Morphology to the rescue: molecular data and the signal of morphological characters in combined phylogenetic analyses-a case study from mysmenid spiders (Araneae, Mysmenidae), with comments on the evolution of web architecture

A comparative morphology of trichobothrial bases in araneoid spiders and its significance for the phylogeny and system of the superfamily Araneoidea (Arachnida, Araneae)

Bothrial morphology was studied by SEM in 137 araneoid genera representing all 22 currently recognized extant families and all 42 conventional subfamilies of the Araneoidea. The ancestral type in the superfamily Araneoidea is a 'hooded' bothrium with a single well-developed transverse ridge, dividing its proximal and distal plates ('Erigone-type'); the advanced type is a solid dome-like bothrium without vestiges of the ridge ('Theridion-type'); there are several intermediate types reflecting various pathways and stages of the ridge reduction (united here as 'Argiope-type'). The parallel trends in bothrial evolution, recognized as continuous series from the ancestral type up to the advanced one through some intermediate stages, are distinguished in each of the seven main phylogenetic lineages of the superfamily: 'tetragnathoids', 'araneoids', 'cyatholipoids', and 'theridioids' possess a complete set of the three types, while 'malkariods', 'symphytognathoids'. and 'linyphioids' lack the advanced, dome-like type ('Theridion-type'). Only three taxa have been proposed earlier as the sister group of the superfamily Araneoidea: Nicodamoidea, Deinopoidea, and Leptonetoidea; morphology of bothria, as well as other cuticular microstructures, clearly supports the araneoid-nicodamoid relationship hypothesis, purely 'molecular' to date. Bothrial morphology provides the additional arguments for several taxonomic acts, e.g., for the reranking the Agnarsson's (2004) 'clade 35' (Theonoe, Carniella, Robertus, and Pholcomma) up to the Theonoeinae Simon, 1894, stat. nov., and for the revalidation the micropholcommatid Plectochetos Butler, 1932, gen. revalid. and zygiellid Parazygiella Wunderlich, 2004, gen. revalid.

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.

Phylogenetic placement of eight poorly known spiders of Microdipoena (Araneae, Mysmenidae), with descriptions of five new species

Ten species of the spider genus Microdipoena Banks, 1895 are reported from China, Laos, Indonesia, Georgia, and Seychelles. DNA sequences of the eight species are obtained to confirm their correct identification. The molecular phylogenetic analysis based on five gene fragments (16S, 18S, 28S, COI, and H3) were used to test the relationships and taxonomic placements of eight Microdipoena species, of which five species are documented as new to science: i.e., M.huisunsp. nov. (♀, China), M.lisusp. nov. (♀, China), M.shenyangsp. nov. (♂♀, China), M.thatitousp. nov. (♀, Laos), and M.zhulinsp. nov. (♂♀, China). Five known species are redescribed: M.elsae Saaristo, 1978 (♂♀, Seychelles), M.gongi (Yin, Peng & Bao, 2004) (♂♀, China), M.menglunensis (Lin & Li, 2008) (♂♀, China), M.jobi (Kraus, 1967) (♂♀, Georgia), and M.yinae (Lin & Li, 2013) (♂♀, China). All but M.menglunensis are diagnosed and illustrated. The family Mysmenidae is also the first recorded from Laos and Georgia.

On the symphytognathoid spider genus Mysmenopsis Simon, 1898 (Araneae: Mysmenidae) from the Brazilian Amazonian region: description of five new species and new records

Five new species of Mysmenopsis from the Brazilian Amazonian region are described: M. rodriguesae n. sp. and M. nadineae n. sp. known by males and females, M snethlageae n. sp., M. lopardoae n. sp. and M. regiae n. sp. known only by males. Three species, M. cienaga Müller, 1987 (previously known from Peru and Colombia), M. penai Platnick & Shadab, 1978 (Ecuador and Colombia), and M. shushufindi Dupérré & Tapia, 2020 (Ecuador) are recorded for the first time in Brazilian Amazonian region. An additional record of M. penai from northeastern Brazil is included.

