Tarantula phylogenomics: A robust phylogeny of deep theraphosid clades inferred from transcriptome data sheds light on the prickly issue of urticating setae evolution.

Mygalomorph spiders of the family Theraphosidae, known to the broader public as tarantulas, are among the most recognizable arachnids on earth due to their large size and widespread distribution. Their use of urticating setae is a notable adaptation that has evolved exclusively in certain New World theraphosids. Thus far, the evolutionary history of Theraphosidae remains poorly understood; theraphosid systematics still largely relies on morphological datasets, which suffer from high degrees of homoplasy, and traditional Sanger sequencing of preselected genes failed to provide strong support for supra-generic clades. In this study, we provide the first robust phylogenetic hypothesis of theraphosid evolution inferred from transcriptome data. A core ortholog approach was used to generate a phylogeny from 2460 orthologous genes across 25 theraphosid genera, representing all of the major theraphosid subfamilies, except Selenogyrinae. Our phylogeny recovers an unprecedented monophyletic group that comprises the vast majority of New World theraphosid subfamilies including Aviculariinae, Schismatothelinae and Theraphosinae. Concurrently, we provide additional evidence for the integrity of questionable subfamilies, such as Poecilotheriinae and Psalmopoeinae, and support the non-monophyly of Ischnocolinae. The deeper relationships between almost all subfamilies are confidently inferred. We also used our phylogeny in tandem with published morphological data to perform ancestral state analyses on urticating setae, and contextualize our reconstructions with emphasis on the complex evolutionary history of the trait.

Description of a new species of Eucynorta (Opiliones, Cosmetidae) from Cortés, Honduras.

A new species, Eucynorta rooneyi sp. nov. (Opiliones, Cosmetidae), is described from Parque Nacional Cusuco, Cortés, Honduras, a tropical montane cloud forest habitat. This is the thirty-fifth species of Eucynorta Roewer, 1912, and is characterized by the combination of three sexually dimorphic characters in males: enlarged chelicerae, some armature on femur III and IV, and swollen basitarsi on leg I. This new species is distinct from other Eucynorta species due to its unique pattern of yellow markings on area I of the dorsal scutum, and unarmed free tergites with line markings.

Discovering the silk road: Nuclear and mitochondrial sequence data resolve the phylogenetic relationships among theraphosid spider subfamilies.

The mygalomorph spiders in the family Theraphosidae, also known as "tarantulas", are one of the most popular and diverse groups of arachnids, but their evolutionary history remains poorly understood because morphological analyses have only provided mostly controversial results, and a broad molecular perspective has been lacking until now. In this study we provide a preliminary molecular phylogenetic hypothesis of relationships among theraphosid subfamilies, based on 3.5 kbp of three nuclear and three mitochondrial markers, for 52 taxa representing 10 of the 11 commonly accepted subfamilies. Our analysis confirms the monophyly of the Theraphosidae and of most recognized theraphosid subfamilies, supports the validity of the Stromatopelminae and Poecilotheriinae, and indicates paraphyly of the Schismatothelinae. The placement of representatives of Schismatothelinae also indicates possible non-monophyly of Aviculariinae and supports the distinction of the previously contentious subfamily Psalmopoeinae. Major clades typically corresponded to taxa occurring in the same biogeographic region, with two of them each occurring in Africa, South America and Asia. Because relationships among these major clades were poorly supported, more extensive molecular data sets are required to test the hypothesis of independent colonization and multiple dispersal events among these continents.

Revised generic placement of Brachypelma embrithes (Chamberlin & Ivie, 1936) and Brachypelma angustum Valerio, 1980, with definition of the taxonomic features for identification of female Sericopelma Ausserer, 1875 (Araneae, Theraphosidae).

