Sequence Capture Phylogenomics of True Spiders Reveals Convergent Evolution of Respiratory Systems

A targeted gene phylogenetic framework to investigate diversification in the highly diverse yet geographically restricted red devil spiders (Araneae, Dysderidae)

The family Dysderidae is a highly diverse group of nocturnal ground-dwelling and active-hunter spiders. Dysderids are mostly restricted to the Western Palearctic, and particularly rich and abundant around the Mediterranean region. Interestingly, the distribution of species richness among its 24 genera and three subfamilies is highly biased-80% of its 644 documented species belong to just two genera, Dysdera (326) and Harpactea (211). Dysderidae provides an excellent study case for evolutionary and ecological research. It includes cases of trophic specialization, which are uncommon among spiders, and exhibit other remarkable biological (e.g. holocentric chromosomes), behavioural (e.g. cryptic female choice), evolutionary (e.g. adaptive radiation) and ecological features (e.g. recurrent colonization of the subterranean environment). The lack of a quantitative hypothesis on its phylogenetic structure has hampered its potential as a testing ground for evolutionary, biogeographical and ecological hypotheses. Here, we present the results of a target, multi-locus phylogenetic analysis, using mitochondrial (cox1, 16s and 12s) and nuclear genes (h3, 28s and 18s), of the most exhaustive taxonomic sample within Dysderidae (104 spp.) to date and across related families (Synspermiata) (83 spp.). We estimate divergence times using a combination of fossil and biogeographic node calibrations and use this timeline to identify shifts in diversification rates. Our results support the monophyly of the Dysderidae subfamilies Rhodinae and Dysderinae but reject Harpacteinae as currently defined. Moreover, the clades recovered within Harpacteinae do not support its current taxonomy. The origin of the family most likely post-dated the break-up of Pangea, and cave colonization may be older than previously considered. After correcting for the taxonomic artefacts, we identified a significant shift in diversification rates at the base of the genus Dysdera. Although the unique coexistence of specialist and generalist diets within the lineage could be suggested as the potential driver for the rate acceleration, further quantitative analyses would be necessary to test this hypothesis.

Burma Terrane Amber Fauna Shows Connections to Gondwana and Transported Gondwanan Lineages to the Northern Hemisphere (Araneae: Palpimanoidea)

Burmese amber is a significant source of fossils that documents the mid-Cretaceous biota. This deposit was formed around 99 Ma on the Burma Terrane, which broke away from Gondwana and later collided with Asia, although the timing is disputed. Palpimanoidea is a dispersal-limited group that was a dominant element of the Mesozoic spider fauna, and has an extensive fossil record, particularly from Burmese amber. Using morphological and molecular data, evolutionary relationships of living and fossil Palpimanoidea are examined. Divergence dating with fossils as terminal tips shows timing of diversification is contemporaneous with continental breakup.Ancestral range estimations show widespread ancestral ranges that divide into lineages that inherit different Pangean fragments, consistent with vicariance. Our results suggest that the Burmese amber fauna has ties to Gondwana due to a historical connection in the Early Cretaceous, and that the Burma Terrane facilitated biotic exchange by transporting lineages from Gondwana into the Holarctic in the Cretaceous.

Advances in the reconstruction of the spider tree of life: A roadmap for spider systematics and comparative studies

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

The Non-Dereliction in Evolution: Trophic Specialisation Drives Convergence in the Radiation of Red Devil Spiders (Araneae: Dysderidae) in the Canary Islands

Natural selection plays a key role in deterministic evolution, as clearly illustrated by the multiple cases of repeated evolution of ecomorphological characters observed in adaptive radiations. Unlike most spiders, Dysdera species display a high variability of cheliceral morphologies, which has been suggested to reflect different levels of specialization to feed on isopods. In this study, we integrate geometric morphometrics and experimental trials with a fully resolved phylogeny of the highly diverse endemic species from the Canary Islands to 1) quantitatively delimit the different cheliceral morphotypes present in the archipelago, 2) test their association with trophic specialization, as reported for continental species, 3) reconstruct the evolution of these ecomorphs throughout the diversification of the group, 4) test the hypothesis of convergent evolution of the different morphotypes, and 5) examine whether specialization constitutes a case of evolutionary irreversibility in this group. We show the existence of 9 cheliceral morphotypes and uncovered their significance for trophic ecology. Further, we demonstrate that similar ecomorphs evolved multiple times in the archipelago, providing a novel study system to explain how convergent evolution and irreversibility due to specialization may be combined to shape phenotypic diversification in adaptive radiations.

