Repeated and Time-Correlated Morphological Convergence in Cave-Dwelling Harvestmen (Opiliones, Laniatores) from Montane Western North America

BACKGROUND: Many cave-dwelling animal species display similar morphologies (troglomorphism) that have evolved convergent within and among lineages under the similar selective pressures imposed by cave habitats. Here we study such ecomorphological evolution in cave-dwelling Sclerobuninae harvestmen (Opiliones) from the western United States, providing general insights into morphological homoplasy, rates of morphological change, and the temporal context of cave evolution. METHODOLOGY/PRINCIPAL FINDINGS: We gathered DNA sequence data from three independent gene regions, and combined these data with Bayesian hypothesis testing, morphometrics analysis, study of penis morphology, and relaxed molecular clock analyses. Using multivariate morphometric analysis, we find that phylogenetically unrelated taxa have convergently evolved troglomorphism; alternative phylogenetic hypotheses involving less morphological convergence are not supported by Bayesian hypothesis testing. In one instance, this morphology is found in specimens from a high-elevation stony debris habitat, suggesting that troglomorphism can evolve in non-cave habitats. We discovered a strong positive relationship between troglomorphy index and relative divergence time, making it possible to predict taxon age from morphology. Most of our time estimates for the origin of highly-troglomorphic cave forms predate the Pleistocene. CONCLUSIONS/SIGNIFICANCE: While several regions in the eastern and central United States are well-known hotspots for cave evolution, few modern phylogenetic studies have addressed the evolution of cave-obligate species in the western United States. Our integrative studies reveal the recurrent evolution of troglomorphism in a perhaps unexpected geographic region, at surprisingly deep time depths, and in sometimes surprising habitats. Because some newly discovered troglomorphic populations represent undescribed species, our findings stress the need for further biological exploration, integrative systematic research, and conservation efforts in western US cave habitats

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.Fil: Hedin, Marshal. San Diego State University; Estados UnidosFil: Derkarabetian, Shahan. University of California; Estados Unidos. San Diego State University; Estados UnidosFil: Ramirez, Martin Javier. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”; ArgentinaFil: Vink, Cor. Canterbury Museum Christchurch; Nueva ZelandaFil: Bond, Jason E.. Auburn University; Estados Unido

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

Phylogenomics, Integrative Taxonomy, and Population Genomics in the Travunioidea (Arachnida, Opiliones, Laniatores)

My dissertation research utilizes next-generation sequencing (NGS) technology and associated bioinformatics processing to answer systematic and evolutionary questions in Opiliones (harvestmen) at different taxonomic scales, focusing on the Laniatores superfamily Travunioidea and particularly the travunioid genus Sclerobunus. Opiliones are a diverse group of arachnids with over 6500 described species distributed on every continent except Antarctica. Despite relatively high diversity (e.g., more described species than mammals), harvestmen are poorly studied. This dissertation research has three main projects. The first chapter is a higher-level phylogenetics and taxonomic study of the Travunioidea, a clade of ~80 species of harvestmen distributed throughout the Holarctic. Here I utilized ultraconserved elements (UCE) for phylogenomic reconstruction using multiple types of phylogenetic reconstruction methods. Based on results, a new taxonomic classification is proposed for the Travunioidea, including the identification and diagnosis of a new family, and I reassess the phylogenetic utility of morphological characters used to differentiate and diagnose travunioid taxa. The second chapter focuses on species delimitation of the western North American travunioid genus Sclerobunus. I utilized modern integrative taxonomic methods, using both discovery-based and validation-based approaches by combining morphometrics, mitochondrial genetic data, genitalic morphology, and nuclear genetic data derived from newly developed genes based on a comparative transcriptomics approach. This research resulted in a revision of the genus including synonymy of the genus Cyptobunus, elevation of four subspecies, and the description of five new species. The third chapter is a phylogeographic analysis of Sclerobunus robustus, a species distributed throughout the southwestern United States. A hypothesis-based framework was adopted, where stable habitats (i.e., potential refugia) were identified through ecological niche modeling, and hypotheses regarding genetic patterns associated with these refugia were developed. Hypotheses were tested by using genetic data in the form of loci and SNPs derived from double-digest RAD sequencing methods. Two large refugial regions were identified and population genomic analyses supported the presence of both