The tarantula genus Sericopelma was originally defined based on male specimens, most notably lacking tibial spurs on leg I. Early female specimens were unrecognised as Sericopelma, and typically placed in Eurypelma - a dumping ground for problem specimens. The first females were only later recognised, but authors failed to adequately define female Sericopelma. Here, the holotypes of the southern-most alleged Brachypelma species, Brachypelma embrithes (Chamberlin & Ivie, 1936) and Brachypelma angustum Valerio, 1980 were examined, and finding both to possess defining characteristics of Sericopelma were transferred. The taxonomic attributes to define Sericopelma relative to Brachypelma and select other Neotropical genera are discussed, especially for females. As important diagnostic characters for Sericopelma, the single (unilobar) spermathecae swollen at the apex forming a P-shaped cross-section, metatarsus IV with trace scopula, femur IV with a dense retrolateral pad of plumose hair, plus other attributes. Some past confusion in these characters are clarified and Sericopelma relative to Brachypelma and Megaphobema mesomelas are discussed. Finally recommendations are given about these taxonomic changes for CITES regulations.

A new scorpion species of genus Diplocentrus Peters, 1861 (Scorpiones: Diplocentridae) endemic to Islas de la Bahia, Honduras.

Three species of genus Diplocentrus are found in north-northwestern Honduras. These species represent the southern east limits of Diplocentrus' distribution. In recent years, a broad survey of arachnids in Honduras has yielded a collection of several specimens of an undescribed species from two islands in northern Honduras. This new species represents the second species of the genus inhabiting an island. The present contribution describes this new species, and compares it against its most similar relatives. A dichotomous key for the identification of the species of Diplocentrus in Honduras is also included.

MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda.

Morphological data traditionally group Tardigrada (water bears), Onychophora (velvet worms), and Arthropoda (e.g., spiders, insects, and their allies) into a monophyletic group of invertebrates with walking appendages known as the Panarthropoda. However, molecular data generally do not support the inclusion of tardigrades within the Panarthropoda, but instead place them closer to Nematoda (roundworms). Here we present results from the analyses of two independent genomic datasets, expressed sequence tags (ESTs) and microRNAs (miRNAs), which congruently resolve the phylogenetic relationships of Tardigrada. Our EST analyses, based on 49,023 amino acid sites from 255 proteins, significantly support a monophyletic Panarthropoda including Tardigrada and suggest a sister group relationship between Arthropoda and Onychophora. Using careful experimental manipulations--comparisons of model fit, signal dissection, and taxonomic pruning--we show that support for a Tardigrada + Nematoda group derives from the phylogenetic artifact of long-branch attraction. Our small RNA libraries fully support our EST results; no miRNAs were found to link Tardigrada and Nematoda, whereas all panarthropods were found to share one unique miRNA (miR-276). In addition, Onychophora and Arthropoda were found to share a second miRNA (miR-305). Our study confirms the monophyly of the legged ecdysozoans, shows that past support for a Tardigrada + Nematoda group was due to long-branch attraction, and suggests that the velvet worms are the sister group to the arthropods.

A congruent solution to arthropod phylogeny: phylogenomics, microRNAs and morphology support monophyletic Mandibulata.

While a unique origin of the euarthropods is well established, relationships between the four euarthropod classes-chelicerates, myriapods, crustaceans and hexapods-are less clear. Unsolved questions include the position of myriapods, the monophyletic origin of chelicerates, and the validity of the close relationship of euarthropods to tardigrades and onychophorans. Morphology predicts that myriapods, insects and crustaceans form a monophyletic group, the Mandibulata, which has been contradicted by many molecular studies that support an alternative Myriochelata hypothesis (Myriapoda plus Chelicerata). Because of the conflicting insights from published molecular datasets, evidence from nuclear-coding genes needs corroboration from independent data to define the relationships among major nodes in the euarthropod tree. Here, we address this issue by analysing two independent molecular datasets: a phylogenomic dataset of 198 protein-coding genes including new sequences for myriapods, and novel microRNA complements sampled from all major arthropod lineages. Our phylogenomic analyses strongly support Mandibulata, and show that Myriochelata is a tree-reconstruction artefact caused by saturation and long-branch attraction. The analysis of the microRNA dataset corroborates the Mandibulata, showing that the microRNAs miR-965 and miR-282 are present and expressed in all mandibulate species sampled, but not in the chelicerates. Mandibulata is further supported by the phylogenetic analysis of a comprehensive morphological dataset covering living and fossil arthropods, and including recently proposed, putative apomorphies of Myriochelata. Our phylogenomic analyses also provide strong support for the inclusion of pycnogonids in a monophyletic Chelicerata, a paraphyletic Cycloneuralia, and a common origin of Arthropoda (tardigrades, onychophorans and arthropods), suggesting that previous phylogenies grouping tardigrades and nematodes may also have been subject to tree-reconstruction artefacts.