Miniaturization does not change conserved spider anatomy, a case study on spider Rayforstia (Araneae: Anapidae)

Miniaturization is an evolutionary trend observed in many animals. Some arachnid groups, such as spiders and mites, demonstrate a strong tendency toward miniaturization. Some of the most miniaturized spiders belong to the family Anapidae. In this study, using light and confocal microscopy and 3D modelling, we provide the first detailed description of the anatomy of a spider of the genus Rayforstia, which is only 900 µm long. In comparison with larger spiders, Rayforstia has no branching of the midgut in the prosoma and an increased relative brain volume. In contrast to many miniature insects and mites, the spider shows no reduction of whole organ systems, no allometry of the digestive and reproductive systems, and also no reduction of the set of muscles. Thus, miniature spider shows a more conserved anatomy than insects of a similar size. These findings expand our knowledge of miniaturization in terrestrial arthropods.

Phylogenomics illuminates the evolution of orb webs, respiratory systems and the biogeographic history of the world's smallest orb-weaving spiders (Araneae, Araneoidea, Symphytognathoids)

The miniature orb weaving spiders (symphytognathoids) are a group of small spiders (< 2 mm), including the smallest adult spider Patu digua (0.37 mm in body length), that have been classified into five families. The species of one of its constituent lineages, the family Anapidae, build a remarkable diversity of webs (ranging from orbs to sheet webs and irregular tangles) and even include a webless kleptoparasitic species. Anapids are also exceptional because of the extraordinary diversity of their respiratory systems. The phylogenetic relationships of symphytognathoid families have been recalcitrant with different classes of data, such as, monophyletic with morphology and its concatenation with Sanger-based six markers, paraphyletic (including a paraphyletic Anapidae) with solely Sanger-based six markers, and polyphyletic with transcriptomes. In this study, we capitalized on a large taxonomic sampling of symphytognathoids, focusing on Anapidae, and using de novo sequenced ultraconserved elements (UCEs) combined with UCEs recovered from available transcriptomes and genomes. We evaluated the conflicting relationships using a variety of support metrics and topology tests. We found support for the phylogenetic hypothesis proposed using morphology to obtain the "symphytognathoids'' clade, Anterior Tracheal System (ANTS) Clade and monophyly of the family Anapidae. Anapidae can be divided into three major lineages, the Vichitra Clade (including Teutoniella, Holarchaea, Sofanapis and Acrobleps), the subfamily Micropholcommatinae and the Orb-weaving anapids (Owa) Clade. Biogeographic analyses reconstructed a hypothesis of multiple long-distance transoceanic dispersal events, potentially influenced by the Antarctic Circumpolar Current and West Wind Drift. In symphytognathoids, the ancestral anterior tracheal system transformed to book lungs four times and reduced book lungs five times. The posterior tracheal system was lost six times. The orb web structure was lost four times independently and transformed into sheet web once.

Evolution and comparative morphology of raptorial feet in spiders

Spiders are among the most diverse animals, which developed different morphological and behavioral traits for capturing prey. We studied the anatomy and functionality of the rare and apomorphic raptorial spider feet using 3D reconstruction modeling, among other imaging techniques. The evolutionary reconstruction of the raptorial feet (tarsus plus pretarsus) features using a composite tree of spiders, indicating that similar traits emerged three times independently in Trogloraptoridae, Gradungulinae, and Doryonychus raptor (Tetragnathidae). The characteristics defining the raptorial feet are an interlocked complex merging of the base of the elongated prolateral claw with the pretarsal sclerotized ring, with the former clasping against the tarsus. Raptorial feet even flex over robust raptorial macrosetae forming a reduced tarsal version of a catching basket to encase prey during hunting. Our results show that Celaeniini (Araneidae) and Heterogriffus berlandi (Thomisidae), taxa previously compared with raptorial spiders, lack the raptorial feet key characteristics and the tarsal-catching basket. We make predictions about the possible behavior of the abovementioned taxa that will need to be tested by observing living specimens. We conclude that multiple morphological tarsal and pretarsal micro-structures define the raptorial foot functional unit and recommend a comprehensive evaluation before assigning this configuration to any spider taxa.

A novel probe set for the phylogenomics and evolution of RTA spiders

Spiders are important models for evolutionary studies of web building, sexual selection and adaptive radiation. The recent development of probes for UCE (ultra-conserved element)-based phylogenomic studies has shed light on the phylogeny and evolution of spiders. However, the two available UCE probe sets for spider phylogenomics (Spider and Arachnida probe sets) have relatively low capture efficiency within spiders, and are not optimized for the retrolateral tibial apophysis (RTA) clade, a hyperdiverse lineage that is key to understanding the evolution and diversification of spiders. In this study, we sequenced 15 genomes of species in the RTA clade, and using eight reference genomes, we developed a new UCE probe set (41 845 probes targeting 3802 loci, labelled as the RTA probe set). The performance of the RTA probes in resolving the phylogeny of the RTA clade was compared with the Spider and Arachnida probes through an in-silico test on 19 genomes. We also tested the new probe set empirically on 28 spider species of major spider lineages. The results showed that the RTA probes recovered twice and four times as many loci as the other two probe sets, and the phylogeny from the RTA UCEs provided higher support for certain relationships. This newly developed UCE probe set shows higher capture efficiency empirically and is particularly advantageous for phylogenomic and evolutionary studies of RTA clade and jumping spiders.

