supercontraction. The MA silk from Darwin's bark spider (Caerostris darwini) is estimated to be two to three times tougher than the MA silk from other spider species. Previous research suggests that a unique MaSp4 protein incorporates proline into a novel glycine-proline-glycine-proline motif and may explain C. darwini MA silk's extraordinary toughness. However, no direct correlation has been made between the silk's molecular structure and its mechanical properties for C. darwini. Here, we correlate the relative protein secondary structure composition of MA silk from C. darwini and four other spider species with mechanical properties before and after supercontraction to understand the effect of the additional MaSp4 protein. Our results demonstrate that C. darwini MA silk possesses a unique protein composition with a lower ratio of helices (31%) and β-sheets (20%) than other species. Before supercontraction, toughness, modulus and tensile strength correlate with percentages of β-sheets, unordered or random coiled regions and β-turns. However, after supercontraction, only modulus and strain at break correlate with percentages of β-sheets and β-turns. Our study highlights that additional information including crystal size and crystal and chain orientation is necessary to build a complete structure-property correlation model.

DNA barcodes combined with multi-locus data of representative taxa can generate reliable higher-level phylogenies

Taxa are frequently labeled incertae sedis when their placement is debated at ranks above the species level, such as their subgeneric, generic, or subtribal placement. This is a pervasive problem in groups with complex systematics due to difficulties in identifying suitable synapomorphies. In this study, we propose combining DNA barcodes with a multilocus backbone phylogeny in order to assign taxa to genus or other higher-level categories. This sampling strategy generates molecular matrices containing large amounts of missing data that are not distributed randomly: barcodes are sampled for all representatives, and additional markers are sampled only for a small percentage. We investigate the effects of the degree and randomness of missing data on phylogenetic accuracy using simulations for up to 100 markers in 1000-tips trees, as well as a real case: the subtribe Polyommatina (Lepidoptera: Lycaenidae), a large group including numerous species with unresolved taxonomy. Our simulation tests show that when a strategic and representative selection of species for higher-level categories has been made for multigene sequencing (approximately one per simulated genus), the addition of this multigene backbone DNA data for as few as 5–10% of the specimens in the total data set can produce high-quality phylogenies, comparable to those resulting from 100% multigene sampling. In contrast, trees based exclusively on barcodes performed poorly. This approach was applied to a 1365-specimen data set of Polyommatina (including ca. 80% of described species), with nearly 8% of representative species included in the multigene backbone and the remaining 92% included only by mitochondrial COI barcodes, a phylogeny was generated that highlighted potential misplacements, unrecognized major clades, and placement for incertae sedis taxa. We use this information to make systematic rearrangements within Polyommatina, and to describe two new genera. Finally, we propose a systematic workflow to assess higher-level taxonomy in hyperdiverse groups. This research identifies an additional, enhanced value of DNA barcodes for improvements in higher-level systematics using large data sets. [Birabiro; DNA barcoding; incertae sedis; Kipepeo; Lycaenidae; missing data; phylogenomic; phylogeny; Polyommatina; supermatrix; systematics; taxonomy]

Complete mitochondrial genomes and phylogenetic relationships of the genera Nephila and Trichonephila (Araneae, Araneoidea)

Spiders of the genera Nephila and Trichonephila are large orb-weaving spiders. In view of the lack of study on the mitogenome of these genera, and the conflicting systematic status, we sequenced (by next generation sequencing) and annotated the complete mitogenomes of N. pilipes, T. antipodiana and T. vitiana (previously N. vitiana) to determine their features and phylogenetic relationship. Most of the tRNAs have aberrant clover-leaf secondary structure. Based on 13 protein-coding genes (PCGs) and 15 mitochondrial genes (13 PCGs and two rRNA genes), Nephila and Trichonephila form a clade distinctly separated from the other araneid subfamilies/genera. T. antipodiana forms a lineage with T. vitiana in the subclade containing also T. clavata, while N. pilipes forms a sister clade to Trichonephila. The taxon vitiana is therefore a member of the genus Trichonephila and not Nephila as currently recognized. Studies on the mitogenomes of other Nephila and Trichonephila species and related taxa are needed to provide a potentially more robust phylogeny and systematics.