Rare genomic changes and mitochondrial sequences provide independent support for congruent relationships among the sea spiders (Arthropoda, Pycnogonida).

Pycnogonids, or sea spiders, are an enigmatic group of arthropods. Their unique anatomical features have made them difficult to place within the broader group Arthropoda. Most attempts to classify members of Pycnogonida have focused on utilizing these anatomical features to infer relatedness. Using data from mitochondrial genomes, we show that pycnogonids are placed as derived chelicerates, challenging the hypothesis that they diverged early in arthropod history. Our increased taxon sampling of three new mitochondrial genomes also allows us to infer phylogenetic relatedness among major pycnogonid lineages. Phylogenetic analyses based on all 13 mitochondrial protein-coding genes yield well-resolved relationships among the sea spider lineages. Gene order and tRNA secondary structure characters provide independent lines of evidence for these inferred phylogenetic relationships among pycnogonids, and show a minimal amount of homoplasy. Additionally, rare changes in three tRNA genes unite pycnogonids as a clade; these include changes in anticodon identity in tRNA(Lys) and tRNA(Ser(AGN)) and the shared loss of D-arm sequence in the tRNA(Ala) gene. Using mitochondrial genome changes and tRNA structural changes is especially useful for resolving relationships among the major lineages of sea spiders in light of the fact that there have been multiple independent evolutionary changes in nucleotide strand bias among sea spiders. Such reversed nucleotide biases can mislead phylogeny reconstruction based on sequences, although the use of appropriate methods can overcome these effects. With pycnogonids, we find that applying methods to compensate for strand bias and that using genome-level characters yield congruent phylogenetic signals.

Ribosomal protein genes of holometabolan insects reject the Halteria, instead revealing a close affinity of Strepsiptera with Coleoptera.

The phylogenetic relationships among holometabolan insect orders remain poorly known, despite a wealth of previous studies. In particular, past attempts to clarify the sister-group of the enigmatic order Strepsiptera with rRNA genes have led to intense debate about long-branch attraction (the 'Strepsiptera problem'), without resolving the taxonomic question at hand. Here, we appealed to alternative nuclear sequences of 27 ribosomal proteins (RPs) to generate a data matrix of 10,731 nucleotides for 22 holometabolan taxa, including two strepsipteran species. Phylogenetic relationships among holometabolan insects were analyzed under several nucleotide-coding schemes to explore differences in signal and systematic biases. Saturation and compositional bias particularly affected third positions, which greatly differed in AT content (18-72%). Such confounding factors were best reduced by R-Y coding and removal of third codon positions, resulting in more strongly supported topologies, whereas amino acid coding gave poor resolution. The placement of Strepsiptera with Coleoptera (the Coleopterida) was recovered under most coding schemes and analytical methods, if often with modest support and ambiguity. In contrast, an alternative sister-group with Diptera (the Halteria) was only found in one analysis using parsimony, and weakly supported. The topologies here generally support a Coleoptera+Strepsiptera as sister-group to Mecopterida (Siphonaptera+Mecoptera+Diptera+Lepidoptera+Trichoptera), while Hymenoptera were always recovered as sister-group to the remaining Holometabola.

Arachnid relationships based on mitochondrial genomes: asymmetric nucleotide and amino acid bias affects phylogenetic analyses.

