Early Cretaceous greenhouse pumped higher taxa diversification in spiders

Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication

Gene duplication generates new genetic material that can contribute to the evolution of gene regulatory networks and phenotypes. Duplicated genes can undergo subfunctionalization to partition ancestral functions and/or neofunctionalization to assume a new function. We previously found there had been a whole genome duplication (WGD) in an ancestor of arachnopulmonates, the lineage including spiders and scorpions but excluding other arachnids like mites, ticks, and harvestmen. This WGD was evidenced by many duplicated homeobox genes, including two Hox clusters, in spiders. However, it was unclear which homeobox paralogues originated by WGD versus smaller-scale events such as tandem duplications. Understanding this is a key to determining the contribution of the WGD to arachnopulmonate genome evolution. Here we characterized the distribution of duplicated homeobox genes across eight chromosome-level spider genomes. We found that most duplicated homeobox genes in spiders are consistent with an origin by WGD. We also found two copies of conserved homeobox gene clusters, including the Hox, NK, HRO, Irx, and SINE clusters, in all eight species. Consistently, we observed one copy of each cluster was degenerated in terms of gene content and organization while the other remained more intact. Focussing on the NK cluster, we found evidence for regulatory subfunctionalization between the duplicated NK genes in the spider Parasteatoda tepidariorum compared to their single-copy orthologues in the harvestman Phalangium opilio. Our study provides new insights into the relative contributions of multiple modes of duplication to the homeobox gene repertoire during the evolution of spiders and the function of NK genes.

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.

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.

Genomic signatures of recent convergent transitions to social life in spiders

The transition from solitary to social life is a major phenotypic innovation, but its genetic underpinnings are largely unknown. To identify genomic changes associated with this transition, we compare the genomes of 22 spider species representing eight recent and independent origins of sociality. Hundreds of genes tend to experience shifts in selection during the repeated transition to social life. These genes are associated with several key functions, such as neurogenesis, behavior, and metabolism, and include genes that previously have been implicated in animal social behavior and human behavioral disorders. In addition, social species have elevated genome-wide rates of molecular evolution associated with relaxed selection caused by reduced effective population size. Altogether, our study provides unprecedented insights into the genomic signatures of social evolution and the specific genetic changes that repeatedly underpin the evolution of sociality. Our study also highlights the heretofore unappreciated potential of transcriptomics using ethanol-preserved specimens for comparative genomics and phylotranscriptomics.

Karyotype differentiation and male meiosis in European clades of the spider genus Pholcus (Araneae, Pholcidae)

Haplogyne araneomorphs are a diverse spider clade. Their karyotypes are usually predominated by biarmed (i.e., metacentric and submetacentric) chromosomes and have a specific sex chromosome system, X₁X₂Y. These features are probably ancestral for haplogynes. Nucleolus organizer regions (NORs) spread frequently from autosomes to sex chromosomes in these spiders. This study focuses on pholcids (Pholcidae), a highly diverse haplogyne family. Despite considerable recent progress in pholcid cytogenetics, knowledge on many clades remains insufficient including the most species-rich pholcid genus, Pholcus Walckenaer, 1805. To characterize the karyotype differentiation of Pholcus in Europe, we compared karyotypes, sex chromosomes, NORs, and male meiosis of seven species [P.alticeps Spassky, 1932; P.creticus Senglet, 1971; P.dentatus Wunderlich, 1995; P.fuerteventurensis Wunderlich, 1992; P.phalangioides (Fuesslin, 1775); P.opilionoides (Schrank, 1781); P.silvai Wunderlich, 1995] representing the dominant species groups in this region. The species studied show several features ancestral for Pholcus, namely the 2n♂ = 25, the X₁X₂Y system, and a karyotype predominated by biarmed chromosomes. Most taxa have a large acrocentric NOR-bearing pair, which evolved from a biarmed pair by a pericentric inversion. In some lineages, the acrocentric pair reverted to biarmed. Closely related species often differ in the morphology of some chromosome pairs, probably resulting from pericentric inversions and/or translocations. Such rearrangements have been implicated in the formation of reproductive barriers. While the X₁ and Y chromosomes retain their ancestral metacentric morphology, the X₂ chromosome shows a derived (acrocentric or subtelocentric) morphology. Pairing of this element is usually modified during male meiosis. NOR patterns are very diverse. The ancestral karyotype of Pholcus contained five or six terminal NORs including three X chromosome-linked loci. The number of NORs has been frequently reduced during evolution. In the Macaronesian clade, there is only a single NOR-bearing pair. Sex chromosome-linked NORs are lost in Madeiran species and in P.creticus. Our study revealed two cytotypes in the synanthropic species P.phalangioides (Madeiran and Czech), which differ by their NOR pattern and chromosome morphology. In the Czech cytotype, the large acrocentric pair was transformed into a biarmed pair by pericentric inversion.