Geometric regularity in webs of non-orb-weaving spiders

Geometric regularity of spider webs has been intensively studied in orb-weaving spiders, although it is not exclusive of orb weavers. Here, we document the geometrically regular, repetitive elements in the webs of the non-orb-weaving groups Leptonetidae and Telemidae for the first time. Similar to orb weavers, we found areas with regularly spaced parallel lines in the webs of Calileptoneta helferi, Sulcia sp., and cf. Pinelema sp. Furthermore, we provide a detailed account of the regular webs of Ochyrocera (Ochyroceratidae). The sections of the web with regularly disposed parallel lines are built as U-shaped modules reminiscent of orb webs. It has been suggested that the regularly spaced parallel lines in the webs of Ochyroceratidae and Psilodercidae may be produced in a single sweep of their posterior lateral spinnerets, which have regularly spaced aciniform gland spigots, perhaps involving expansion of the spinnerets. To test this hypothesis, we compared the spacing between parallel lines with the spacing between spigots, searched for expansible membranes in the spinnerets, and examined the junctions of regularly spaced lines. The distance between parallel lines was 10-20 times the distance between spigots, and we found no expansible membranes, and the intersection of parallel lines are cemented, which opposes the single sweep hypothesis. Furthermore, we found cues of viscid silk in the parallel lines of the psilodercid Althepus and broadened piriform gland spigots that may be responsible of its production. Finally, we evaluated the presence or absence of geometrically regular web elements across the spider tree of life. We found reports of regular webs in 31 spider families, including 20 families that are not orb weavers and hypothesize that the two basic aspects of regularity (parallel lines spaced at regular intervals, and radial lines spaced at regular angles) probably appeared many times in the evolution of spiders.

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.

Correlation with a limited set of behavioral niches explains the convergence of somatic morphology in mygalomorph spiders

Understanding the drivers of morphological convergence requires investigation into its relationship with behavior and niche space, and such investigations in turn provide insights into evolutionary dynamics, functional morphology, and life history. Mygalomorph spiders (trapdoor spiders and their kin) have long been associated with high levels of morphological homoplasy, and many convergent features can be intuitively associated with different behavioral niches. Using genus-level phylogenies based on recent genomic studies and a newly assembled matrix of discrete behavioral and somatic morphological characters, we reconstruct the evolution of burrowing behavior in the Mygalomorphae, compare the influence of behavior and evolutionary history on somatic morphology, and test hypotheses of correlated evolution between specific morphological features and behavior. Our results reveal the simplicity of the mygalomorph adaptive landscape, with opportunistic, web-building taxa at one end, and burrowing/nesting taxa with structurally modified burrow entrances (e.g., a trapdoor) at the other. Shifts in behavioral niche, in both directions, are common across the evolutionary history of the Mygalomorphae, and several major clades include taxa inhabiting both behavioral extremes. Somatic morphology is heavily influenced by behavior, with taxa inhabiting the same behavioral niche often more similar morphologically than more closely related but behaviorally divergent taxa, and we were able to identify a suite of 11 somatic features that show significant correlation with particular behaviors. We discuss these findings in light of the function of particular morphological features, niche dynamics within the Mygalomorphae, and constraints on the mygalomorph adaptive landscape relative to other spiders.

Phylogeny and biogeography of the ancient spider family Filistatidae (Araneae) is consistent both with long-distance dispersal and vicariance following continental drift

