Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction.

Ultraconserved genomic elements (UCEs) are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes does not require prior knowledge of genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here, we characterized UCEs from 11 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated four different sets of UCE markers by genomic category from five different studies including: birds, mammals, fish, Hymenoptera (ants, wasps, and bees), and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by two or more UCEs, corresponding to nonoverlapping segments of a single gene. We considered these UCEs to be nonindependent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging cogenic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees was significantly improved across all data sets apparently driven by the increase in loci length. Additionally, we conducted simulations and found that gene trees generated from merged UCEs were more accurate than those generated by unmerged UCEs. As loci length improves gene tree accuracy, this modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses. [Anchored hybrid enrichment; ants; ASTRAL; bait capture; carangimorph; Coleoptera; conserved nonexonic elements; exon capture; gene tree; Hymenoptera; mammal; phylogenomic markers; songbird; species tree; ultraconserved elements; weevils.].

Towards a synthesis of the Caribbean biogeography of terrestrial arthropods.

BACKGROUND: The immense geologic and ecological complexity of the Caribbean has created a natural laboratory for interpreting when and how organisms disperse through time and space. However, competing hypotheses compounded with this complexity have resulted in a lack of unifying principles of biogeography for the region. Though new data concerning the timing of geologic events and dispersal events are emerging, powerful new analytical tools now allow for explicit hypothesis testing. Arthropods, with varying dispersal ability and high levels of endemism in the Caribbean, are an important, albeit understudied, biogeographic model system. Herein, we include a comprehensive analysis of every publicly available genetic dataset (at the time of writing) of terrestrial Caribbean arthropod groups using a statistically robust pipeline to explicitly test the current extent of biogeographic hypotheses for the region. RESULTS: Our findings indicate several important biogeographic generalizations for the region: the South American continent is the predominant origin of Caribbean arthropod fauna; GAARlandia played a role for some taxa in aiding dispersal from South America to the Greater Antilles; founder event dispersal explains the majority of dispersal events by terrestrial arthropods, and distance between landmasses is important for dispersal; most dispersal events occurred via island hopping; there is evidence of 'reverse' dispersal from islands to the mainland; dispersal across the present-day Isthmus of Panama generally occurred prior to 3 mya; the Greater Antilles harbor more lineage diversity than the Lesser Antilles, and the larger Greater Antilles typically have greater lineage diversity than the smaller islands; basal Caribbean taxa are primarily distributed in the Greater Antilles, the basal-most being from Cuba, and derived taxa are mostly distributed in the Lesser Antilles; Jamaican taxa are usually endemic and monophyletic. CONCLUSIONS: Given the diversity and deep history of terrestrial arthropods, incongruence of biogeographic patterns is expected, but focusing on both similarities and differences among divergent taxa with disparate life histories emphasizes the importance of particular qualities responsible for resulting diversification patterns. Furthermore, this study provides an analytical toolkit that can be used to guide researchers interested in answering questions pertaining to Caribbean biogeography using explicit hypothesis testing.

The house spider genome reveals an ancient whole-genome duplication during arachnid evolution.

BACKGROUND: The duplication of genes can occur through various mechanisms and is thought to make a major contribution to the evolutionary diversification of organisms. There is increasing evidence for a large-scale duplication of genes in some chelicerate lineages including two rounds of whole genome duplication (WGD) in horseshoe crabs. To investigate this further, we sequenced and analyzed the genome of the common house spider Parasteatoda tepidariorum. RESULTS: We found pervasive duplication of both coding and non-coding genes in this spider, including two clusters of Hox genes. Analysis of synteny conservation across the P. tepidariorum genome suggests that there has been an ancient WGD in spiders. Comparison with the genomes of other chelicerates, including that of the newly sequenced bark scorpion Centruroides sculpturatus, suggests that this event occurred in the common ancestor of spiders and scorpions, and is probably independent of the WGDs in horseshoe crabs. Furthermore, characterization of the sequence and expression of the Hox paralogs in P. tepidariorum suggests that many have been subject to neo-functionalization and/or sub-functionalization since their duplication. CONCLUSIONS: Our results reveal that spiders and scorpions are likely the descendants of a polyploid ancestor that lived more than 450 MYA. Given the extensive morphological diversity and ecological adaptations found among these animals, rivaling those of vertebrates, our study of the ancient WGD event in Arachnopulmonata provides a new comparative platform to explore common and divergent evolutionary outcomes of polyploidization events across eukaryotes.

Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal.

Scorpions represent an iconic lineage of arthropods, historically renowned for their unique bauplan, ancient fossil record and venom potency. Yet, higher level relationships of scorpions, based exclusively on morphology, remain virtually untested, and no multilocus molecular phylogeny has been deployed heretofore towards assessing the basal tree topology. We applied a phylogenomic assessment to resolve scorpion phylogeny, for the first time, to our knowledge, sampling extensive molecular sequence data from all superfamilies and examining basal relationships with up to 5025 genes. Analyses of supermatrices as well as species tree approaches converged upon a robust basal topology of scorpions that is entirely at odds with traditional systematics and controverts previous understanding of scorpion evolutionary history. All analyses unanimously support a single origin of katoikogenic development, a form of parental investment wherein embryos are nurtured by direct connections to the parent's digestive system. Based on the phylogeny obtained herein, we propose the following systematic emendations: Caraboctonidae is transferred to Chactoidea new superfamilial assignment: ; superfamily Bothriuroidea revalidated: is resurrected and Bothriuridae transferred therein; and Chaerilida and Pseudochactida are synonymized with Buthida new parvordinal synonymies: .