Phylogeny of Micronesian emperor fishes and evolution of trophic types

Island communities that rely on reef fish are currently faced with declining marine resources due to unsustainable fishing and climate change. Identification of genetic stocks through phylogenetic analyses has become a growing field of study with conservation implications, but genetic information on reef fish in Micronesia is limited. In this study we focus on Lethrinidae, one of the most commonly fished reef fish families in Micronesia. Our main goal was to establish a phylogeny for Lethrinidae based on Micronesian data with the intent to help future conservation efforts and clarify the evolutionary history of trophic types in this family. Thirty-eight Lethrinidae specimens collected across five Micronesian islands were used to build a phylogeny with three mitochondrial and one nuclear gene. The phylogenetic analyses allowed us to clarify the identity and position of 11 commonly harvested species and provided a novel genetic identification for Monotaxis heterodon in Micronesia. Our improved and dated phylogeny supports a new hypothesis for the ancestral trophic type of emperor fishes: "stalkers" with low-bodies and conical teeth. We correlated the radiation of most Lethrinidae species with the radiation of major scleractinian coral lineages in the middle Miocene, highlighting the tight relationships between declining reefs and the survival of emperor fishes.

Exploring diversification drivers in golden orbweavers

Heterogeneity in species diversity is driven by the dynamics of speciation and extinction, potentially influenced by organismal and environmental factors. Here, we explore macroevolutionary trends on a phylogeny of golden orbweavers (spider family Nephilidae). Our initial inference detects heterogeneity in speciation and extinction, with accelerated extinction rates in the extremely sexually size dimorphic Nephila and accelerated speciation in Herennia, a lineage defined by highly derived, arboricolous webs, and pronounced island endemism. We evaluate potential drivers of this heterogeneity that relate to organisms and their environment. Primarily, we test two continuous organismal factors for correlation with diversification in nephilids: phenotypic extremeness (female and male body length, and sexual size dimorphism as their ratio) and dispersal propensity (through range sizes as a proxy). We predict a bell-shaped relationship between factor values and speciation, with intermediate phenotypes exhibiting highest diversification rates. Analyses using SSE-class models fail to support our two predictions, suggesting that phenotypic extremeness and dispersal propensity cannot explain patterns of nephilid diversification. Furthermore, two environmental factors (tropical versus subtropical and island versus continental species distribution) indicate only marginal support for higher speciation in the tropics. Although our results may be affected by methodological limitations imposed by a relatively small phylogeny, it seems that the tested organismal and environmental factors play little to no role in nephilid diversification. In the phylogeny of golden orbweavers, the recent hypothesis of universal diversification dynamics may be the simplest explanation of macroevolutionary patterns.

A chromosome-level genome of the spider Trichonephila antipodiana reveals the genetic basis of its polyphagy and evidence of an ancient whole-genome duplication event

Background

The spider Trichonephila antipodiana (Araneidae), commonly known as the batik golden web spider, preys on arthropods with body sizes ranging from ∼2 mm in length to insects larger than itself (>20‒50 mm), indicating its polyphagy and strong dietary detoxification abilities. Although it has been reported that an ancient whole-genome duplication event occurred in spiders, lack of a high-quality genome has limited characterization of this event.

Results

We present a chromosome‐level T. antipodiana genome constructed on the basis of PacBio and Hi-C sequencing. The assembled genome is 2.29 Gb in size with a scaffold N50 of 172.89 Mb. Hi‐C scaffolding assigned 98.5% of the bases to 13 pseudo-chromosomes, and BUSCO completeness analysis revealed that the assembly included 94.8% of the complete arthropod universal single-copy orthologs (n = 1,066). Repetitive elements account for 59.21% of the genome. We predicted 19,001 protein-coding genes, of which 96.78% were supported by transcriptome-based evidence and 96.32% matched protein records in the UniProt database. The genome also shows substantial expansions in several detoxification-associated gene families, including cytochrome P450 mono-oxygenases, carboxyl/cholinesterases, glutathione-S-transferases, and ATP-binding cassette transporters, reflecting the possible genomic basis of polyphagy. Further analysis of the T. antipodiana genome architecture reveals an ancient whole-genome duplication event, based on 2 lines of evidence: (i) large-scale duplications from inter-chromosome synteny analysis and (ii) duplicated clusters of Hox genes.