New Insights into the Origin and Evolution of Mysmenid Spiders (Araneae, Mysmenidae) Based on the First Four Complete Mitochondrial Genomes

The mitochondrial genome (mitogenome) is recognized as an effective molecular marker for studying molecular evolution and phylogeny. The family Mysmenidae is a group of widely distributed and covert-living spiders, of which the mitogenomic information is largely unclear. In this study, we obtained the first four complete mitogenomes of mysmenid spiders (one aboveground species: Trogloneta yuensis, and three cave-dwelling species: T. yunnanense, Yamaneta kehen and Y. paquini). Comparative analyses revealed that their lengths ranged from 13,771 bp (T. yuensis) to 14,223 bp (Y. kehen), containing a standard set of 37 genes and an A + T-rich region with the same gene orientation as other spider species. The mitogenomic size of T. yunnanense was more similar to that of Yamaneta mitogenomes than that of T. yuensis, which might indicate the convergent evolution of cave spiders. High variability was detected between the genera Trogloneta and Yamaneta. The A + T content, the amino acid frequency of protein-coding genes (PCGs) and the secondary structures of tRNAs showed large differences. Yamaneta kehen and Y. paquini contained almost identical truncated tRNAs, and their intergenic spacers and overlaps exhibited high uniformity. The two Yamaneta species also possessed a higher similarity of start/stop codons for PCGs than the two Trogloneta species. In selective pressure analysis, compared to Yamaneta, Trogloneta had much higher Ka/Ks values, which implies that selection pressure may be affected by habitat changes. In our study, the phylogenetic analysis based on the combination of 13 PCGs and two rRNAs showed that Mysmenidae is a sister clade to the family Tetragnathidae. Our data and findings will contribute to the better understanding of the origin and evolution of mysmenid spiders.

Systematic notes on three troglobitic Anapistula (Araneae, Symphytognathidae) spiders from China, with the descriptions of two new species

Three cave-dwelling spider species belonging to the family Symphytognathidae Hickman, 1931, i.e., Anapistulasanjiao sp. nov. (♂♀), A.walayaku sp. nov. (♂♀), and A.panensis Lin, Tao & Li, 2013 (♂♀), are reported from southwest China. DNA sequences and detailed illustrations of the habitus, male palps and epigynes are provided, and their distributions are mapped. Their phylogenetic position within symphytognathids and relationships were tested and assessed using previously published phylogenetic analyses on symphytognathoids. The results showed that they form a clade with A.choojaiae Rivera-Quiroz, Petcharad & Miller, 2021 from Thailand.

Chimena gen. nov., a new spider genus (Araneae, Mysmenidae) from China, with descriptions of two new species and a new combination

A new mysmenid genus, Chimena gen. nov., is reported from China. Two new species: C.qiong sp. nov. (Hainan, ♂♀, the type species) and C.nantou sp. nov. (Taiwan, ♀) are illustrated and described in detail. A new combination is suggested: Chimenataiwanica (Ono, 2007) comb. nov. (Taiwan, ♂♀, transferred from Mysmena Simon, 1894). The molecular phylogeny and morphological characters were used to discuss the taxonomy and circumscription of the newly erected genus.

Biological challenges to conclusions from molecular phylogenies: behaviour strongly favours orb web monophyly, contradicting molecular analyses

This first-ever extensive review of the construction behaviour of orb webs, of webs secondarily derived from orbs, and of non-orbs shows that the evidence favouring monophyly over convergent evolution of orbs is stronger than previously appreciated. The two major orb-weaving groups, Uloboridae and Araneoidea, share 31 construction behaviour traits, 20 of which are likely to be both derived and to have feasible alternatives, making convergence an unlikely explanation. Convergence in two lineages seems unlikely, and convergence in five different lineages, as proposed in some recent molecular studies of phylogeny, is even less credible. A further set of seven shared responses in orb design to experimentally constrained spaces also supports orb monophyly. Finally, a ‘control’ case of confirmed convergence on similar ‘pseudo-orbs’ in a taxonomically distant group also supports this argument, as it shows a low frequency of behavioural similarities. I argue that the omission of behavioural data from recent molecular studies of orb web evolution represents a failure of the analytic techniques, not the data, and increases the risk of making mistakes. In general, phylogenetic studies that aim to understand the evolution of particular phenotypes can benefit from including careful study of the phenotypes themselves.

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.

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.

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.