Filistatids, the crevice weavers, are an ancient family of cribellate spiders without extant close relatives. As one of the first lineages of araneomorph spiders, they present a complicated mixture of primitive and derived characters that make them a key taxon to elucidate the phylogeny of spiders, as well as the evolution of phenotypic characters in this group. Their moderate diversity (187 species in 19 genera) is distributed mainly in arid and semi-arid subtropical zones of all continents, except Antarctica. The objective of this paper is to generate a comprehensive phylogenetic hypothesis for this family to advance the understanding of its morphological evolution and biogeography, as well as lay the basis for a natural classification scheme. By studying the morphology using optical and electronic microscopy techniques, we produced a matrix of 302 morphological characters coded for a sample of 103 species of filistatids chosen to represent the phylogenetic diversity of the family. In addition, we included sequences of four molecular markers (COI, 16S, H3 and 28S; 3787 aligned positions) of 70 filistatid species. The analysis of the data (morphological, molecular, and combined) consistently indicates the separation of the Filistatidae into two subfamilies, Prithinae and Filistatinae, in addition to supporting several groups of genera: Filistata, Zaitunia and an undescribed genus from Madagascar; Sahastata and Kukulcania; all Prithinae except Filistatinella and Microfilistata; Antilloides and Filistatoides; a large Old World group including Pritha, Tricalamus, Afrofilistata, Labahitha, Yardiella, Wandella and putative new genera; and a South American group formed by Lihuelistata, Pikelinia and Misionella. Pholcoides is transferred to Filistatinae and Microfilistata is transferred to Prithinae, and each represents the sister group to the remaining genera of its own subfamily. Most genera are valid, although Pikelinia is paraphyletic with respect to Misionella, so we consider the two genera as synonyms and propose a few new generic combinations. Considering the new phylogenetic hypothesis, we discuss the evolution of some morphological character systems and the biogeography of the family. The ages of divergence between clades were estimated using a total-evidence tip-dating approach by including fossils of Filistatidae and early spider clades; this approach resulted in younger age estimates than those obtained with traditional node-dating. Filistatidae is an ancient family that started diversifying in the Mesozoic and most genera date to the Cretaceous. Clades displaying transcontinental distributions were most likely affected by continental drift, but at least one clade shows unequivocal signs of transoceanic long-distance dispersal.

Evolutionary morphology of sperm in pholcid spiders (Pholcidae, Synspermiata)

Background

Pholcidae represent one of the largest and most diverse spider families and have been subject to various studies regarding behavior and reproductive biology. In contrast to the solid knowledge on phylogeny and general reproductive morphology, the primary male reproductive system is strongly understudied, as it has been addressed only for few species. Those studies however suggested a high diversity of sperm and seminal secretions across the family. To address this disparity and reconstruct the evolution of sperm traits, we investigate the primary male reproductive system of pholcid spiders by means of light, X-ray, and transmission electron microscopy using a comprehensive taxon sampling with 46 species from 33 genera, representing all five subfamilies.

Results

Our data show a high disparity of sperm morphology and seminal secretions within pholcids. We document several sperm characters that are unique for pholcids, such as a helical band (Pholcinae) or a lamellate posterior centriolar adjunct material (Modisiminae). Character mapping revealed several putative synapomorphies for individual taxa. With regard to sperm transfer forms, we found that synspermia occur only in the subfamily Ninetinae, whereas the other subfamilies have cleistospermia. In several species with cleistospermia, we demonstrate that spermatids remain fused until late stages of spermiogenesis before ultimately separating shortly before the coiling process. Additionally, we explored the previously hypothesized correlation between sperm size and minimum diameter of the spermophor in the male palpal organ. We show that synspermia differ strongly in size whereas cleistospermia are rather uniform, but neither transfer form is positively correlated with the diameter of the spermophor.

Conclusions

Our data revealed a dynamic evolution of sperm characters, with convergences across all subfamilies and a high level of homoplasy. The present diversity can be related to subfamily level and allows for assignments of specific subtypes of spermatozoa. Our observations support the idea that Ninetinae are an ancestral clade within Pholcidae that have retained synspermia and that synspermia represent the ancestral sperm transfer form of Pholcidae.

Phylogenomics of paleoendemic lampshade spiders (Araneae, Hypochilidae, Hypochilus), with the description of a new species from montane California

Hypochilus is a relictual lineage of Nearctic spiders distributed disjunctly across the United States in three montane regions (California, southern Rocky Mountains, southern Appalachia). Phylogenetic resolution of species relationships in Hypochilus has been challenging, and conserved morphology coupled with extreme genetic divergence has led to uncertain species limits in some complexes. Here, Hypochilus interspecies relationships have been reconstructed and cryptic speciation more critically evaluated using a combination of ultraconserved elements, mitochondrial CO1 by-catch, and morphology. Phylogenomic data strongly support the monophyly of regional clades and support a ((California, Appalachia), southern Rocky Mountains) topology. In Appalachia, five species are resolved as four lineages (H.thorelli Marx, 1888 and H.coylei Platnick, 1987 are clearly sister taxa), but the interrelationships of these four lineages remain unresolved. The Appalachian species H.pococki Platnick, 1987 is recovered as monophyletic but is highly genetically structured at the nuclear level. While algorithmic analyses of nuclear data indicate many species (e.g., all H.pococki populations as species), male morphology instead reveals striking stasis. Within the California clade, nuclear and mitochondrial lineages of H.petrunkevitchi Gertsch, 1958 correspond directly to drainage basins of the southern Sierra Nevada, with H.bernardino Catley, 1994 nested within H.petrunkevitchi and sister to the southernmost basin populations. Combining nuclear, mitochondrial, geographical, and morphological evidence a new species from the Tule River and Cedar Creek drainages is described, Hypochilusxomotesp. nov. We also emphasize the conservation issues that face several microendemic, habitat-specialized species in this remarkable genus.

