Broken Ring Speciation in California Mygalomorph Spiders (Nemesiidae, Calisoga).

AbstractIdealized ring species, with approximately continuous gene flow around a geographic barrier but singular reproductive isolation at a ring terminus, are rare in nature. A broken ring species model preserves the geographic setting and fundamental features of an idealized model but accommodates varying degrees of gene flow restriction over complex landscapes through evolutionary time. Here we examine broken ring species dynamics in Calisoga spiders, which, like the classic ring species Ensatina salamanders, are distributed around the Central Valley of California. Using nuclear and mitogenomic data, we test key predictions of common ancestry, ringlike biogeography, biogeographic timing, population connectivity, and terminal overlap. We show that a ring complex of populations shares a single common ancestor, and from an ancestral area in the Sierra Nevada mountains, two distributional and phylogenomic arms encircle the Central Valley. Isolation by distance occurs along these distributional arms, although gene flow restriction is also evident. Where divergent lineages meet in the South Coast Ranges, we find rare lineage sympatry, without evidence for nuclear gene flow and with clear evidence for morphological and ecological divergence. We discuss general insights provided by broken ring species and how such a model could be explored and extended in other systems and future studies.

Phylogeny and biogeography of harmochirine jumping spiders (Araneae: Salticidae).

We use ultraconserved elements (UCE) and Sanger data to study the phylogeny, age, and biogeographical history of harmochirine jumping spiders, a group that includes the species-rich genus Habronattus, whose remarkable courtship has made it the focus of studies of behaviour, sexual selection, and diversification. We recovered 1947 UCE loci from 43 harmochirine taxa and 4 outgroups, yielding a core dataset of 193 UCEs with at least 50 % occupancy. Concatenated likelihood and ASTRAL analyses confirmed the separation of harmochirines into two major clades, here designated the infratribes Harmochirita and Pellenita. Most are African or Eurasian with the notable exception of a clade of pellenites containing Habronattus and Pellenattus of the Americas and Havaika and Hivanua of the Pacific Islands. Biogeographical analysis using the DEC model favours a dispersal of the clade's ancestor from Eurasia to the Americas, from which Havaika's ancestor dispersed to Hawaii and Hivanua's ancestor to the Marquesas Islands. Divergence time analysis on 32 loci with 85 % occupancy, calibrated by fossils and island age, dates the dispersal to the Americas at approximately 4 to 6 million years ago. The explosive radiation of Habronattus perhaps began only about 4 mya. The phylogeny clarifies both the evolution of sexual traits (e.g., the terminal apophyses was enlarged in Pellenes and not subsequently lost) and the taxonomy. Habronattus is confirmed as monophyletic. Pellenattus is raised to the status of genus, and 13 species moved into it as new combinations. Bianor stepposus Logunov, 1991 is transferred to Sibianor, and Pellenes bulawayoensis Wesolowska, 1999 is transferred to Neaetha. A molecular clock rate estimate for spider UCEs is presented and its utility to inform prior distributions is discussed.

Species delimitation, biogeography, and natural history of dwarf funnel web spiders (Mygalomorphae, Hexurellidae, Hexurella) from the United States / Mexico borderlands.

The rarely encountered spider genus Hexurella Gertsch & Platnick, 1979 includes some of the smallest mygalomorph spiders in the world, with four poorly known taxa from central and southeastern montane Arizona, southern California, and northern Baja California Norte. At time of description the genus was known from fewer than 20 individuals, with sparse natural history information suggesting a vagrant, web-building, litter-dwelling natural history. Here the first published taxonomic and natural history information for this taxon is provided in more than 50 years, working from extensive new geographic sampling, consideration of male and female morphology, and sequence capture-based nuclear phylogenomics and mitogenomics. Several new species are easily diagnosed based on distinctive male morphologies, while a complex of populations from central and northern Arizona required an integrative combination of genomic algorithmic species delimitation analyses and morphological study. Four new species are described, including H.ephedrasp. nov., H.uwiiltilsp. nov., H.xericasp. nov., and H.zassp. nov. Females of H.encina Gertsch & Platnick, 1979 are also described for the first time. It is predicted that additional new species will ultimately be found in the mountains of central and northwestern Arizona, northern mainland Mexico, and the Mojave Desert of California.