First records and three new species of the family Symphytognathidae (Arachnida, Araneae) from Thailand, and the circumscription of the genus Crassignatha Wunderlich, 1995

The family Symphytognathidae is reported from Thailand for the first time. Three new species: Anapistula choojaiae sp. nov., Crassignatha seeliam sp. nov., and Crassignatha seedam sp. nov. are described and illustrated. Distribution is expanded and additional morphological data are reported for Patu shiluensis Lin & Li, 2009. Specimens were collected in Thailand between July and August 2018. The newly described species were found in the north mountainous region of Chiang Mai, and Patu shiluensis was collected in the coastal region of Phuket. DNA sequences are provided for all the species here studied. The relations of these symphytognathid species were tested using previously published phylogenetic analyses on micro orb-weavers. Also, we used micro CT analysis to build 3D models of the male genitalia and somatic characters of two species of Crassignatha Wunderlich, 1995. The molecular phylogeny and 3D models were used to discuss the taxonomy and circumscription of the currently valid symphytognathid genera, with focus on Crassignatha and Patu Marples, 1951. Based on this, three new combinations are suggested: Crassignatha bicorniventris (Lin & Li, 2009), comb. nov., Crassignatha quadriventris (Lin & Li, 2009), comb. nov., and Crassignatha spinathoraxi (Lin & Li, 2009), comb. nov. A new record of Crassignatha danaugirangensisMiller et al. 2014 is reported from Brunei.

Molecular phylogeny of the orb-weaving spider genus Leucauge and the intergeneric relationships of Leucauginae (Araneae, Tetragnathidae)

The tetragnathid genus Leucauge includes some of the most common orb-weaving spiders in the tropics. Although some species in this genus have attained relevance as model systems for several aspects of spider biology, our understanding of the generic diversity and evolutionary relationships among the species is poor. In this study we present the first attempt to determine the phylogenetic structure within Leucauge and the relationship of this genus with other genera of Leucauginae. This is based on DNA sequences from the five loci commonly used and Histone H4, used for the first time in spider phylogenetics. We also assess the informativeness of the standard markers and test for base composition biases in the dataset. Our results suggest that Leucauge is not monophyletic since species of the genera Opas, Opadometa, Mecynometa and Alcimosphenus are included within the current circumscription of the genus. Based on a phylogenetic re-circumscription of the genus to fulfil the requirement for monophyly of taxa, Leucauge White, 1841 is deemed to be a senior synonym of the genera Opas Pickard-Cambridge, 1896 revalidated synonymy, Mecynometa Simon, 1894 revalidated synonymy, Opadometa Archer, 1951 new synonymy and Alcimosphenus Simon, 1895 new synonymy. We identify groups of taxa critical for resolving relationships within Leucauginae and describe the limitations of the standard loci for accomplishing these resolutions.

Phylogenetic placement of the stone-nest orb-weaving spider Nemoscolus Simon, 1895 (Araneae : Araneidae) and the description of the first species from Australia

The spider genus Nemoscolus Simon, 1895 (Araneidae) has been neglected taxonomically despite the unique retreat that several species construct in their horizontal orb-webs, composed of pebbles and other detritus. The distribution of Nemoscolus is poorly known and the genus includes species from Africa and Europe. Nemoscolus is placed in Simon’s Cycloseae species group along with Cyclosa Menge, 1866, Acusilas Simon, 1895, Arachnura Vinson, 1863, Witica O. Pickard-Cambridge, 1895, among others. Here we describe a new species from Queensland, Australia, N. sandersi, sp. nov., drastically expanding the distribution range of the genus. We use nucleotide sequence data to phylogenetically place Nemoscolus using model-based inference methods within Araneidae and to explore its affinities to Simon’s Cycloseae. The data support propinquity of Nemoscolus with Acusilas and Arachnura but not with Cyclosa. Our analyses suggest that Cycloseae is not a clade, with Cyclosa, Acusilas, Witica and Nemoscolus not sharing a recent common ancestor. This use of an integrated granular retreat represents at least the second independent evolution of such a structure within Araneidae. These results improve our understanding of both phylogeny and retreat evolution in araneid spiders.