Phylogenetic analyses based on mitochondrial DNA have yielded widely differing relationships among members of the arthropod lineage Arachnida, depending on the nucleotide coding schemes and models of evolution used. We enhanced taxonomic coverage within the Arachnida greatly by sequencing seven new arachnid mitochondrial genomes from five orders. We then used all 13 mitochondrial protein-coding genes from these genomes to evaluate patterns of nucleotide and amino acid biases. Our data show that two of the six orders of arachnids (spiders and scorpions) have experienced shifts in both nucleotide and amino acid usage in all their protein-coding genes, and that these biases mislead phylogeny reconstruction. These biases are most striking for the hydrophobic amino acids isoleucine and valine, which appear to have evolved asymmetrical exchanges in response to shifts in nucleotide composition. To improve phylogenetic accuracy based on amino acid differences, we tested two recoding methods: (1) removing all isoleucine and valine sites and (2) recoding amino acids based on their physiochemical properties. We find that these methods yield phylogenetic trees that are consistent in their support of ancient intraordinal divergences within the major arachnid lineages. Further refinement of amino acid recoding methods may help us better delineate interordinal relationships among these diverse organisms.

The nematode-arthropod clade revisited: phylogenomic analyses from ribosomal protein genes misled by shared evolutionary biases.

Phylogenetic analysis of major groups of Metazoa using genomic data tends to recover the sister relationships of arthropods and chordates, contradicting the proposed Ecdysozoa (the molting animals), which group the arthropods together with nematodes and relatives. Ribosomal protein genes have been a major data source in phylogenomic studies because they are readily detected as Expressed Sequence Tags (ESTs) due to their high transcription rates. Here we address the debate about the recovery of Ecdysozoa in genomic data by building a new matrix of carefully curated EST and genome sequences for 25 ribosomal protein genes of the small subunit, with focus on new insect sequences in addition to the Diptera sequences generally used to represent the arthropods. Individually, each ribosomal protein gene showed low phylogenetic signal, but in simultaneous analysis strong support emerged for many expected groups, with support increasing linearly with increased gene number. In agreement with most studies of metazoan relationships from genomic data, our analyses contradicted the Ecdysozoa (the putative sister relationship of arthropods and nematodes), and instead supported the affinity of arthropods with chordates. In addition, relationships among holometabolan insects resulted in an unlikely basal position for Diptera. To test for biases in the data that might produce an erroneous arthropod-chordate affinity we simulated sequence data on tree topologies with the alternative arthropod-nematode sister relationships, applying a model of amino acid sequence evolution estimated from the real data. Tree searches on these simulated data still revealed an arthropod-chordate grouping, i.e., the topologies used to simulate the data were not recovered correctly. This suggests that the arthropod-chordate relationships may be obtained erroneously also from the real data even if the alternative topology (Ecdysozoa) represents the true phylogeny. Whereas denser taxon sampling in the future may recover the Ecdysozoa, our analyses demonstrate that recent phylogenomic studies may be affected by as yet unspecified biases in amino acid sequence composition in the model organisms with available genomic data.

Dense taxonomic EST sampling and its applications for molecular systematics of the Coleoptera (beetles).

Expressed sequence tag (EST) sequences can provide a wealth of data for phylogenetic and genomic studies, but the utility of these resources is restricted by poor taxonomic sampling. Here, we use small EST libraries (<1,000 clones) to generate phylogenetic markers across a broad sample of insects, focusing on the species-rich Coleoptera (beetles). We sequenced over 23,000 ESTs from 34 taxa, which produced 8,728 unique sequences after clustering nonredundant sequences. Between taxa, the sequences could be grouped into 731 gene clusters, with the largest corresponding to mitochondrial DNA transcripts and gene families chymotrypsin, actin, troponin, and tubulin. While levels of paralogy were high in most gene clusters, several midsized clusters including many ribosomal protein (RP) genes appeared to be free of expressed paralogs. To evaluate the utility of EST data for molecular systematics, we curated available transcripts for 66 RP genes from representatives of the major groups of Coleoptera. Using supertree and supermatrix approaches for phylogenetic analysis, the results were consistent with the emerging phylogenetic conclusions about basal relationships in Coleoptera. Numerous small EST libraries from a taxonomically densely sampled lineage can provide a core set of genes that together act as a scaffold in phylogenetic reconstruction, comparative genomics, and studies of gene evolution.