Conclusions

The high-quality T. antipodiana genome represents a valuable resource for spider research and provides insights into this species’ adaptation to the environment.

Many paths, one destination: mapping the movements of a kleptoparasitic spider on the host's web

Kleptoparasitic spiders live and forage in the webs of other spiders. Using vibratory cues generated by the host spider during prey capture, they leave their resting positions in the upper peripheries of the host web and move towards the centre of the web where they feed along with the host spider or steal small pieces of prey. While the triggers for initiating the foraging raids are known, there is little information about the fine-scale trajectory dynamics in this model system. We mapped the movement of the kleptoparasite Argyrodes elevatus in the web of the host Trichonephila clavipes. We filmed the movement of the kleptoparasite spiders and quantified the trajectory shape, speed, heading directions and path revisitation. Our results show that kleptoparasitic spider movement is spatially structured, with higher levels of speed at the peripheries and slower in the centre of the web. We found a high level of variation in trajectory shapes between individuals. We found that the majority of heading orientations were away from the hub suggesting that detouring or repeated approaches are an essential component of kleptoparasite movement strategies. Our results of the revisitation rate also confirm this pattern, where locations close to the hub were revisited more often than in the periphery. The kleptoparasite-host spider system is a promising model to study fine-scale movement patterns in small bounded spaces.

Spider Diversification Through Space and Time

Spiders (Araneae) make up a remarkably diverse lineage of predators that have successfully colonized most terrestrial ecosystems. All spiders produce silk, and many species use it to build capture webs with an extraordinary diversity of forms. Spider diversity is distributed in a highly uneven fashion across lineages. This strong imbalance in species richness has led to several causal hypotheses, such as codiversification with insects, key innovations in silk structure and web architecture, and loss of foraging webs. Recent advances in spider phylogenetics have allowed testing of some of these hypotheses, but results are often contradictory, highlighting the need to consider additional drivers of spider diversification. The spatial and historical patterns of diversity and diversification remain contentious. Comparative analyses of spider diversification will advance only if we continue to make progress with studies of species diversity, distribution, and phenotypic traits, together with finer-scale phylogenies and genomic data.

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.].

Spiders in space-orb-web-related behaviour in zero gravity

Gravity is very important for many organisms, including web-building spiders. Probably the best approach to study the relevance of gravity on organisms is to bring them to the International Space Station. Here, we describe the results of such an experiment where two juvenile Trichonephila clavipes (L.) (Araneae, Nephilidae) spiders were observed over a 2-month period in zero gravity and two control spiders under otherwise identical conditions on Earth. During that time, the spiders and their webs were photographed every 5 min. Under natural conditions, Trichonephila spiders build asymmetric webs with the hub near the upper edge of the web, and they always orient themselves downwards when sitting on the hub whilst waiting for prey. As these asymmetries are considered to be linked to gravity, we expected the spiders experiencing no gravity to build symmetric webs and to show a random orientation when sitting on the hub. We found that most, but not all, webs built in zero gravity were indeed quite symmetric. Closer analysis revealed that webs built when the lights were on were more asymmetric (with the hub near the lights) than webs built when the lights were off. In addition, spiders showed a random orientation when the lights were off but faced away from the lights when they were on. We conclude that in the absence of gravity, the direction of light can serve as an orientation guide for spiders during web building and when waiting for prey on the hub.

Molecular dating for phylogenies containing a mix of populations and species by using Bayesian and RelTime approaches

Simultaneous molecular dating of population and species divergences is essential in many biological investigations, including phylogeography, phylodynamics and species delimitation studies. In these investigations, multiple sequence alignments consist of both intra- and interspecies samples (mixed samples). As a result, the phylogenetic trees contain interspecies, interpopulation and within-population divergences. Bayesian relaxed clock methods are often employed in these analyses, but they assume the same tree prior for both inter- and intraspecies branching processes and require specification of a clock model for branch rates (independent vs. autocorrelated rates models). We evaluated the impact of a single tree prior on Bayesian divergence time estimates by analysing computer-simulated data sets. We also examined the effect of the assumption of independence of evolutionary rate variation among branches when the branch rates are autocorrelated. Bayesian approach with coalescent tree priors generally produced excellent molecular dates and highest posterior densities with high coverage probabilities. We also evaluated the performance of a non-Bayesian method, RelTime, which does not require the specification of a tree prior or a clock model. RelTime's performance was similar to that of the Bayesian approach, suggesting that it is also suitable to analyse data sets containing both populations and species variation when its computational efficiency is needed.