Exploring the impact of morphology, multiple sequence alignment and choice of optimality criteria in phylogenetic inference: a case study with the Neotropical orb-weaving spider genus Wagneriana (Araneae: Araneidae)

We present a total evidence phylogenetic analysis of the Neotropical orb-weaving spider genus Wagneriana and discuss the phylogenetic impacts of methodological choices. We analysed 167 phenotypic characters and nine loci scored for 115 Wagneriana and outgroups, including 46 newly sequenced species. We compared total evidence analyses and molecular-only analyses to evaluate the impact of phenotypic evidence, and we performed analyses using the programs POY, TNT, RAxML, GARLI, IQ-TREE and MrBayes to evaluate the effects of multiple sequence alignment and optimality criteria. In all analyses, Wagneriana carimagua and Wagneriana uropygialis were nested in the genera Parawixia and Alpaida, respectively, and the remaining species of Wagneriana fell into three main clades, none of which formed a pair of sister taxa. However, sister-group relationships among the main clades and their internal relationships were strongly influenced by methodological choices. Alignment methods had comparable topological effects to those of optimality criteria in terms of ‘subtree pruning and regrafting’ moves. The inclusion of phenotypic evidence, 2.80–3.05% of the total evidence matrices, increased support irrespective of the optimality criterion used. The monophyly of some groups was recovered only after the addition of morphological characters. A new araneid genus, Popperaneus gen. nov., is erected, and Paraverrucosa is resurrected. Four new synonymies and seven new combinations are proposed.

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

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

Further study of two Chinese cave spiders (Araneae, Mysmenidae), with description of a new genus

The current paper expands knowledge of two Chinese cave spider species originally described in the genus Maymena Gertsch, 1960: M. paquini Miller, Griswold & Yin, 2009 and M. kehen Miller, Griswold & Yin, 2009. With the exception of these two species, the genus Maymena is endemic to the western hemisphere, and new evidence presented here supports the creation of a new genus for the Chinese species, which we name Yamaneta gen. nov. The male of Y. kehen is described for the first time. Detailed illustrations of the habitus, male palps and epigyne are provided for these two species, as well as descriptions of their webs. DNA sequences are provided for both Yamaneta species. We build on a previously published phylogenetic analysis of Mysmenidae to assess the phylogenetic position of Yamaneta and its relationship to true Maymena.

Phylogenomics, Diversification Dynamics, and Comparative Transcriptomics across the Spider Tree of Life

Dating back to almost 400 mya, spiders are among the most diverse terrestrial predators [1]. However, despite considerable effort [1-9], their phylogenetic relationships and diversification dynamics remain poorly understood. Here, we use a synergistic approach to study spider evolution through phylogenomics, comparative transcriptomics, and lineage diversification analyses. Our analyses, based on ca. 2,500 genes from 159 spider species, reject a single origin of the orb web (the "ancient orb-web hypothesis") and suggest that orb webs evolved multiple times since the late Triassic-Jurassic. We find no significant association between the loss of foraging webs and increases in diversification rates, suggesting that other factors (e.g., habitat heterogeneity or biotic interactions) potentially played a key role in spider diversification. Finally, we report notable genomic differences in the main spider lineages: while araneoids (ecribellate orb-weavers and their allies) reveal an enrichment in genes related to behavior and sensory reception, the retrolateral tibial apophysis (RTA) clade-the most diverse araneomorph spider lineage-shows enrichment in genes related to immune responses and polyphenic determination. This study, one of the largest invertebrate phylogenomic analyses to date, highlights the usefulness of transcriptomic data not only to build a robust backbone for the Spider Tree of Life, but also to address the genetic basis of diversification in the spider evolutionary chronicle.

Modular patterns in behavioural evolution: webs derived from orbs

Imperfect knowledge of ancestral behaviour often hampers tracing behavioural evolution. This limitation is reduced in orb weaving spiders, because spider orb web construction behaviour and the cues used by modern orb-weavers are well-studied and highly conserved. Several species in orb-weaving families build non-orb webs that are clearly derived from orbs, allowing transitions from ancestral to modern behaviours to be described with high confidence. Three major patterns of general evolutionary significance were found in 69 phylogenetically independent transitions in 15 groups in 8 families: ancestral traits were often maintained as units; the most frequent of the eight different types of ancestral trait change was transfer of an ancestral behaviour to a new context; and ‘new’ traits that had no clear homology with ancestral traits were also common. Changes occurred in all major stages of orb construction. This may be the most extensive summary of evolutionary transitions in behaviour yet compiled.