New species in old mountains: integrative taxonomy reveals ten new species and extensive short-range endemism in Nesticus spiders (Araneae, Nesticidae) from the southern Appalachian Mountains.

This revision is based on sampling efforts over the past three decades in the southern Appalachian Mountains which have provided Nesticus (Araneae, Nesticidae) collections of approximately 2100 adult specimens from more than 475 unique collecting events. Using a "morphology first" framework we examined recently collected specimens plus museum material to formulate morphology-based species hypotheses for putative new taxa (discovery phase). Using sequence capture of nuclear ultraconserved elements (UCEs) we analyzed 801 nuclear loci to validate new (and prior) morphology-based species hypotheses (validation phase) and reconstructed a robust backbone phylogeny including all described and new species. Sanger sequencing and UCE-bycatch were also used to gather mitochondrial data for more than 240 specimens. Based on our integrative taxonomic framework ten new Nesticus species are herein described, including N.binfordaesp. nov., N.bondisp. nov., N.caneisp. nov., N.cherokeensissp. nov., N.dellingerisp. nov., N.dykemanaesp. nov., N.jemisinaesp. nov., N.lowderisp. nov., N.roanensissp. nov., and N.templetonisp. nov. Previously unknown males are also described for N.bishopi Gertsch, 1984, N.crosbyi Gertsch, 1984, and N.silvanus Gertsch, 1984, as well as the previously unknown female for N.mimus Gertsch, 1984. Based on combined evidence N.cooperi Gertsch, 1984 is placed in synonymy with N.reclusus Gertsch, 1984. Overall, the montane radiation of Appalachian Nesticus reveals a general lack of species sympatry and compelling biogeographic patterns. Several regional Nesticus taxa are rare, microendemic habitat specialists that deserve conservation attention and detailed future monitoring as conservation sentinels.

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, Hypochilusxomote sp. nov. We also emphasize the conservation issues that face several microendemic, habitat-specialized species in this remarkable genus.

Using natural history to guide supervised machine learning for cryptic species delimitation with genetic data.

The diversity of biological and ecological characteristics of organisms, and the underlying genetic patterns and processes of speciation, makes the development of universally applicable genetic species delimitation methods challenging. Many approaches, like those incorporating the multispecies coalescent, sometimes delimit populations and overestimate species numbers. This issue is exacerbated in taxa with inherently high population structure due to low dispersal ability, and in cryptic species resulting from nonecological speciation. These taxa present a conundrum when delimiting species: analyses rely heavily, if not entirely, on genetic data which over split species, while other lines of evidence lump. We showcase this conundrum in the harvester Theromaster brunneus, a low dispersal taxon with a wide geographic distribution and high potential for cryptic species. Integrating morphology, mitochondrial, and sub-genomic (double-digest RADSeq and ultraconserved elements) data, we find high discordance across analyses and data types in the number of inferred species, with further evidence that multispecies coalescent approaches over split. We demonstrate the power of a supervised machine learning approach in effectively delimiting cryptic species by creating a "custom" training data set derived from a well-studied lineage with similar biological characteristics as Theromaster. This novel approach uses known taxa with particular biological characteristics to inform unknown taxa with similar characteristics, using modern computational tools ideally suited for species delimitation. The approach also considers the natural history of organisms to make more biologically informed species delimitation decisions, and in principle is broadly applicable for taxa across the tree of life.

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.

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.].

Sitticine jumping spiders: phylogeny, classification, and chromosomes (Araneae, Salticidae, Sitticini).