Comparative mitogenomic analyses provide evolutionary insights into the retrolateral tibial apophysis clade (Araneae: Entelegynae)

The retrolateral tibial apophysis (RTA) clade is the largest spider lineage within Araneae. To better understand the diversity and evolution, we newly determined mitogenomes of ten RTA species from six families and performed a comparative mitogenomics analysis by combining them with 40 sequenced RTA mitogenomes available on GenBank. The ten mitogenomes encoded 37 typical mitochondrial genes and included a large non-coding region (putative control region). Nucleotide composition and codon usage were well conserved within the RTA clade, whereas diversity in sequence length and structural features was observed in control region. A reversal of strand asymmetry in nucleotide composition, i.e., negative AT-skews and positive GC-skews, was observed in each RTA species, likely resulting from mitochondrial gene rearrangements. All protein-coding genes were evolving under purifying selection, except for atp8 whose Ka/Ks was larger than 1, possibly due to positive selection or selection relaxation. Both mutation pressure and natural selection might contribute to codon usage bias of 13 protein-coding genes in the RTA lineage. Phylogenetic analyses based on mitogenomic data recovered a family-level phylogeny within the RTA; {[(Oval calamistrum clade, Dionycha), Marronoid clade], Sparassidae}. This study characterized RTA mitogenomes and provided some new insights into the phylogeny and evolution of the RTA clade.

The Angiosperm Terrestrial Revolution and the origins of modern biodiversity

Biodiversity today has the unusual property that 85% of plant and animal species live on land rather than in the sea, and half of these live in tropical rainforests. An explosive boost to terrestrial diversity occurred from c. 100-50 million years ago, the Late Cretaceous and early Palaeogene. During this interval, the Earth-life system on land was reset, and the biosphere expanded to a new level of productivity, enhancing the capacity and species diversity of terrestrial environments. This boost in terrestrial biodiversity coincided with innovations in flowering plant biology and evolutionary ecology, including their flowers and efficiencies in reproduction; coevolution with animals, especially pollinators and herbivores; photosynthetic capacities; adaptability; and ability to modify habitats. The rise of angiosperms triggered a macroecological revolution on land and drove modern biodiversity in a secular, prolonged shift to new, high levels, a series of processes we name here the Angiosperm Terrestrial Revolution.

Widespread retention of ohnologs in key developmental gene families following whole-genome duplication in arachnopulmonates