Comprehensive species sampling and sophisticated algorithmic approaches refute the monophyly of Arachnida

Deciphering the evolutionary relationships of Chelicerata (arachnids, horseshoe crabs, and allied taxa) has proven notoriously difficult, due to their ancient rapid radiation and the incidence of elevated evolutionary rates in several lineages. Although conflicting hypotheses prevail in morphological and molecular data sets alike, the monophyly of Arachnida is nearly universally accepted, despite historical lack of support in molecular data sets. Some phylotranscriptomic analyses have recovered arachnid monophyly, but these did not sample all living orders, whereas analyses including all orders have failed to recover Arachnida. To understand this conflict, we assembled a data set of 506 high-quality genomes and transcriptomes, sampling all living orders of Chelicerata with high occupancy and rigorous approaches to orthology inference. Our analyses consistently recovered the nested placement of horseshoe crabs within a paraphyletic Arachnida. This result was insensitive to variation in evolutionary rates of genes, complexity of the substitution models, and alternative algorithmic approaches to species tree inference. Investigation of sources of systematic bias showed that genes and sites that recover arachnid monophyly are enriched in noise and exhibit low information content. To test the impact of morphological data, we generated a 514-taxon morphological data matrix of extant and fossil Chelicerata, analyzed in tandem with the molecular matrix. Combined analyses recovered the clade Merostomata (the marine orders Xiphosura, Eurypterida, and Chasmataspidida), but merostomates appeared nested within Arachnida. Our results suggest that morphological convergence resulting from adaptations to life in terrestrial habitats has driven the historical perception of arachnid monophyly, paralleling the history of numerous other invertebrate terrestrial groups.

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.

Micro-Computed Tomography Reveals a Remarkable Twin Intromittent Organ in Spiders – A Novelty for Arachnids With Direct Sperm Transfer

The modification of male pedipalps into secondary sexual intromittent organs is one of the hallmark characteristics of spiders, yet understanding the development and evolution of male genitalia across the order remains a challenging prospect. The embolus – the sclerite bearing the efferent spermatic duct or spermophor, and used to deliver sperm directly to the female genitalia during copulation – has always been considered the single unambiguously homologous palpal sclerite shared by all spider species, fundamental to the bauplan of the order and to the evolution and functional morphology of spider reproductive systems. Indeed, after two centuries of comparative research on spider reproduction, the presence of a single spermophor and embolus on each of a male spider’s two pedipalps remains a central tenet of evolutionary arachnology. Our findings challenge this premise, and reveal a remarkable twin intromittent organ sperm transfer system in a lineage of Australian palpimanoid spiders, characterized by a bifurcate spermophor and the presence of two efferent ducts leading to a pair of embolic sclerites on each pedipalp. This is the first time such a remarkable conformation has been observed in any group of arachnids with direct sperm transfer, complicating our understanding of palpal sclerite homologies, and challenging ideas about the evolution of spider genitalia.

Whole-Genome Phylogenetic Reconstruction as a Powerful Tool to Reveal Homoplasy and Ancient Rapid Radiation in Waterflea Evolution

Although phylogeny estimation is notoriously difficult in radiations that occurred several hundred million years ago, phylogenomic approaches offer new ways to examine relationships among ancient lineages and evaluate hypotheses that are key to evolutionary biology. Here, we reconstruct the deep-rooted relationships of one of the oldest living arthropod clades, the branchiopod crustaceans, using a kaleidoscopic approach. We use concatenation and coalescent tree-building methods to analyze a large multigene data set at the nucleotide and amino acid level and examine gene tree versus species tree discordance. We unequivocally resolve long-debated relationships among extant orders of the Cladocera, the waterfleas, an ecologically relevant zooplankton group in global aquatic and marine ecosystems that is famous for its model systems in ecology and evolution. To build the data set, we assembled eight de novo genomes of key taxa including representatives of all extant cladoceran orders and suborders. Our phylogenetic analysis focused on a BUSCO-based set of 823 conserved single-copy orthologs shared among 23 representative taxa spanning all living branchiopod orders, including 11 cladoceran families. Our analysis supports the monophyly of the Cladocera and reveals remarkable homoplasy in their body plans. We found large phylogenetic distances between lineages with similar ecological specializations, indicating independent evolution in major body plans, such as in the pelagic predatory orders Haplopoda and Onychopoda (the “Gymnomera”). In addition, we assessed rapid cladogenesis by estimating relative timings of divergence in major lineages using reliable fossil-calibrated priors on eight nodes in the branchiopod tree, suggesting a Paleozoic origin around 325 Ma for the cladoceran ancestor and an ancient rapid radiation around 252 Ma at the Perm/Triassic boundary. These findings raise new questions about the roles of homoplasy and rapid radiation in the diversification of the cladocerans and help examine trait evolution from a genomic perspective in a functionally well understood, ancient arthropod group. [Cladocera; Daphnia; evolution; homoplasy; molecular clock; phylogenomics; systematics; waterfleas.]