Machine learning approaches identify male body size as the most accurate predictor of species richness

BACKGROUND

A major challenge in biodiversity science is to understand the factors contributing to the variability of species richness -the number of different species in a community or region - among comparable taxonomic lineages. Multiple biotic and abiotic factors have been hypothesized to have an effect on species richness and have been used as its predictors, but identifying accurate predictors is not straightforward. Spiders are a highly diverse group, with some 48,000 species in 120 families; yet nearly 75% of all species are found within just the ten most speciose families. Here we use a Random Forest machine learning algorithm to test the predictive power of different variables hypothesized to affect species richness of spider genera.

RESULTS

We test the predictive power of 22 variables from spiders' morphological, genetic, geographic, ecological and behavioral landscapes on species richness of 45 genera selected to represent the phylogenetic and biological breath of Araneae. Among the variables, Random Forest analyses find body size (specifically, minimum male body size) to best predict species richness. Multiple Correspondence analysis confirms this outcome through a negative relationship between male body size and species richness. Multiple Correspondence analyses furthermore establish that geographic distribution of congeneric species is positively associated with genus diversity, and that genera from phylogenetically older lineages are species poorer. Of the spider-specific traits, neither the presence of ballooning behavior, nor sexual size dimorphism, can predict species richness.

CONCLUSIONS

We show that machine learning analyses can be used in deciphering the factors associated with diversity patterns. Since no spider-specific biology could predict species richness, but the biologically universal body size did, we believe these conclusions are worthy of broader biological testing. Future work on other groups of organisms will establish whether the detected associations of species richness with small body size and wide geographic ranges hold more broadly.

Ocrepeira klamt sp. n. (Araneae: Araneidae), a novel spider species from an Andean páramo in Colombia

Herein we describe Ocrepeira klamt sp. n. (Araneae: Araneidae), a new orb-weaving spider species from a Colombian páramo, which was formerly inaccessible for scientific studies due to decades long armed conflicts. Both, phenotypic and molecular data are used to confirm genus affiliation, and the new species is placed into phylogenetic context with other araneid spiders. Morphological characteristics and ecological notes of Ocrepeira klamt sp. n. are reported together with the sequence of the barcoding region of cytochrome c oxidase subunit I (COI) to provide a comprehensive description of the spider, facilitating future identification beyond taxonomic experts. With this study we contribute to the taxonomic knowledge that is required to inventory the hyper diverse yet threatened ecosystem of the Colombian páramos.

Revealing the Venomous Secrets of the Spider's Web

Orb-weaving spiders use a highly strong, sticky and elastic web to catch their prey. These web properties alone would be enough for the entrapment of prey; however, these spiders may be hiding venomous secrets in the web, which current research is revealing. Here, we provide strong proteotranscriptomic evidence for the presence of toxin/neurotoxin-like proteins, defensins, and proteolytic enzymes on the web silk from Nephila clavipes spider. The results from quantitative-based transcriptomic and proteomic approaches showed that silk-producing glands produce an extensive repertoire of toxin/neurotoxin-like proteins, similar to those already reported in spider venoms. Meanwhile, the insect toxicity results demonstrated that these toxic components can be lethal and/or paralytic chemical weapons used for prey capture on the web, and the presence of fatty acids in the web may be a responsible mechanism opening the way to the web toxins for accessing the interior of prey's body, as shown here. Comparative phylogenomic-level evolutionary analyses revealed orthologous genes among two spider groups, Araneomorphae and Mygalomorphae, and the findings showed protein sequences similar to toxins found in the taxa Scorpiones and Hymenoptera in addition to Araneae. Overall, these data represent a valuable resource to further investigate other spider web toxin systems and also suggest that N. clavipes web is not a passive mechanical trap for prey capture, but it exerts an active role in prey paralysis/killing using a series of neurotoxins.