Whole-genome duplications (WGDs) have occurred multiple times during animal evolution, including in lineages leading to vertebrates, teleosts, horseshoe crabs, and arachnopulmonates. These dramatic events initially produce a wealth of new genetic material, generally followed by extensive gene loss. It appears, however, that developmental genes such as homeobox genes, signaling pathway components and microRNAs are frequently retained as duplicates (so-called ohnologs) following WGD. These not only provide the best evidence for WGD, but an opportunity to study its evolutionary consequences. Although these genes are well studied in the context of vertebrate WGD, similar comparisons across the extant arachnopulmonate orders are patchy. We sequenced embryonic transcriptomes from two spider species and two amblypygid species and surveyed three important gene families, Hox, Wnt, and frizzled, across these and 12 existing transcriptomic and genomic resources for chelicerates. We report extensive retention of putative ohnologs, further supporting the ancestral arachnopulmonate WGD. We also found evidence of consistent evolutionary trajectories in Hox and Wnt gene repertoires across three of the six arachnopulmonate orders, with interorder variation in the retention of specific paralogs. We identified variation between major clades in spiders and are better able to reconstruct the chronology of gene duplications and losses in spiders, amblypygids, and scorpions. These insights shed light on the evolution of the developmental toolkit in arachnopulmonates, highlight the importance of the comparative approach within lineages, and provide substantial new transcriptomic data for future study.

Phylogenomics reveals accelerated late Cretaceous diversification of bee flies (Diptera: Bombyliidae)

Bombyliidae is a very species-rich and widespread family of parasitoid flies with more than 250 genera classified into 17 extant subfamilies. However, little is known about their evolutionary history or how their present-day diversity was shaped. Transcriptomes of 15 species and anchored hybrid enrichment (AHE) sequence captures of 86 species, representing 94 bee fly species and 14 subfamilies, were used to reconstruct the phylogeny of Bombyliidae. We integrated data from transcriptomes across each of the main lineages in our AHE tree to build a data set with more genes (550 loci versus 216 loci) and higher support levels. Our overall results show strong congruence with the current classification of the family, with 11 out of 14 included subfamilies recovered as monophyletic. Heterotropinae and Mythicomyiinae are successive sister groups to the remainder of the family. We examined the evolution of key morphological characters through our phylogenetic hypotheses and show that neither the "sand chamber subfamilies" nor the "Tomophthalmae" are monophyletic in our phylogenomic analyses. Based on our results, we reinstate two tribes at the subfamily level (Phthiriinae stat. rev. and Ecliminae stat. rev.) and we include the genus Sericosoma Macquart (previously incertae sedis) in the subfamily Oniromyiinae, bringing the total number of bee fly subfamilies to 19. Our dating analyses indicate a Jurassic origin of the family (165-194 Ma), with the sand chamber evolving early in bee fly evolution, in the late Jurassic or mid-Cretaceous (100-165 Ma). We hypothesize that the angiosperm radiation and the hothouse climate established during the late Cretaceous accelerated the diversification of bee flies, by providing an expanded range of resources for the parasitoid larvae and nectarivorous adults.

Repeated colonization, adaptive radiation and convergent evolution in the sheet-weaving spiders (Linyphiidae) of the south Pacific Archipelago of Juan Fernandez

We report on the colonization and diversification of linyphiid spiders in the Pacific oceanic archipelago of Juan Fernandez. About 50 spider species occur naturally in these islands, most of them endemic and about half of them are linyphiids. Linyphiidae includes no fewer than 15 species of Laminacauda and three of Neomaso (with several additional undescribed species in the latter genus), all of them single island endemics. There are three additional linyphiid endemic genera, two monotypic and one, Juanfernandezia, with two species. Unlike the rather uniform somatic morphology and small ground sheet webs of the continental Laminacauda and Neomaso species, the Juan Fernandez endemics exhibit morphological features and life history traits that are very rare or unknown in any other linyphiids. A multi-locus phylogenetic analysis confirms at least five independent Juan Fernandez colonizations of Linyphiidae, two within the same genus, and three of which underwent subsequent local diversification. Different calibrations suggest alternative colonization timelines, some at odds with island ages, but all agree on similar diversification timings of the endemic lineages. Rare phenotypic traits (e.g. gigantism, massive chelicerae or elongated legs) evolved multiple times independently within the islands. Based on the remarkable levels of eco-phenotypic differentiation in locally diversified species showing densely packed distributions, we propose that Laminacauda, and probably Neomaso, constitute a case of adaptive radiation.