The systematics of sitticine jumping spiders is reviewed, with a focus on the Palearctic and Nearctic regions, in order to revise their generic classification, clarify the species of one region (Canada), and study their chromosomes. A genome-wide molecular phylogeny of 23 sitticine species, using more than 700 loci from the arachnid Ultra-Conserved Element (UCE) probeset, confirms the Neotropical origins of sitticines, whose basal divergence separates the new subtribeAillutticina (a group of five Neotropical genera) from the subtribe Sitticina (five genera of Eurasia and the Americas). The phylogeny shows that most Eurasian sitticines form a relatively recent and rapid radiation, which we unite into the genus Attulus Simon, 1868, consisting of the subgenera Sitticus Simon, 1901 (seven described species), Attulus (41 described species), and Sittilong Prószynski, 2017 (one species). Five species of Attulus occur natively in North America, presumably through dispersals back from the Eurasian radiation, but an additional three species were more recently introduced from Eurasia. Attus palustris Peckham & Peckham, 1883 is considered to be a full synonym of Euophrys floricola C. L. Koch, 1837 (not a distinct subspecies). Attus sylvestris Emerton, 1891 is removed from synonymy and recognized as a senior synonym of Sitticus magnus Chamberlin & Ivie, 1944. Thus, the five native Attulus in North America are Attulus floricola, A. sylvestris, A. cutleri, A. striatus, and A. finschi. The other sitticines of Canada and the U.S.A. are placed in separate genera, all of which arose from a Neotropical radiation including Jollas Simon, 1901 and Tomis F.O.Pickard-Cambridge, 1901: (1) Attinella Banks, 1905 (A. dorsata, A. concolor, A. juniperi), (2) Tomis (T. welchi), and (3) Sittisax Prószynski, 2017 (S. ranieri). All Neotropical and Caribbean "Sitticus" are transferred to either Jollas (12 species total) or Tomis (14 species). Attinella (three species) and Tomis are both removed from synonymy with Sitticus; the synonymy of Sitticus cabellensis Prószynski, 1971 with Pseudattulus kratochvili Caporiacco, 1947 is restored; Pseudattulus Caporiacco, 1947 is synonymized with Tomis. Six generic names are newly synonymized with Attulus and one with Attinella. Two Neotropical species are described as new, Jollas cupreus sp. nov. and Tomis manabita sp. nov. Forty-six new combinations are established and three are restored. Three species synonymies are restored, one is new, and two are rejected. Across this diversity of species is a striking diversification of chromosome complements, with X-autosome fusions occurring at least four times to produce neo-Y sex chromosome systems (X1X2Y and X1X2X3Y), some of which (Sittisax ranieri and S. saxicola) are sufficiently derived as to no longer preserve the simple traces of ancestral X material. The correlated distribution of neo-Y and a base autosome number of 28 suggests that neo-Y origins occurred preferentially in lineages with the presence of an extra pair of autosomes.

Phylogenetic Systematics and Evolution of the Spider Infraorder Mygalomorphae Using Genomic Scale Data.

The infraorder Mygalomorphae is one of the three main lineages of spiders comprising over 3000 nominal species. This ancient group has a worldwide distribution that includes among its ranks large and charismatic taxa such as tarantulas, trapdoor spiders, and highly venomous funnel-web spiders. Based on past molecular studies using Sanger-sequencing approaches, numerous mygalomorph families (e.g., Hexathelidae, Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae) have been identified as non-monophyletic. However, these data were unable to sufficiently resolve the higher-level (intra- and interfamilial) relationships such that the necessary changes in classification could be made with confidence. Here, we present a comprehensive phylogenomic treatment of the spider infraorder Mygalomorphae. We employ 472 loci obtained through anchored hybrid enrichment to reconstruct relationships among all the mygalomorph spider families and estimate the timeframe of their diversification. We sampled nearly all currently recognized families, which has allowed us to assess their status, and as a result, propose a new classification scheme. Our generic-level sampling has also provided an evolutionary framework for revisiting questions regarding silk use in mygalomorph spiders. The first such analysis for the group within a strict phylogenetic framework shows that a sheet web is likely the plesiomorphic condition for mygalomorphs, as well as providing insights to the ancestral foraging behavior for all spiders. Our divergence time estimates, concomitant with detailed biogeographic analysis, suggest that both ancient continental-level vicariance and more recent dispersal events have played an important role in shaping modern day distributional patterns. Based on our results, we relimit the generic composition of the Ctenizidae, Cyrtaucheniidae, Dipluridae, and Nemesiidae. We also elevate five subfamilies to family rank: Anamidae (NEW RANK), Euagridae (NEW RANK), Ischnothelidae (NEW RANK), Pycnothelidae (NEW RANK), and Bemmeridae (NEW RANK). Three families Entypesidae (NEW FAMILY), Microhexuridae (NEW FAMILY), and Stasimopidae (NEW FAMILY), and one subfamily Australothelinae (NEW SUBFAMILY) are newly proposed. Such a major rearrangement in classification, recognizing nine newly established family-level rank taxa, is the largest the group has seen in over three decades. [Biogeography; molecular clocks; phylogenomics; spider web foraging; taxonomy.].