Take a deep breath… The evolution of the respiratory system of symphytognathoid spiders (Araneae, Araneoidea)

Spiders are unique in having a dual respiratory system with book lungs and tracheae, and most araneomorph spiders breathe simultaneously via book lungs and tracheae, or tracheae alone. The respiratory organs of spiders are diverse but relatively conserved within families. The small araneoid spiders of the symphytognathoid clade exhibit a remarkably high diversity of respiratory organs and arrangements, unparalleled by any other group of ecribellate orb weavers. In the present study, we explore and review the diversity of symphytognathoid respiratory organs. Using a phylogenetic comparative approach, we reconstruct the evolution of the respiratory system of symphytognathoids based on the most comprehensive phylogenetic frameworks to date. There are no less than 22 different respiratory system configurations in symphytognathoids. The phylogenetic reconstructions suggest that the anterior tracheal system evolved from fully developed book lungs and, conversely, reduced book lungs have originated independently at least twice from its homologous tracheal conformation. Our hypothesis suggests that structurally similar book lungs might have originated through different processes of tracheal transformation in different families. In symphytognathoids, the posterior tracheal system has either evolved into a highly branched and complex system or it is completely lost. No evident morphological or behavioral features satisfactorily explains the exceptional variation of the symphytognathoid respiratory organs.

What Is an “Arachnid”? Consensus, Consilience, and Confirmation Bias in the Phylogenetics of Chelicerata

The basal phylogeny of Chelicerata is one of the opaquest parts of the animal Tree of Life, defying resolution despite application of thousands of loci and millions of sites. At the forefront of the debate over chelicerate relationships is the monophyly of Arachnida, which has been refuted by most analyses of molecular sequence data. A number of phylogenomic datasets have suggested that Xiphosura (horseshoe crabs) are derived arachnids, refuting the traditional understanding of arachnid monophyly. This result is regarded as controversial, not least by paleontologists and morphologists, due to the widespread perception that arachnid monophyly is unambiguously supported by morphological data. Moreover, some molecular datasets have been able to recover arachnid monophyly, galvanizing the belief that any result that challenges arachnid monophyly is artefactual. Here, we explore the problems of distinguishing phylogenetic signal from noise through a series of in silico experiments, focusing on datasets that have recently supported arachnid monophyly. We assess the claim that filtering by saturation rate is a valid criterion for recovering Arachnida. We demonstrate that neither saturation rate, nor the ability to assemble a molecular phylogenetic dataset supporting a given outcome with maximal nodal support, is a guarantor of phylogenetic accuracy. Separately, we review empirical morphological phylogenetic datasets to examine characters supporting Arachnida and the downstream implication of a single colonization of terrestrial habitats. We show that morphological support of arachnid monophyly is contingent upon a small number of ambiguous or incorrectly coded characters, most of these tautologically linked to adaptation to terrestrial habitats.

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.

Combining genomic, phenotypic and Sanger sequencing data to elucidate the phylogeny of the two-clawed spiders (Dionycha)

The importance of morphology in the phylogenomic era has recently gained attention, but relatively few studies have combined both types of information when inferring phylogenetic relationships. Sanger sequencing legacy data can also be important for understanding evolutionary relationships. The possibility of combining genomic, morphological and Sanger data in one analysis seems compelling, permitting a more complete sampling and yielding a comprehensive view of the evolution of a group. Here we used these three data types to elucidate the systematics and evolution of the Dionycha, a highly diverse group of spiders relatively underrepresented in phylogenetic studies. The datasets were analyzed separately and combined under different inference methods, including a novel approach for analyzing morphological matrices with commonly used evolutionary models. We tested alternative hypotheses of relationships and performed simulations to investigate the accuracy of our findings. We provide a comprehensive and thorough phylogenetic hypothesis for Dionycha that can serve as a robust framework to test hypotheses about the evolution of key characters. We also show that morphological data might have a phylogenetic impact, even when massively outweighed by molecular data. Our approach to analyze morphological data may serve as an alternative to the proposed practice of arbitrarily partitioning, weighting, and choosing between parsimony and stochastic models. As a result of our findings, we propose Trachycosmidae new rank for a group of Australian genera formerly included in Trochanteriidae and Gallieniellidae, and consider Ammoxenidae as a junior synonym of Gnaphosidae. We restore the family rank for Prodidomidae, but transfer the subfamily Molycriinae to Gnaphosidae. Drassinella is transferred to Liocranidae, Donuea to Corinnidae, and Mahafalytenus to Viridasiidae.