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

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

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.

Evolutionary pattern of karyotypes and meiosis in pholcid spiders (Araneae: Pholcidae): implications for reconstructing chromosome evolution of araneomorph spiders

BACKGROUND

Despite progress in genomic analysis of spiders, their chromosome evolution is not satisfactorily understood. Most information on spider chromosomes concerns the most diversified clade, entelegyne araneomorphs. Other clades are far less studied. Our study focused on haplogyne araneomorphs, which are remarkable for their unusual sex chromosome systems and for the co-evolution of sex chromosomes and nucleolus organizer regions (NORs); some haplogynes exhibit holokinetic chromosomes. To trace the karyotype evolution of haplogynes on the family level, we analysed the number and morphology of chromosomes, sex chromosomes, NORs, and meiosis in pholcids, which are among the most diverse haplogyne families. The evolution of spider NORs is largely unknown.

RESULTS

Our study is based on an extensive set of species representing all major pholcid clades. Pholcids exhibit a low 2n and predominance of biarmed chromosomes, which are typical haplogyne features. Sex chromosomes and NOR patterns of pholcids are diversified. We revealed six sex chromosome systems in pholcids (X0, XY, X1X20, X1X2X30, X1X2Y, and X1X2X3X4Y). The number of NOR loci ranges from one to nine. In some clades, NORs are also found on sex chromosomes.

CONCLUSIONS

The evolution of cytogenetic characters was largely derived from character mapping on a recently published molecular phylogeny of the family. Based on an extensive set of species and mapping of their characters, numerous conclusions regarding the karyotype evolution of pholcids and spiders can be drawn. Our results suggest frequent autosome-autosome and autosome-sex chromosome rearrangements during pholcid evolution. Such events have previously been attributed to the reproductive isolation of species. The peculiar X1X2Y system is probably ancestral for haplogynes. Chromosomes of the X1X2Y system differ considerably in their pattern of evolution. In some pholcid clades, the X1X2Y system has transformed into the X1X20 or XY systems, and subsequently into the X0 system. The X1X2X30 system of Smeringopus pallidus probably arose from the X1X20 system by an X chromosome fission. The X1X2X3X4Y system of Kambiwa probably evolved from the X1X2Y system by integration of a chromosome pair. Nucleolus organizer regions have frequently expanded on sex chromosomes, most probably by ectopic recombination. Our data suggest the involvement of sex chromosome-linked NORs in achiasmatic pairing.

Spider Diversification Through Space and Time

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

Tropical Niche Conservatism Explains the Eocene Migration from India to Southeast Asia in Ochyroceratid Spiders

Biological migrations between India and Southeast (SE) Asia provide an ideal system for exploring the effects of geology and climate on species ranges. Geologists have confirmed that the direct collision between India and Eurasia occurred in the Early Eocene, but most migrations occurred between the Indian subcontinent and SE Asia rather than the former and the southern margin of Eurasia. To explain this seemingly paradoxical disconnect between the routes of plate movement and biological migration, we studied the evolutionary history of the tropical spider family Ochyroceratidae based on 101 globally distributed species. We infer a robust dated phylogeny using both transcriptomic data and a data set of classical markers and relate these to biogeographic and climatic analyses. Our results indicate that the monophyly of Ochyroceratidae is strongly supported, and the divergence times suggest a Cretaceous Gondwanan origin of the family. Reconstructed biogeographic histories support a dispersal event from the Indian subcontinent to islands of SE Asia 55-38 Ma. Climatic analyses and the fossil record reveal that ochyroceratids are characterized by a high degree of tropical niche conservatism, and that the ancestor of the Indian and SE Asian clades originated in very warm, wet environments. Early Eocene tropical, perhumid climates in India, and SE Asia may have facilitated ochyroceratid migration, whereas the dry or seasonal climate extending from the eastern coast of China to Central Asia may have acted as a barrier, preventing dispersal. Our analyses suggest that climate plays a more important role than geology in biological migration from the Indian subcontinent to SE Asia, providing new insights into the Indian-Asian biogeographic link. [Biogeography; ecology; geological connections; macroevolution; paleoclimate.].