Data from: Integrative taxonomy and species delimitation in harvestmen: a revision of the western North American genus Sclerobunus (Opiliones: Laniatores: Travunioidea)

Alpha taxonomy, and specifically the delimitation of species, is becoming increasingly objective and integrative. The use of coalescent-based methods applied to genetic data is providing new tools for the discovery and delimitation of species. Here, we use an integrative approach via a combination of discovery-based multivariate morphological analyses to detect potential new species. These potential species are then used as a priori species in hypothesis-driven validation analyses with genetic data. This research focuses on the harvestmen genus Sclerobunus found throughout the mountainous regions of western North America. Based on our analyses, we conduct a revision of Sclerobunus resulting in synonymy of Cyptobunus with Sclerobunus including transfer of S. cavicolens comb. nov. and elevation of both subspecies of S. ungulatus: S. ungulatus comb. nov. and S. madhousensis comb. nov., stat. nov. The three subspecies of S. robustus are elevated, S. robustus, S. glorietus stat. nov., and S. idahoensis stat. nov. Additionally, five new species of Sclerobunus are described from New Mexico and Colorado, including S. jemez sp. nov., S. klomax sp. nov., S. skywalkeri sp. nov., S. speoventus sp. nov., and S. steinmanni sp. nov. Several of the newly described species are single-cave endemics, and our findings suggest that further exploration of western North American cave habitats will likely yield additional new species

Nomenclatorial changes in Triaenonychidae: Sclerobunus parvus Roewer is a junior synonym of Paranonychus brunneus (Banks), Mutusnonychus Suzuki is a junior synonym of Paranonychus Briggs, and Kaolinonychinae Suzuki is a junior synonym of Paranonychinae Briggs (Opiliones: Triaenonychidae).

Shear, William A., Derkarabetian, Shahan (2008): Nomenclatorial changes in Triaenonychidae: Sclerobunus parvus Roewer is a junior synonym of Paranonychus brunneus (Banks), Mutusnonychus Suzuki is a junior synonym of Paranonychus Briggs, and Kaolinonychinae Suzuki is a junior synonym of Paranonychinae Briggs (Opiliones: Triaenonychidae). Zootaxa 1809 (1): 67-68, DOI: 10.11646/zootaxa.1809.1.5, URL: http://dx.doi.org/10.11646/zootaxa.1809.1.

65/65 CORE 50% coverage matrix

Concatenated UCE matrix for the 65/65 CORE dataset with 50% taxon coverag

65/65 CORE 50% coverage UCE loci

All individual UCE loci included in the 65/65 CORE 50% coverage matri

65/65 CORE 50% coverage tree

Resulting RAxML phylogeny for the 65/65 CORE dataset with 50% taxon coverag

Habitus morphology of the <i>robustus</i> group.

<p>A) <i>S. speoventus</i>, paratype male (Cave of the Winds, CO) [835868]. B) <i>S. steinmanni</i>, holotype male (Mallory Cave, CO) [835871]. C) <i>S. robustus</i> male (Apex Valley, CO) [835865]. D) <i>S. glorietus</i>, male (Glorieta Canyon, NM) [835850]. E) <i>S. klomax</i>, holotype female (Taos Ski Valley, NM) [835857]. F) <i>S. jemez</i>, holotype male (Terrero Cave, NM) [835856]. G) <i>S. skywalkeri</i>, paratype male, image horizontally reflected (Manzano Mountains, NM) [835867]. Scale bars = 1 mm. Morphbank numbers indicated in brackets.</p