New specimens from Mid-Cretaceous Myanmar amber illuminate the phylogenetic placement of Lagonomegopidae (Arachnida: Araneae)

New lagonomegopid spiders are described from Mid-Cretaceous Myanmar (Burmese) amber. Two new genera and species based on single specimens, Scopomegops fax gen. & sp. nov. and Hiatomegops spinalis gen. & sp. nov. are described. Two specimens belonging to Lineaburmops beigeli are further described. Additionally, after re-examining the holotype of Odontomegops titan, a detailed description of its basal ventral abdomen is added here. A phylogenetic analysis was performed to investigate the phylogenetic placement of Lagonomegopidae. A matrix of 79 morphological characters, scored for six lagonomegopid taxa and 26 non-lagonomegopid taxa, was analysed through parsimony and Bayesian phylogenetic inference. Our results recover extant Palpimanoidea as a monophyletic group and partly suggest that Lagonomegopidae is the sister-group to extant Palpimanoidea. The external sexual organs, retrolateral tibial apophysis on the male palp and tracheal spiracle in lagonomegopids are discussed.

Taxonomic Sampling and Rare Genomic Changes Overcome Long-Branch Attraction in the Phylogenetic Placement of Pseudoscorpions

Long-branch attraction is a systematic artifact that results in erroneous groupings of fast-evolving taxa. The combination of short, deep internodes in tandem with long-branch attraction artifacts has produced empirically intractable parts of the Tree of Life. One such group is the arthropod subphylum Chelicerata, whose backbone phylogeny has remained unstable despite improvements in phylogenetic methods and genome-scale data sets. Pseudoscorpion placement is particularly variable across data sets and analytical frameworks, with this group either clustering with other long-branch orders or with Arachnopulmonata (scorpions and tetrapulmonates). To surmount long-branch attraction, we investigated the effect of taxonomic sampling via sequential deletion of basally branching pseudoscorpion superfamilies, as well as varying gene occupancy thresholds in supermatrices. We show that concatenated supermatrices and coalescent-based summary species tree approaches support a sister group relationship of pseudoscorpions and scorpions, when more of the basally branching taxa are sampled. Matrix completeness had demonstrably less influence on tree topology. As an external arbiter of phylogenetic placement, we leveraged the recent discovery of an ancient genome duplication in the common ancestor of Arachnopulmonata as a litmus test for competing hypotheses of pseudoscorpion relationships. We generated a high-quality developmental transcriptome and the first genome for pseudoscorpions to assess the incidence of arachnopulmonate-specific duplications (e.g., homeobox genes and miRNAs). Our results support the inclusion of pseudoscorpions in Arachnopulmonata (new definition), as the sister group of scorpions. Panscorpiones (new name) is proposed for the clade uniting Scorpiones and Pseudoscorpiones.

Interrogating Genomic-Scale Data to Resolve Recalcitrant Nodes in the Spider Tree of Life

Genome-scale data sets are converging on robust, stable phylogenetic hypotheses for many lineages; however, some nodes have shown disagreement across classes of data. We use spiders (Araneae) as a system to identify the causes of incongruence in phylogenetic signal between three classes of data: exons (as in phylotranscriptomics), noncoding regions (included in ultraconserved elements [UCE] analyses), and a combination of both (as in UCE analyses). Gene orthologs, coded as amino acids and nucleotides (with and without third codon positions), were generated by querying published transcriptomes for UCEs, recovering 1,931 UCE loci (codingUCEs). We expected that congeners represented in the codingUCE and UCEs data would form clades in the presence of phylogenetic signal. Noncoding regions derived from UCE sequences were recovered to test the stability of relationships. Phylogenetic relationships resulting from all analyses were largely congruent. All nucleotide data sets from transcriptomes, UCEs, or a combination of both recovered similar topologies in contrast with results from transcriptomes analyzed as amino acids. Most relationships inferred from low-occupancy data sets, containing several hundreds of loci, were congruent across Araneae, as opposed to high occupancy data matrices with fewer loci, which showed more variation. Furthermore, we found that low-occupancy data sets analyzed as nucleotides (as is typical of UCE data sets) can result in more congruent relationships than high occupancy data sets analyzed as amino acids (as in phylotranscriptomics). Thus, omitting data, through amino acid translation or via retention of only high occupancy loci, may have a deleterious effect in phylogenetic reconstruction.