Monophyly, Taxon Sampling, and the Nature of Ranks in the Classification of Orb-Weaving Spiders (Araneae: Araneoidea)

We address some of the taxonomic and classification changes proposed by Kuntner et al. (2019) in a comparative study on the evolution of sexual size dimorphism in nephiline spiders. Their proposal to recircumscribe araneids and to rank the subfamily Nephilinae as a family is fundamentally flawed as it renders the family Araneidae paraphyletic. We discuss the importance of monophyly, outgroup selection, and taxon sampling, the subjectivity of ranks, and the implications of the age of origin criterion to assign categorical ranks in biological classifications. We explore the outcome of applying the approach of Kuntner et al. (2019) to the classification of spiders with emphasis on the ecribellate orb-weavers (Araneoidea) using a recently published dated phylogeny. We discuss the implications of including the putative sister group of Nephilinae (the sexually dimorphic genus Paraplectanoides) and the putative sister group of Araneidae (the miniature, monomorphic family Theridiosomatidae). We propose continuation of the phylogenetic classification put forth by Dimitrov et al. (2017), and we formally rank Nephilinae and Phonognathinae as subfamilies of Araneidae. Our classification better reflects the understanding of the phylogenetic placement and evolutionary history of nephilines and phonognathines while maintaining the diagnosability of Nephilinae. It also fulfills the fundamental requirement that taxa must be monophyletic, and thus avoids the paraphyly of Araneidae implied by Kuntner et al. (2019).

Photoreflectance/scattering measurements of spider silks informed by standard optics

The silks of certain orb weaving spiders are emerging as high-quality optical materials. This motivates study of the optical properties of such silk and particularly the comparative optical properties of the silks of different species. Any differences in optical properties may impart biological advantage for a spider species and make the silks interesting for biomimetic prospecting as optical materials. A prior study of the reflectance of spider silks from 18 species reported results for three species of modern orb weaving spiders (Nephila clavipes, Argiope argentata and Micrathena Schreibersi) as having reduced reflectance in the UV range. (Modern in the context used here means more recently derived.) The reduced UV reflectance was interpreted as an adaptive advantage in making the silks less visible to insects. Herein, a standard, experimental technique for measuring the reflectance spectrum of diffuse surfaces, using commercially available equipment, has been applied to samples of the silks of four modern species of orb weaving spiders: Phonognatha graeffei, Eriophora transmarina, Nephila plumipes and Argiope keyserlingi. This is a different technique than used in the previous study. Three of the four silks measured have a reduced signal in the UV. By taking the form of the silks as optical elements into account, it is shown that this is attributable to a combination of wavelength-dependent absorption and scattering by the silks rather than differences in reflectance for the different silks. Phonognatha graeffei dragline silk emerges as a very interesting spider silk with a flat 'reflectance'/scattering spectrum which may indicate it is a low UV absorbing dielectric micro-fibre. Overall the measurement emerges as having the potential to compare the large numbers of silks from different species to prospect for those which have desirable optical properties.

Ultrastructures and Mechanics of Annealed Nephila clavipes Major Ampullate Silk

The semicrystalline protein structure and impressive mechanical properties of major ampullate (MA) spider silk make it a promising natural alternative to polyacrylonitrile (PAN) fibers for carbon fiber manufacture. However, when annealed using a similar procedure to carbon fiber production, the tensile strength and Young's modulus of MA silk decrease. Despite this, MA silk fibers annealed at 600 °C remain stronger and tougher than similarly annealed PAN but have a lower Young's modulus. Although MA silk and PAN graphitize to similar extents, annealing disrupts the hydrogen bonding that controls crystal alignment within MA silk. Consequently, unaligned graphite crystals form in annealed MA silk, causing it to weaken, while graphite crystals in PAN maintain alignment along the fiber axis, strengthening the fibers. These shortcomings of spider silk when annealed provide insights into the selection and design of future alternative carbon fiber precursors.