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.

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

The common ancestor of spiders likely used silk to line burrows or make simple webs, with specialized spinning organs and aerial webs originating with the evolution of the megadiverse "true spiders" (Araneomorphae). The base of the araneomorph tree also concentrates the greatest number of changes in respiratory structures, a character system whose evolution is still poorly understood, and that might be related to the evolution of silk glands. Emphasizing a dense sampling of multiple araneomorph lineages where tracheal systems likely originated, we gathered genomic-scale data and reconstructed a phylogeny of true spiders. This robust phylogenomic framework was used to conduct maximum likelihood and Bayesian character evolution analyses for respiratory systems, silk glands, and aerial webs, based on a combination of original and published data. Our results indicate that in true spiders, posterior book lungs were transformed into morphologically similar tracheal systems six times independently, after the evolution of novel silk gland systems and the origin of aerial webs. From these comparative data, we put forth a novel hypothesis that early-diverging web-building spiders were faced with new energetic demands for spinning, which prompted the evolution of similar tracheal systems via convergence; we also propose tests of predictions derived from this hypothesis.[Book lungs; discrete character evolution; respiratory systems; silk; spider web evolution; ultraconserved elements.].

Taxonomic revision of Telemidae (Arachnida, Araneae) from East and Southeast Asia

Species of the spider family Telemidae Fage, 1913 from East and Southeast Asia are revised. Four new genera are erected: Mekonglema Zhao & Li, gen. nov. with the type species Mekonglemabailang Zhao & Li, sp. nov. (♂♀, Yunnan, China), Siamlema Zhao & Li, gen. nov. with the type species Siamlemachanghai Zhao & Li, sp. nov. (♂♀, southern Thailand), Sundalema Zhao & Li, gen. nov. with the type species Sundalemabonjol Zhao & Li, sp. nov. (♂♀, Sumatra), and Zhuanlema Zhao & Li, gen. nov. with the type species Zhuanlemapeteri Zhao & Li, sp. nov. (♂♀, northern Laos). Eight additional new species are described: Mekonglemakaorao Zhao & Li, sp. nov. (♂♀, northern Laos), M.walayaku Zhao & Li, sp. nov. (♂♀, Yunnan, China), M.yan Zhao & Li, sp. nov. (♂♀, Yunnan, China), Pinelemadaguaiwan Zhao & Li, sp. nov. (♂♀, Guangxi, China), P.shiba Zhao & Li, sp. nov. (♂♀, Guangxi, China), P.tham Zhao & Li, sp. nov. (♂♀, northern Laos), Siamlemasuea Zhao & Li, sp. nov. (♂♀, southern Thailand), and Sundalemakhaorakkiat Zhao & Li, sp. nov. (♂♀, southern Thailand). Thirty species are transferred from the genus Telema Simon, 1882 to the genera Pinelema Wang & Li, 2012, Sundalemagen. nov., and Telemofila Wunderlich, 1995. Seychelliaxinpingi Lin & Li, 2008 is transferred to Mekonglemagen. nov. as M.xinpingicomb. nov. Furthermore, the genus Pinelema is divided into seven species groups based on male morphological characters.