There is no evidence that Podoctidae carry eggs of their own species: Reply to Machado and Wolff (2017)

In our recent publication (Sharma et al., 2017), we tested the hypothesis that eggs attached to the legs of male Podoctidae (Opiliones, Laniatores) constituted a case of paternal care, using molecular sequence data in tandem with multiple sequence alignments to test the prediction that sequences of the eggs and the adults that carried them would indicate conspecific identity. We discovered that the sequences of the eggs belonged to spiders, and thus rejected the paternal care hypothesis for these species. Machado and Wolff (2017) recently critiqued our work, which they regarded as a non-critical interpretation and over-reliance on molecular sequence data, and defended the traditional argument that the eggs attached to podoctids are in fact harvestman eggs. Here we show that additional molecular sequence data also refute the identity of the eggs as conspecific harvestman eggs, using molecular cloning techniques to rule out contamination. We show that individual gene trees consistently and reliably place the egg and adult sequences in disparate parts of the tree topology. Phylogenetic methods consistently place all egg sequences within the order Araneae (spiders). We submit that evidence for the paternal care hypothesis based on behavioral, morphological, and natural history approaches is either absent or insufficient for concluding that the eggs of podoctids are conspecific.

A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology

Current sequencing technologies are making available unprecedented amounts of genetic data for a large variety of species including nonmodel organisms. Although many phylogenomic surveys spend considerable time finding orthologs from the wealth of sequence data, these results do not transcend the original study and after being processed for specific phylogenetic purposes these orthologs do not become stable orthology hypotheses. We describe a procedure to detect and document the phylogenetic distribution of orthologs allowing researchers to use this information to guide selection of loci best suited to test specific evolutionary questions. At the core of this pipeline is a new phylogenetic orthology method that is neither affected by the position of the root nor requires explicit assignment of outgroups. We discuss the properties of this new orthology assessment method and exemplify its utility for phylogenomics using a small insects dataset. In addition, we exemplify the pipeline to identify and document stable orthologs for the group of orb-weaving spiders (Araneoidea) using RNAseq data. The scripts used in this study, along with sample files and additional documentation, are available at https://github.com/ballesterus/UPhO.

Mysmenidae, a spider family newly recorded from Tibet (Arachnida, Araneae)

The spider family Mysmenidae is reported from Tibet for the first time. Two new species, Chanea voluta sp. n. (male and female) and Mysmena lulanga sp. n. (male and female) are found in eastern Tibet in high altitude. Morphological descriptions, diagnoses and comparative photos are provided for the two new species.

Gastrulation occurs in multiple phases at two distinct sites in Latrodectus and Cheiracanthium spiders

BACKGROUND

The longstanding canonical model of spider gastrulation posits that cell internalization occurs only at a unitary central blastopore; and that the cumulus (dorsal organizer) arises from within the early deep layer by cell-cell interaction. Recent work has begun to challenge the canonical model by demonstrating cell internalization at extra-blastoporal sites in two species (Parasteatoda tepidariorum and Zygiella x-notata); and showing in Zygiella that the prospective cumulus internalizes first, before other cells are present in the deep layer. The cell behaviors making up spider gastrulation thus appear to show considerable variation, and a wider sampling of taxa is indicated.

RESULTS

We evaluated the model in three species from two families by direct observation of living embryos. Movements of individual cells were traced from timelapse recordings and the origin and fate of the cumulus determined by CM-DiI labeling. We show that there are two distinct regions of internalization: most cells enter the deep layer via the central blastopore but many additional cells ingress via an extra-blastoporal ring, either at the periphery of the germ disc (Latrodectus spp.) or nearer the central field (Cheiracanthium mildei). In all species, the cumulus cells internalize first; this is shown by tracing cells in timelapse, histology, and by CM-DiI injection into the deep layer. Injection very early in gastrulation labels only cumulus mesenchyme cells whereas injections at later stages label non-cumulus mesoderm and endoderm.

CONCLUSIONS

We propose a revised model to accommodate the new data. Our working model has the prospective cumulus cells internalizing first, at the central blastopore. The cumulus cells begin migration before other cells enter the deep layer. This is consistent with early specification of the cumulus and suggests that cell-cell interaction with other deep layer cells is not required for its function. As the cumulus migrates, additional mesendoderm internalizes at two distinct locations: through the central blastopore and at an extra-blastoporal ring. Our work thus demonstrates early, cell-autonomous behavior of the cumulus and variation in subsequent location and timing of cell internalization during gastrulation in spiders.