Evolutionary divergences mirror Pleistocene paleodrainages in a rapidly-evolving complex of oasis-dwelling jumping spiders (Salticidae, Habronattus tarsalis).

We aimed to understand the diversification history of jumping spiders in the Habronattus tarsalis species complex, with particular emphasis on how history in this system might illuminate biogeographic patterns and processes in deserts of the western United States. Desert populations of H. tarsalis are now confined to highly discontinuous oasis-like habitats, but these habitats would have been periodically more connected during multiple pluvial periods of the Pleistocene. We estimated divergence times using relaxed molecular clock analyses of published transcriptome datasets. Geographic patterns of diversification history were assessed using phylogenetic and cluster analyses of original sequence capture, RADSeq and morphological data. Clock analyses of multiple replicate transcriptome datasets suggest mid- to late-Pleistocene divergence dates within the H. tarsalis group complex. Coalescent and concatenated phylogenetic analyses indicate four early-diverging lineages (H. mustaciata, H. ophrys, and H. tarsalis from the Lahontan and Owens drainage basins), with remaining samples separated into larger clades from the Mojave desert, and western populations from the California Floristic Province of California and northern Baja California. Focusing on desert populations, there is a strong correspondence between RAD lineages and modern and/or paleodrainages, mirrored more finely in STRUCTURE and machine learning results. Non-metric multidimensional scaling analysis reveals strong congruence between morphological clusters and genetic lineages, whether the latter represent previously described species or H. tarsalis RAD lineages. Here we have uncovered a system that adds to our regional biogeographic knowledge in unique ways, using multiple types of evidence in a broadly-distributed terrestrial taxon. At the same time, we have discovered rapid evolution of both novel morphological forms and diverging genetic lineages. The hierarchical nature of variation in the H. tarsalis complex, the minute range sizes of many forms, the high likelihood that geographic distributions have shrunk and expanded through time, and signs of introgression all align with an ephemeral speciation model.

A demonstration of unsupervised machine learning in species delimitation.

One major challenge to delimiting species with genetic data is successfully differentiating population structure from species-level divergence, an issue exacerbated in taxa inhabiting naturally fragmented habitats. Many fields of science are now using machine learning, and in evolutionary biology supervised machine learning has recently been used to infer species boundaries. These supervised methods require training data with associated labels. Conversely, unsupervised machine learning (UML) uses inherent data structure and does not require user-specified training labels, potentially providing more objectivity in species delimitation. In the context of integrative taxonomy, we demonstrate the utility of three UML approaches (random forests, variational autoencoders, t-distributed stochastic neighbor embedding) for species delimitation in an arachnid taxon with high population genetic structure (Opiliones, Laniatores, Metanonychus). We find that UML approaches successfully cluster samples according to species-level divergences and not high levels of population structure, while model-based validation methods severely over-split putative species. UML offers intuitive data visualization in two-dimensional space, the ability to accommodate various data types, and has potential in many areas of systematic and evolutionary biology. We argue that machine learning methods are ideally suited for species delimitation and may perform well in many natural systems and across taxa with diverse biological characteristics.

Phylogenomic analysis and revised classification of atypoid mygalomorph spiders (Araneae, Mygalomorphae), with notes on arachnid ultraconserved element loci.

