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.

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.].

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.

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.

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.

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.

Population genomic evidence for multiple Pliocene refugia in a montane-restricted harvestman (Arachnida, Opiliones, Sclerobunus robustus) from the southwestern United States.

The integration of ecological niche modelling into phylogeographic analyses has allowed for the identification and testing of potential refugia under a hypothesis-based framework, where the expected patterns of higher genetic diversity in refugial populations and evidence of range expansion of nonrefugial populations are corroborated with empirical data. In this study, we focus on a montane-restricted cryophilic harvestman, Sclerobunus robustus, distributed throughout the heterogeneous Southern Rocky Mountains and Intermontane Plateau of southwestern North America. We identified hypothetical refugia using ecological niche models (ENMs) across three time periods, corroborated these refugia with population genetic methods using double-digest RAD-seq data and conducted population-level phylogenetic and divergence dating analyses. ENMs identify two large temporally persistent regions in the mid-latitude highlands. Genetic patterns support these two hypothesized refugia with higher genetic diversity within refugial populations and evidence for range expansion in populations found outside hypothesized refugia. Phylogenetic analyses identify five to six genetically divergent, geographically cohesive clades of S. robustus. Divergence dating analyses suggest that these separate refugia date to the Pliocene and that divergence between clades pre-dates the late Pleistocene glacial cycles, while diversification within clades was likely driven by these cycles. Population genetic analyses reveal effects of both isolation by distance (IBD) and isolation by environment (IBE), with IBD more important in the continuous mountainous portion of the distribution, while IBE was stronger in the populations inhabiting the isolated sky islands of the south. Using model-based coalescent approaches, we find support for postdivergence migration between clades from separate refugia.

Phylogenomic analyses resolve an ancient trichotomy at the base of Ischyropsalidoidea (Arachnida, Opiliones) despite high levels of gene tree conflict and unequal minority resolution frequencies.

Phylogenetic resolution of ancient rapid radiations has remained problematic despite major advances in statistical approaches and DNA sequencing technologies. Here we report on a combined phylogenetic approach utilizing transcriptome data in conjunction with Sanger sequence data to investigate a tandem of ancient divergences in the harvestmen superfamily Ischyropsalidoidea (Arachnida, Opiliones, Dyspnoi). We rely on Sanger sequences to resolve nodes within and between closely related genera, and use RNA-seq data from a subset of taxa to resolve a short and ancient internal branch. We use several analytical approaches to explore this succession of ancient diversification events, including concatenated and coalescent-based analyses and maximum likelihood gene trees for each locus. We evaluate the robustness of phylogenetic inferences using a randomized locus sub-sampling approach, and find congruence across these methods despite considerable incongruence across gene trees. Incongruent gene trees are not recovered in frequencies expected from a simple multispecies coalescent model, and we reject incomplete lineage sorting as the sole contributor to gene tree conflict. Using these approaches we attain robust support for higher-level phylogenetic relationships within Ischyropsalidoidea.

High-stakes species delimitation in eyeless cave spiders (Cicurina, Dictynidae, Araneae) from central Texas.

A remarkable radiation of completely eyeless, cave-obligate spider species (Cicurina) has been described from limestone caves of Texas. This radiation includes over 50 described species, with a large number of hypothesized single-cave endemics, and four species listed as US Federally Endangered. Because of this conservation importance, species delimitation in the group is 'high-stakes'- it is imperative that species hypotheses are data rich, objective, and robust. This study focuses on a complex of four cave-dwelling Cicurina distributed on the northwestern edge of Austin, Texas. Several of the existing species hypotheses in this complex are weak, based on morphological comparisons of small samples of adult female specimens; one species description (for C. wartoni) is based on a single adult specimen. Species limits in this group were newly assessed using morphological, mitochondrial and nuclear DNA sequence data evidence, analysed using a variety of approaches. All data support a clear lineage separation between C. buwata versus the C. travisae complex (including C. travisae, C. wartoni and C. reddelli). Observed congruence across multiple analyses indicate that the C. travisae complex represents a single species, and the formal species synonymy presented here has important conservation implications. The integrative framework utilized in this study serves as a potential model for other Texas cave Cicurina, including US Federally Endangered species. More generally, this study illustrates how and why taxon-focused conservation efforts must prioritize modern species delimitation research (if the existing taxonomy is weak), before devoting precious downstream resources to conservation efforts. The study also highlights the issue of taxonomic type II error that diversity biologists increasingly face as species delimitation moves into the genomics era.