A Cambrian-Ordovician Terrestrialization of Arachnids

Understanding the temporal context of terrestrialization in chelicerates depends on whether terrestrial groups, the traditional Arachnida, have a single origin and whether or not horseshoe crabs are primitively or secondarily marine. Molecular dating on a phylogenomic tree that recovers arachnid monophyly, constrained by 27 rigorously vetted fossil calibrations, estimates that Arachnida originated during the Cambrian or Ordovician. After the common ancestor colonized the land, the main lineages appear to have rapidly radiated in the Cambrian-Ordovician boundary interval, coinciding with high rates of molecular evolution. The highest rates of arachnid diversification are detected between the Permian and Early Cretaceous. A pattern of ancient divergence estimates for terrestrial arthropod groups in the Cambrian while the oldest fossils are Silurian (seen in both myriapods and arachnids) is mirrored in the molecular and fossil records of land plants. We suggest the discrepancy between molecular and fossil evidence for terrestrialization is likely driven by the extreme sparseness of terrestrial sediments in the rock record before the late Silurian.

The fossil record of spiders revisited: implications for calibrating trees and evidence for a major faunal turnover since the Mesozoic

Studies in evolutionary biology and biogeography increasingly rely on the estimation of dated phylogenetic trees using molecular clocks. In turn, the calibration of such clocks is critically dependent on external evidence (i.e. fossils) anchoring the ages of particular nodes to known absolute ages. In recent years, a plethora of new fossil spiders, especially from the Mesozoic, have been described, while the number of studies presenting dated spider phylogenies based on fossil calibrations increased sharply. We critically evaluate 44 of these studies, which collectively employed 67 unique fossils in 180 calibrations. Approximately 54% of these calibrations are problematic, particularly regarding unsupported assignment of fossils to extant clades (44%) and crown (rather than stem) dating (9%). Most of these cases result from an assumed equivalence between taxonomic placement of fossils and their phylogenetic position. To overcome this limitation, we extensively review the literature on fossil spiders, with a special focus on putative synapomorphies and the phylogenetic placement of fossil species with regard to their importance for calibrating higher taxa (families and above) in the spider tree of life. We provide a curated list including 41 key fossils intended to be a basis for future estimations of dated spider phylogenies. In a second step, we use a revised set of 23 calibrations to estimate a new dated spider tree of life based on transcriptomic data. The revised placement of key fossils and the new calibrated tree are used to resolve a long-standing debate in spider evolution - we tested whether there has been a major turnover in the spider fauna between the Mesozoic and Cenozoic. At least 17 (out of 117) extant families have been recorded from the Cretaceous, implying that at least 41 spider lineages in the family level or above crossed the Cretaeous-Paleogene (K-Pg) boundary. The putative phylogenetic affinities of families known only from the Mesozoic suggest that at least seven Cretaceous families appear to have no close living relatives and might represent extinct lineages. There is no unambiguous fossil evidence of the retrolateral tibial apophysis clade (RTA-clade) in the Mesozoic, although molecular clock analyses estimated the major lineages within this clade to be at least ∼100 million years old. Our review of the fossil record supports a major turnover showing that the spider faunas in the Mesozoic and the Cenozoic are very distinct at high taxonomic levels, with the Mesozoic dominated by Palpimanoidea and Synspermiata, while the Cenozoic is dominated by Araneoidea and RTA-clade spiders.

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.

On the genera Qiongocera and Relictocera (Araneae, Psilodercidae) from Southeast Asia

Four new species are described in two psilodercid genera, Qiongocera Li & Li, 2017 and Relictocera Li & Li, 2017: Qiongoceraluoxuan Li & Li, sp. nov. (♂♀) from China, Relictocerawugen Li & Li, sp. nov. (♂♀) and R.sigen Li & Li, sp. nov. (♂) from Vietnam, and R.qianzi Li & Li, sp. nov. (♂♀) from Thailand. These genera were previously thought to be monotypic. In addition, one species of the genus Merizocera Fage, 1912 is transferred to Relictocera: Relictoceramus (Deeleman-Reinhold, 1995), comb. nov. (♂♀). The types of the new species are deposited in the Institute of Zoology, Chinese Academy of Sciences (IZCAS) in Beijing.