The atypoid mygalomorphs include spiders from three described families that build a diverse array of entrance web constructs, including funnel-and-sheet webs, purse webs, trapdoors, turrets and silken collars. Molecular phylogenetic analyses have generally supported the monophyly of Atypoidea, but prior studies have not sampled all relevant taxa. Here we generated a dataset of ultraconserved element loci for all described atypoid genera, including taxa (Mecicobothrium and Hexurella) key to understanding familial monophyly, divergence times, and patterns of entrance web evolution. We show that the conserved regions of the arachnid UCE probe set target exons, such that it should be possible to combine UCE and transcriptome datasets in arachnids. We also show that different UCE probes sometimes target the same protein, and under the matching parameters used here show that UCE alignments sometimes include non-orthologs. Using multiple curated phylogenomic matrices we recover a monophyletic Atypoidea, and reveal that the family Mecicobothriidae comprises four separate and divergent lineages. Fossil-calibrated divergence time analyses suggest ancient Triassic (or older) origins for several relictual atypoid lineages, with late Cretaceous/early Tertiary divergences within some genera indicating a high potential for cryptic species diversity. The ancestral entrance web construct for atypoids, and all mygalomorphs, is reconstructed as a funnel-and-sheet web.

Sequence capture phylogenomics of eyeless Cicurina spiders from Texas caves, with emphasis on US federally-endangered species from Bexar County (Araneae, Hahniidae).

Morphological, mitochondrial, and nuclear phylogenomic data were combined to address phylogenetic and species delimitation questions in cave-limited Cicurina spiders from central Texas. Special effort was focused on specimens and cave locations in the San Antonio region (Bexar County), home to four eyeless species listed as US Federally Endangered. Sequence capture experiments resulted in the recovery of ~200-400 homologous ultra-conserved element (UCE) nuclear loci across taxa, and nearly complete COI mitochondrial DNA sequences from the same set of individuals. Some of these nuclear and mitochondrial sequences were recovered from "standard" museum specimens without special preservation of DNA material, including museum specimens preserved in the 1990s. Multiple phylogenetic analyses of the UCE data agree in the recovery of two major lineages of eyeless Cicurina in Texas. These lineages also differ in mitochondrial clade membership, female genitalic morphology, degree of troglomorphy (as measured by relative leg length), and are mostly allopatric across much of Texas. Rare sympatry was confirmed in Bexar County, where members of the two major clades sometimes co-exist in the same karst feature. Both nuclear phylogenomic and mitochondrial data indicate the existence of undescribed species from the San Antonio region, although further sampling and collection of adult specimens is needed to explicitly test these hypotheses. Our data support the two following species synonymies (Cicurina venii Gertsch, 1992 = Cicurina madla Gertsch, 1992; Cicurina loftini Cokendolpher, 2004 = Cicurina vespera Gertsch, 1992), formally proposed here. Overall, our taxonomy-focused research has many important conservation implications, and again highlights the fundamental importance of robust taxonomy in conservation research.

A stable phylogenomic classification of Travunioidea (Arachnida, Opiliones, Laniatores) based on sequence capture of ultraconserved elements.

Molecular phylogenetics has transitioned into the phylogenomic era, with data derived from next-generation sequencing technologies allowing unprecedented phylogenetic resolution in all animal groups, including understudied invertebrate taxa. Within the most diverse harvestmen suborder, Laniatores, most relationships at all taxonomic levels have yet to be explored from a phylogenomics perspective. Travunioidea is an early-diverging lineage of laniatorean harvestmen with a Laurasian distribution, with species distributed in eastern Asia, eastern and western North America, and south-central Europe. This clade has had a challenging taxonomic history, but the current classification consists of ~77 species in three families, the Travuniidae, Paranonychidae, and Nippononychidae. Travunioidea classification has traditionally been based on structure of the tarsal claws of the hind legs. However, it is now clear that tarsal claw structure is a poor taxonomic character due to homoplasy at all taxonomic levels. Here, we utilize DNA sequences derived from capture of ultraconserved elements (UCEs) to reconstruct travunioid relationships. Data matrices consisting of 317-677 loci were used in maximum likelihood, Bayesian, and species tree analyses. Resulting phylogenies recover four consistent and highly supported clades; the phylogenetic position and taxonomic status of the enigmatic genus Yuria is less certain. Based on the resulting phylogenies, a revision of Travunioidea is proposed, now consisting of the Travuniidae, Cladonychiidae, Paranonychidae (Nippononychidae is synonymized), and the new family Cryptomastridae Derkarabetian & Hedin, fam. n., diagnosed here. The phylogenetic utility and diagnostic features of the intestinal complex and male genitalia are discussed in light of phylogenomic results, and the inappropriateness of the tarsal claw in diagnosing higher-level taxa is further corroborated.