Phylogeny, species delimitation and convergence in the South American bothriurid scorpion genus Brachistosternus Pocock 1893: Integrating morphology, nuclear and mitochondrial DNA

A phylogenetic analysis of the scorpion genus Brachistosternus Pocock, 1893 (Bothriuridae Simon, 1880) is presented, based on a dataset including 41 of the 43 described species and five outgroups, 116 morphological characters and more than 4150 base-pairs of DNA sequence from the nuclear 18S rDNA and 28S rDNA gene loci, and the mitochondrial 12S rDNA, 16S rDNA, and Cytochrome c Oxidase Subunit I gene loci. Analyses conducted using parsimony, Maximum Likelihood and Bayesian Inference were largely congruent with high support for most clades. The results confirmed the monophyly of Brachistosternus, the nominal subgenus, and subgenus Ministernus Francke, 1985, as in previous analyses based only on morphology, but differed in several other respects. Species from the plains of the Atacama Desert diverged basally whereas the high altitude Andean species radiated from a more derived ancestor, presumably as a consequence of Andean uplift and associated changes in climate. Species limits were assessed among species that contain intraspecific variation (e.g., different morphs), are difficult to separate morphologically, and/or exhibit widespread or disjunct distributions. The extent of convergence in morphological adaptation to life on sandy substrata (psammophily) and the complexity of the male genitalia, or hemispermatophores, was investigated. Psammophily evolved on at least four independent occasions. The lobe regions of the hemispermatophore increased in complexity on three independent occasions, and decreased in complexity on another three independent occasions.

Phylogenomic analysis of spiders reveals nonmonophyly of orb weavers

Spiders constitute one of the most successful clades of terrestrial predators. Their extraordinary diversity, paralleled only by some insects and mites, is often attributed to the use of silk, and, in one of the largest lineages, to stereotyped behaviors for building foraging webs of remarkable biomechanical properties. However, our understanding of higher-level spider relationships is poor and is largely based on morphology. Prior molecular efforts have focused on a handful of genes but have provided little resolution to key questions such as the origin of the orb weavers. We apply a next-generation sequencing approach to resolve spider phylogeny, examining the relationships among its major lineages. We further explore possible pitfalls in phylogenomic reconstruction, including missing data, unequal rates of evolution, and others. Analyses of multiple data sets all agree on the basic structure of the spider tree and all reject the long-accepted monophyly of Orbiculariae, by placing the cribellate orb weavers (Deinopoidea) with other groups and not with the ecribellate orb weavers (Araneoidea). These results imply independent origins for the two types of orb webs (cribellate and ecribellate) or a much more ancestral origin of the orb web with subsequent loss in the so-called RTA clade. Either alternative demands a major reevaluation of our current understanding of the spider evolutionary chronicle.

Evolutionary morphology of the male reproductive system, spermatozoa and seminal fluid of spiders (Araneae, Arachnida)--current knowledge and future directions

The male reproductive system and spermatozoa of spiders are known for their high structural diversity. Spider spermatozoa are flagellate and males transfer them to females in a coiled and encapsulated state using their modified pedipalps. Here, we provide a detailed overview of the present state of knowledge of the primary male reproductive system, sperm morphology and the structural diversity of seminal fluids with a focus on functional and evolutionary implications. Secondly, we conceptualized characters for the male genital system, spermiogenesis and spermatozoa for the first time based on published and new data. In total, we scored 40 characters for 129 species from 56 families representing all main spider clades. We obtained synapomorphies for several taxa including Opisthothelae, Araneomorphae, Dysderoidea, Scytodoidea, Telemidae, Linyphioidea, Mimetidae, Synotaxidae and the Divided Cribellum Clade. Furthermore, we recovered synspermia as a synapomorphy for ecribellate Haplogynae and thus propose Synspermiata as new name for this clade. We hope that these data will not only contribute to future phylogenetic studies but will also stimulate much needed evolutionary studies of reproductive systems in spiders.