Sky island diversification meets the multispecies coalescent - divergence in the spruce-fir moss spider (Microhexura montivaga, Araneae, Mygalomorphae) on the highest peaks of southern Appalachia.

Microhexura montivaga is a miniature tarantula-like spider endemic to the highest peaks of the southern Appalachian mountains and is known only from six allopatric, highly disjunct montane populations. Because of severe declines in spruce-fir forest in the late 20th century, M. montivaga was formally listed as a US federally endangered species in 1995. Using DNA sequence data from one mitochondrial and seven nuclear genes, patterns of multigenic genetic divergence were assessed for six montane populations. Independent mitochondrial and nuclear discovery analyses reveal obvious genetic fragmentation both within and among montane populations, with five to seven primary genetic lineages recovered. Multispecies coalescent validation analyses [guide tree and unguided Bayesian Phylogenetics and Phylogeography (BPP), Bayes factor delimitation (BFD)] using nuclear-only data congruently recover six or seven distinct lineages; BFD analyses using combined nuclear plus mitochondrial data favour seven or eight lineages. In stark contrast to this clear genetic fragmentation, a survey of secondary sexual features for available males indicates morphological conservatism across montane populations. While it is certainly possible that morphologically cryptic speciation has occurred in this taxon, this system may alternatively represent a case where extreme population genetic structuring (but not speciation) leads to an oversplitting of lineage diversity by multispecies coalescent methods. Our results have clear conservation implications for this federally endangered taxon and illustrate a methodological issue expected to become more common as genomic-scale data sets are gathered for taxa found in naturally fragmented habitats.

Multilocus sequence data reveal dozens of putative cryptic species in a radiation of endemic Californian mygalomorph spiders (Araneae, Mygalomorphae, Nemesiidae).

We use mitochondrial and multi-locus nuclear DNA sequence data to infer both species boundaries and species relationships within California nemesiid spiders. Higher-level phylogenetic data show that the California radiation is monophyletic and distantly related to European members of the genus Brachythele. As such, we consider all California nemesiid taxa to belong to the genus Calisoga Chamberlin, 1937. Rather than find support for one or two taxa as previously hypothesized, genetic data reveal Calisoga to be a species-rich radiation of spiders, including perhaps dozens of species. This conclusion is supported by multiple mitochondrial barcoding analyses, and also independent analyses of nuclear data that reveal general genealogical congruence. We discovered three instances of sympatry, and genetic data indicate reproductive isolation when in sympatry. An examination of female reproductive morphology does not reveal species-specific characters, and observed male morphological differences for a subset of putative species are subtle. Our coalescent species tree analysis of putative species lays the groundwork for future research on the taxonomy and biogeographic history of this remarkable endemic radiation.

Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (mygalomorphae, antrodiaetidae, aliatypus).

Species are a fundamental unit for biological studies, yet no uniform guidelines exist for determining species limits in an objective manner. Given the large number of species concepts available, defining species can be both highly subjective and biased. Although morphology has been commonly used to determine species boundaries, the availability and prevalence of genetic data has allowed researchers to use such data to make inferences regarding species limits. Genetic data also have been used in the detection of cryptic species, where other lines of evidence (morphology in particular) may underestimate species diversity. In this study, we investigate species limits in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus) from California. Multiple approaches were used to determine species boundaries in this highly genetically fragmented group, including both multilocus discovery and validation approaches (plus a chimeric approach). Additionally, we introduce a novel tree-based discovery approach using species trees. Results suggest that this complex includes multiple cryptic species, with two groupings consistently recovered across analyses. Due to incongruence across analyses for the remaining samples, we take a conservative approach and recognize a three species complex, and formally describe two new species (Aliatypus roxxiae, sp. nov. and Aliatypus starretti, sp. nov.). This study helps to clarify species limits in a genetically fragmented group and provides a framework for identifying and defining the cryptic lineage diversity that prevails in many organismal groups.