Population genomics and geographical parthenogenesis in Japanese harvestmen (Opiliones, Sclerosomatidae, Leiobunum).

Naturally occurring population variation in reproductive mode presents an opportunity for researchers to test hypotheses regarding the evolution of sex. Asexual reproduction frequently assumes a geographical pattern, in which parthenogenesis-dominated populations are more broadly dispersed than their sexual conspecifics. We evaluate the geographical distribution of genomic signatures associated with parthenogenesis using nuclear and mitochondrial DNA sequence data from two Japanese harvestman sister taxa, Leiobunum manubriatum and Leiobunum globosum. Asexual reproduction is putatively facultative in these species, and female-biased localities are common in habitat margins. Past karyotypic and current cytometric work indicates L. globosum is entirely tetraploid, while L. manubriatum may be either diploid or tetraploid. We estimated species phylogeny, genetic differentiation, diversity, and mitonuclear discordance in females collected across the species range in order to identify range expansion toward marginal habitat, potential for hybrid origin, and persistence of asexual lineages. Our results point to northward expansion of a tetraploid ancestor of L. manubriatum and L. globosum, coupled with support for greater male gene flow in southern L. manubriatum localities. Specimens from localities in the Tohoku and Hokkaido regions were indistinct, particularly those of L. globosum, potentially due to little mitochondrial differentiation or haplotypic variation. Although L. manubriatum overlaps with L. globosum across its entire range, L. globosum was reconstructed as monophyletic with strong support using mtDNA, and marginal support with nuclear loci. Ultimately, we find evidence for continued sexual reproduction in both species and describe opportunities to clarify the rate and mechanism of parthenogenesis.

Phylogenomic reclassification of the world's most venomous spiders (Mygalomorphae, Atracinae), with implications for venom evolution.

Here we show that the most venomous spiders in the world are phylogenetically misplaced. Australian atracine spiders (family Hexathelidae), including the notorious Sydney funnel-web spider Atrax robustus, produce venom peptides that can kill people. Intriguingly, eastern Australian mouse spiders (family Actinopodidae) are also medically dangerous, possessing venom peptides strikingly similar to Atrax hexatoxins. Based on the standing morphology-based classification, mouse spiders are hypothesized distant relatives of atracines, having diverged over 200 million years ago. Using sequence-capture phylogenomics, we instead show convincingly that hexathelids are non-monophyletic, and that atracines are sister to actinopodids. Three new mygalomorph lineages are elevated to the family level, and a revised circumscription of Hexathelidae is presented. Re-writing this phylogenetic story has major implications for how we study venom evolution in these spiders, and potentially genuine consequences for antivenom development and bite treatment research. More generally, our research provides a textbook example of the applied importance of modern phylogenomic research.

Cryptic elevational zonation in trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus janus complex) from the California southern Sierra Nevada.

The relative roles of ecological niche conservatism versus niche divergence in promoting montane speciation remains an important topic in biogeography. Here, our aim was to test whether lineage diversification in a species complex of trapdoor spiders corresponds with riverine barriers or with an ecological gradient associated with elevational tiering. Aliatypus janus was sampled from throughout its range, with emphasis on populations in the southern Sierra Nevada Mountains of California. We collected multi-locus genetic data to generate a species tree for A. janus and its close relatives. Coalescent based hypothesis tests were conducted to determine if genetic breaks within A. janus conform to riverine barriers. Ecological niche models (ENM) under current and Last Glacial Maximum (LGM) conditions were generated and hypothesis tests of niche conservatism and divergence were performed. Coalescent analyses reveal deeply divergent genetic lineages within A. janus, likely corresponding to cryptic species. Two primary lineages meet along an elevational gradient on the western slopes of the southern Sierra Nevada Mountains. ENMs under both current and LGM conditions indicate that these groups occupy largely non-overlapping niches. ENM hypothesis testing rejected niche identity between the two groups, and supported a sharp ecological gradient occurring where the groups meet. However, the niche similarity test indicated that the two groups may not inhabit different background niches. The Sierra Nevada Mountains provide a natural laboratory for simultaneously testing ecological niche divergence and conservatism and their role in speciation across a diverse range of taxa. Aliatypus janus represents a species complex with cryptic lineages that may have diverged due to parapatric speciation along an ecological gradient, or been maintained by the evolution of ecological niche differences following allopatric speciation.