Cribellate thread production as model for spider's spinneret kinematics

Spider silk attracts researchers from the most diverse fields, such as material science or medicine. However, still little is known about silk aside from its molecular structure and material strength. Spiders produce many different silks and even join several silk types to one functional unit. In cribellate spiders, a complex multi-fibre system with up to six different silks affects the adherence to the prey. The assembly of these cribellate capture threads influences the mechanical properties as each fibre type absorbs forces specifically. For the interplay of fibres, spinnerets have to move spatially and come into contact with each other at specific points in time. However, spinneret kinematics are not well described though highly sophisticated movements are performed which are in no way inferior to the movements of other flexible appendages. We describe here the kinematics for the spinnerets involved in the cribellate spinning process of the grey house spider, Badumna longinqua, as an example of spinneret kinematics in general. With this information, we set a basis for understanding spinneret kinematics in other spinning processes of spiders and additionally provide inspiration for biomimetic multiple fibre spinning.

Phylogenomics and biogeography of leptonetid spiders (Araneae:Leptonetidae)

Leptonetidae are rarely encountered spiders, usually associated with caves and mesic habitats, and are disjunctly distributed across the Holarctic. Data from ultraconserved elements (UCEs) were used in concatenated and coalescent-based analyses to estimate the phylogenetic history of the family. Our taxon sample included close outgroups, and 90% of described leptonetid genera, with denser sampling in North America and Mediterranean Europe. Two data matrices were assembled and analysed; the first ‘relaxed’ matrix includes the maximum number of loci and the second ‘strict’ matrix is limited to the same set of core orthologs but with flanking introns mostly removed. A molecular dating analysis incorporating fossil and geological calibration points was used to estimate divergence times, and dispersal–extinction–cladogenesis analysis (DEC) was used to infer ancestral distributions. Analysis of both data matrices using maximum likelihood and coalescent-based methods supports the monophyly of Archoleptonetinae and Leptonetinae. However, relationships among Archoleptonetinae, Leptonetinae, and Austrochiloidea are poorly supported and remain unresolved. Archoleptonetinae is elevated to family rank Archoleptonetidae (new rank) and Leptonetidae (new status) is restricted to include only members of the subfamily Leptonetinae; a taxonomic review with morphological diagnoses is provided for both families. Four well supported lineages within Leptonetidae (new status) are recovered: (1) the Calileptoneta group, (2) the Leptoneta group, (3) the Paraleptoneta group, and (4) the Protoleptoneta group. Most genera within Leptonetidae are monophyletic, although Barusia, Cataleptoneta, and Leptoneta include misplaced species and require taxonomic revision. The origin of Archoleptonetidae (new rank), Leptonetidae, and the four main lineages within Leptonetidae date to the Cretaceous. DEC analysis infers the Leptoneta and Paraleptoneta groups to have ancestral distributions restricted to Mediterranean Europe, whereas the Calileptoneta and Protoleptoneta groups include genera with ancestral distributions spanning eastern and western North America, Mediterranean Europe, and east Asia. Based on a combination of biology, estimated divergence times, and inferred ancestral distributions we hypothesise that Leptonetidae was once widespread across the Holarctic and their present distributions are largely the result of vicariance. Given the wide disjunctions between taxa, we broadly interpret the family as a Holarctic relict fauna and hypothesise that they were once part of the Boreotropical forest ecosystem.

Hooroo mates! Phylogenomic data suggest that the closest relatives of the iconic Tasmanian cave spider Hickmania troglodytes are in Australia and New Zealand, not in South America

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

Evolutionary kinematics of spinneret movements for rapid silk thread anchorage in spiders

Many organisms secrete structural materials from their bodies to enhance protection, foraging or signalling. The function of such secretion products can be further extended by their assembly into complex structures, so-called extended phenotypes, such as shells, nests and biofilms. Understanding the variation in the efficacy of such assembly processes could help to explain why extended phenotypes are common on some lineages and rare in others. Here, I comparatively studied the assembly of sticky silk fibres into thread anchorages by the innate 'printing' behaviour in 92 species of spiders from 45 families, representing the so-far largest comparative study of construction-related motion patterns. I found a global evolutionary trend towards a faster production of silk thread anchorages, in both web builders and hunting spiders. The slowest producers of silk anchors belong to a clade with an ancestral configuration of respiratory organs, suggesting that a major constraint to the evolution of spinning speed is the efficiency of oxygen uptake. Motion patterns were found to contain a high phylogenetic signal, but did not correlate with spinning speeds. These results help to explain the variation in diversity and ecological success among the spider fauna and showcase the value of comparative kinematics in biodiversity studies.