Female genital morphology in the secondarily haplogyne spider genus Glenognatha Simon, 1887 (Araneae, Tetragnathidae), with comments on its phylogenetic significance

Female genital morphology of secondarily haplogyne spiders has been poorly studied, hampering the analysis of its possible phylogenetic significance. We conduct a comparative morphological study of 12 species of the secondarily haplogyne spider genus Glenognatha Simon, 1887 using scanning electron microscopy. Representatives of the closely related genera Pachygnatha Sundevall, 1823 and Dyschiriognatha Simon, 1893 were also examined. The female genitalia of Glenognatha, Dyschiriognatha, and Pachygnatha species examined are composed of a spiracle-shape gonopore, a membranous chamber, a pair of copulatory ducts (CD) leading to spermathecae and a large uterus externus (UE). The most significant variation among Glenognatha species, previously unregistered within Araneoidea, is related with the absence or presence of CD and spermathecae. In addition, several characters as the form and distribution of long stem gland ductules and compartmentalization of the UE may be important for phylogenetic inference at species and generic level. Our results corroborate the close relationship between Dyshiriognatha and Glenognatha. A table with potentially informative female genitalic characters for phylogenetic inference within Glenognatha is provided. Understanding the general structure of the female genitalia in secondarily haplogyne taxa is a crucial step in order to propose characters for phylogenetic inference and to understand its possible functional significance.

Testing mitochondrial marker efficacy for DNA barcoding in spiders: a test case using the dwarf spider genus Oedothorax (Araneae : Linyphiidae : Erigoninae)

The present study focusses on comparatively assessing the efficacy for DNA barcoding of the two most commonly used mitochondrial markers (cox1 and 16S) in a genus of erigonine spiders. In total, 53 specimens representing five species, including four multi-sampled species, were sampled from several European localities. Initial evaluation of species monophyly was performed through parsimony and Bayesian phylogenetic analyses. Efficacy of mitochondrial markers was tested using operational (including distance-, tree-based measures and Barcode Gap) and evolutionary criteria (using the General Mixed Yule-coalescent Model) for species delimitation. We propose that the cox1 marker can potentially overestimate analyses of biodiversity and thus might not be the preferred marker for DNA species identification and delimitation methods in Oedothorax. Instead, our results suggest that the 16S marker appears to be a promising candidate for such endeavour. Evaluating the contribution and suitability of markers to the re-identification of species, measured by their recovery of well established morphological species, is critical for future studies and for reliable results in species identification in spiders.

Systematics, phylogeny, and evolution of orb-weaving spiders

The orb-weaving spiders (Orbiculariae) comprise more than 25% of the approximately 44,000 known living spider species and produce a remarkable variety of webs. The wheel-shaped orb web is primitive to this clade, but most Orbiculariae make webs hardly recognizable as orbs. Orb-weavers date at least to the Jurassic. With no evidence for convergence of the orb web, the monophyly of the two typical orb web taxa, the cribellate Deinopoidea and ecribellate Araneoidea, remains problematic, supported only weakly by molecular studies. The sister group of the Orbiculariae also remains elusive. Despite more than 15 years of phylogenetic scrutiny, a fully resolved cladogram of the Orbiculariae families is not yet possible. More comprehensive taxon sampling, comparative morphology, and new molecular markers are required for a better understanding of orb-weaver evolution.

Two new species of the genera Mysmena and Trogloneta (Mysmenidae, Araneae) from Southwestern China

Two new spider species of the family Mysmenidae Petrunkevitch, 1928 are reported from Southwestern China, i.e., Mysmena wawuensis sp. n. (male and female) from Sichuan and Trogloneta yuensis sp. n. (male) from Chongqing. Diagnoses and illustrations of the new species are provided.

Tangled in a sparse spider web: single origin of orb weavers and their spinning work unravelled by denser taxonomic sampling

In order to study the tempo and the mode of spider orb web evolution and diversification, we conducted a phylogenetic analysis using six genetic markers along with a comprehensive taxon sample. The present analyses are the first to recover the monophyly of orb-weaving spiders based solely on DNA sequence data and an extensive taxon sample. We present the first dated orb weaver phylogeny. Our results suggest that orb weavers appeared by the Middle Triassic and underwent a rapid diversification during the end of the Triassic and Early Jurassic. By the second half of the Jurassic, most of the extant orb-weaving families and web designs were already present. The processes that may have given origin to this diversification of lineages and web architectures are discussed. A combination of biotic factors, such as key innovations in web design and silk composition, as well as abiotic environmental changes, may have played important roles in the diversification of orb weavers. Our analyses also show that increased taxon sampling density in both ingroups and outgroups greatly improves phylogenetic accuracy even when extensive data are missing. This effect is particularly important when addition of character data improves gene overlap.