Comparative transcriptomics of Entelegyne spiders (Araneae, Entelegynae), with emphasis on molecular evolution of orphan genes.

Next-generation sequencing technology is rapidly transforming the landscape of evolutionary biology, and has become a cost-effective and efficient means of collecting exome information for non-model organisms. Due to their taxonomic diversity, production of interesting venom and silk proteins, and the relative scarcity of existing genomic resources, spiders in particular are excellent targets for next-generation sequencing (NGS) methods. In this study, the transcriptomes of six entelegyne spider species from three genera (Cicurina travisae, C. vibora, Habronattus signatus, H. ustulatus, Nesticus bishopi, and N. cooperi) were sequenced and de novo assembled. Each assembly was assessed for quality and completeness and functionally annotated using gene ontology information. Approximately 100 transcripts with evidence of homology to venom proteins were discovered. After identifying more than 3,000 putatively orthologous genes across all six taxa, we used comparative analyses to identify 24 instances of positively selected genes. In addition, between ~ 550 and 1,100 unique orphan genes were found in each genus. These unique, uncharacterized genes exhibited elevated rates of amino acid substitution, potentially consistent with lineage-specific adaptive evolution. The data generated for this study represent a valuable resource for future phylogenetic and molecular evolutionary research, and our results provide new insight into the forces driving genome evolution in taxa that span the root of entelegyne spider phylogeny.

The spider tree of life: phylogeny of Araneae based on target-gene analyses from an extensive taxon sampling.