Crossing the uncrossable: novel trans-valley biogeographic patterns revealed in the genetic history of low-dispersal mygalomorph spiders (Antrodiaetidae, Antrodiaetus) from California.

Antrodiaetus riversi is a dispersal-limited, habitat-specialized mygalomorph spider species endemic to mesic woodlands of northern and central California. Here, we build upon prior phylogeographic research using a much larger geographic sample and include additional nuclear genes, providing more detailed biogeographic insights throughout the range of this complex. Of particular interest is the uncovering of unexpected and replicated trans-valley biogeographic patterns, where in two separate genetic clades western haplotypes in the California south Coast Ranges are phylogenetically closely related to eastern haplotypes from central and northern Sierran foothills. In both instances, these trans-valley phylogenetic patterns are strongly supported by multiple genes. These western and eastern populations are currently separated by the Central Valley, a well-recognized modern-day and historical biogeographic barrier in California. For one clade, the directionality is clearly northeast to southwest, and all available evidence is consistent with a jump dispersal event estimated at 1.2-1.3 Ma. During this time period, paleogeographic data indicate that northern Sierran rivers emptied to the ocean in the south Coast Ranges, rather than at the San Francisco Bay. For the other trans-valley clade genetic evidence is less conclusive regarding the mechanism and directionality of biogeographic exchange, although the estimated timeframe is similar (approximately 1.8 Ma). Despite the large number of biogeographic studies previously conducted in central California, to the best of our knowledge no prior studies have discussed or revealed a northern Sierran to south Coast Range biogeographic connection. This uniqueness may reflect the low-dispersal biology of mygalomorph spiders, where 'post-event' gene exchange rarely erases historical biogeographic signal.

Molecular phylogeny of the harvestmen genus Sabacon (Arachnida: Opiliones: Dyspnoi) reveals multiple Eocene-Oligocene intercontinental dispersal events in the Holarctic.

We investigated the phylogeny and biogeographic history of the Holarctic harvestmen genus Sabacon, which shows an intercontinental disjunct distribution and is presumed to be a relatively old taxon. Molecular phylogenetic relationships of Sabacon were estimated using multiple gene regions and Bayesian inference for a comprehensive Sabacon sample. Molecular clock analyses, using relaxed clock models implemented in BEAST, are applied to date divergence events. Biogeographic scenarios utilizing S-DIVA and Lagrange C++ are reconstructed over sets of Bayesian trees, allowing for the incorporation of phylogenetic uncertainty and quantification of alternative reconstructions over time. Four primary well-supported subclades are recovered within Sabacon: (1) restricted to western North America; (2) eastern North American S. mitchelli and sampled Japanese taxa; (3) a second western North American group and taxa from Nepal and China; and (4) eastern North American S. cavicolens with sampled European Sabacon species. Three of four regional faunas (wNA, eNA, East Asia) are thereby non-monophyletic, and three clades include intercontinental disjuncts. Molecular clock analyses and biogeographic reconstructions support nearly simultaneous intercontinental dispersal coincident with the Eocene-Oligocene transition. We hypothesize that biogeographic exchange in the mid-Tertiary is likely correlated with the onset of global cooling, allowing cryophilic Sabacon taxa to disperse within and among continents. Morphological variation supports the divergent genetic clades observed in Sabacon, and suggests that a taxonomic revision (e.g., splitting Sabacon into multiple genera) may be warranted.

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.

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.