We present a phylogenetic analysis of spiders using a dataset of 932 spider species, representing 115 families (only the family Synaphridae is unrepresented), 700 known genera, and additional representatives of 26 unidentified or undescribed genera. Eleven genera of the orders Amblypygi, Palpigradi, Schizomida and Uropygi are included as outgroups. The dataset includes six markers from the mitochondrial (12S, 16S, COI) and nuclear (histone H3, 18S, 28S) genomes, and was analysed by multiple methods, including constrained analyses using a highly supported backbone tree from transcriptomic data. We recover most of the higher-level structure of the spider tree with good support, including Mesothelae, Opisthothelae, Mygalomorphae and Araneomorphae. Several of our analyses recover Hypochilidae and Filistatidae as sister groups, as suggested by previous transcriptomic analyses. The Synspermiata are robustly supported, and the families Trogloraptoridae and Caponiidae are found as sister to the Dysderoidea. Our results support the Lost Tracheae clade, including Pholcidae, Tetrablemmidae, Diguetidae, Plectreuridae and the family Pacullidae (restored status) separate from Tetrablemmidae. The Scytodoidea include Ochyroceratidae along with Sicariidae, Scytodidae, Drymusidae and Periegopidae; our results are inconclusive about the separation of these last two families. We did not recover monophyletic Austrochiloidea and Leptonetidae, but our data suggest that both groups are more closely related to the Cylindrical Gland Spigot clade rather than to Synspermiata. Palpimanoidea is not recovered by our analyses, but also not strongly contradicted. We find support for Entelegynae and Oecobioidea (Oecobiidae plus Hersiliidae), and ambiguous placement of cribellate orb-weavers, compatible with their non-monophyly. Nicodamoidea (Nicodamidae plus Megadictynidae) and Araneoidea composition and relationships are consistent with recent analyses. We did not obtain resolution for the titanoecoids (Titanoecidae and Phyxelididae), but the Retrolateral Tibial Apophysis clade is well supported. Penestomidae, and probably Homalonychidae, are part of Zodarioidea, although the latter family was set apart by recent transcriptomic analyses. Our data support a large group that we call the marronoid clade (including the families Amaurobiidae, Desidae, Dictynidae, Hahniidae, Stiphidiidae, Agelenidae and Toxopidae). The circumscription of most marronoid families is redefined here. Amaurobiidae include the Amaurobiinae and provisionally Macrobuninae. We transfer Malenellinae (Malenella, from Anyphaenidae), Chummidae (Chumma) (new syn.) and Tasmarubriinae (Tasmarubrius, Tasmabrochus and Teeatta, from Amphinectidae) to Macrobuninae. Cybaeidae are redefined to include Calymmaria, Cryphoeca, Ethobuella and Willisius (transferred from Hahniidae), and Blabomma and Yorima (transferred from Dictynidae). Cycloctenidae are redefined to include Orepukia (transferred from Agelenidae) and Pakeha and Paravoca (transferred from Amaurobiidae). Desidae are redefined to include five subfamilies: Amphinectinae, with Amphinecta, Mamoea, Maniho, Paramamoea and Rangitata (transferred from Amphinectidae); Ischaleinae, with Bakala and Manjala (transferred from Amaurobiidae) and Ischalea (transferred from Stiphidiidae); Metaltellinae, with Austmusia, Buyina, Calacadia, Cunnawarra, Jalkaraburra, Keera, Magua, Metaltella, Penaoola and Quemusia; Porteriinae (new rank), with Baiami, Cambridgea, Corasoides and Nanocambridgea (transferred from Stiphidiidae); and Desinae, with Desis, and provisionally Poaka (transferred from Amaurobiidae) and Barahna (transferred from Stiphidiidae). Argyroneta is transferred from Cybaeidae to Dictynidae. Cicurina is transferred from Dictynidae to Hahniidae. The genera Neoramia (from Agelenidae) and Aorangia, Marplesia and Neolana (from Amphinectidae) are transferred to Stiphidiidae. The family Toxopidae (restored status) includes two subfamilies: Myroinae, with Gasparia, Gohia, Hulua, Neomyro, Myro, Ommatauxesis and Otagoa (transferred from Desidae); and Toxopinae, with Midgee and Jamara, formerly Midgeeinae, new syn. (transferred from Amaurobiidae) and Hapona, Laestrygones, Lamina, Toxops and Toxopsoides (transferred from Desidae). We obtain a monophyletic Oval Calamistrum clade and Dionycha; Sparassidae, however, are not dionychans, but probably the sister group of those two clades. The composition of the Oval Calamistrum clade is confirmed (including Zoropsidae, Udubidae, Ctenidae, Oxyopidae, Senoculidae, Pisauridae, Trechaleidae, Lycosidae, Psechridae and Thomisidae), affirming previous findings on the uncertain relationships of the "ctenids" Ancylometes and Cupiennius, although a core group of Ctenidae are well supported. Our data were ambiguous as to the monophyly of Oxyopidae. In Dionycha, we found a first split of core Prodidomidae, excluding the Australian Molycriinae, which fall distantly from core prodidomids, among gnaphosoids. The rest of the dionychans form two main groups, Dionycha part A and part B. The former includes much of the Oblique Median Tapetum clade (Trochanteriidae, Gnaphosidae, Gallieniellidae, Phrurolithidae, Trachelidae, Gnaphosidae, Ammoxenidae, Lamponidae and the Molycriinae), and also Anyphaenidae and Clubionidae. Orthobula is transferred from Phrurolithidae to Trachelidae. Our data did not allow for complete resolution for the gnaphosoid families. Dionycha part B includes the families Salticidae, Eutichuridae, Miturgidae, Philodromidae, Viridasiidae, Selenopidae, Corinnidae and Xenoctenidae (new fam., including Xenoctenus, Paravulsor and Odo, transferred from Miturgidae, as well as Incasoctenus from Ctenidae). We confirm the inclusion of Zora (formerly Zoridae) within Miturgidae.