Islands within islands: Diversification of tailless whip spiders (Amblypygi, Phrynus) in Caribbean caves.

Islands have played a key role in understanding species formation ever since Darwin's work on the Galapagos and Wallace's work in the Malay Archipelago. Like oceanic islands, habitat 'islands', such as mountaintops and caves similarly may drive diversification. Here we examine patterns of diversification in the tailless whip spider genus Phrynus Larmarck, 1809 (Amblypygida: Phrynidae) a system that shows evidence of diversification under the influence of 'islands within islands'. We estimate phylogeographic history and measure genetic diversity among representatives of three nominal Phrynus species from epigean and cave systems of Puerto Rico and nearby islands. Data from five loci (mitochondrial 12S, 16S, Cox1; nuclear H3, 28S) were used to generate phylogenetic hypotheses and to assess species monophyly and phylogeographic relationships. Genetic divergences and population limits were estimated and assessed using the Geneious barcoding plugin and the genealogical sorting index. We find that mtDNA sequence divergences within each of the three Phrynus species range between 15% and 20%. Genetic divergence is structured at three spatial scales: among islands in a manner consistent with the GAARlandia hypothesis, among bedrock formations within Puerto Rico, and among caves within these formations. Every isolated cave system contains a unique mtDNA genetic lineage of Phrynus, with divergence among cave systems far exceeding that within. In some localities epigean specimens nest among cave taxa, in others caves are monophyletic. Remarkably, clades that show up to 20% mtDNA sequence divergence show little or no variation in the nuclear markers. We interpret this pattern as resulting from extreme conservation of our nuclear markers rather than male sex-biased dispersal, based on high conservation of 28S and H3 between our individuals and other amblypygid genera that are restricted to Africa. While this study includes but a tiny fraction of Caribbean caves, our findings suggest Phrynus may be much more diverse than hitherto thought, at least in terms of mtDNA diversity, and that the arthropod fauna of caves may represent a dimension of biodiversity that is yet to be discovered in the Caribbean biodiversity hotspot.

A new species of Centruroides Marx (Scorpiones: Buthidae) from Panama and new distribution records for Centruroides bicolor (Pocock, 1898) and Centruroides granosus (Thorell, 1876).

A new species, Centruroides panamensis n. sp., from the foothills of Volcán Barú in the Province of Chiriquí, Panama is described with a extremely narrow distributional range. New distribution records of Centruroides bicolor (Pocock, 1898) are also presented.

A new species of alkali-sink Paruroctonus Werner, 1934 (Scorpiones, Vaejovidae) from California's San Joaquin Valley.

Herein a new species of Paruroctonus Werner, 1934 is described from alkali-sink habitats in the San Joaquin Desert of central California, Paruroctonustularesp. nov. It can be differentiated from other Paruroctonus by a combination of morphological features including scalloped pedipalp fingers in males, specific setal counts and morphometric ratios, and specific patterns of fuscous pigmentation. It also inhabits a unique distribution allopatric with all other Paruroctonus species except P.variabilis Hjelle, 1982. Photographs of a large series of live P.tularesp. nov. from across their range and detailed images of several morphological features are provided, their distribution is modeled, a haplotype network is presented, and details about their habitat, ecology, and conservation are discussed.

Two new alkali-sink specialist species of Paruroctonus Werner 1934 (Scorpiones, Vaejovidae) from central California.

Herein we describe two new species of Paruroctonus (Werner 1934) from California: Paruroctonussoda sp. nov. from the Soda Lake playa at the center of the Carrizo Plain in San Luis Obispo county and Paruroctonusconclusus sp. nov. from the Koehn Lake playa in the Mojave Desert of Kern County. They can be differentiated from other Paruroctonus by a combination of morphological features including deeply scalloped pedipalp fingers in males, specific patterns of fuscous pigmentation, unique setal counts, and unique morphometric ratios. They can also be separated from one another by the latter three characters. Photographs of a large selection of live scorpions are provided, including detailed images and figures of many morphological features. Their distributions, habitats, and ecologies are discussed; and important steps towards their conservation are described.

The flattie spiders of the Selenops isopodus/ species group (Araneae: Selenopidae) with a review of Selenops/ records from Colombia.

Here we examine the species of the Selenops isopodus species group: S. isopodus Mello-Leitão, 1941, S. arikok Crews, 2011, and S. curazao Alayón, 2001. We describe the female and male of S. bullerengue sp. nov. from Colombia and synonymize S. marilus Corronca, 1998a with S. isopodus, providing diagnoses and complete descriptions of both sexes of S. isopodus. Detailed images and a key to species in the group are provided. The distribution of all selenopid species in Colombia is reviewed using published records, museum specimens, and citizen science data from inaturalist.org.

Publisher Correction: Island Ancestors and New World Biogeography: A Case Study from the Scorpions (Buthidae: Centruroidinae).

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Gene content evolution in the arthropods.

BACKGROUND: Arthropods comprise the largest and most diverse phylum on Earth and play vital roles in nearly every ecosystem. Their diversity stems in part from variations on a conserved body plan, resulting from and recorded in adaptive changes in the genome. Dissection of the genomic record of sequence change enables broad questions regarding genome evolution to be addressed, even across hyper-diverse taxa within arthropods. RESULTS: Using 76 whole genome sequences representing 21 orders spanning more than 500 million years of arthropod evolution, we document changes in gene and protein domain content and provide temporal and phylogenetic context for interpreting these innovations. We identify many novel gene families that arose early in the evolution of arthropods and during the diversification of insects into modern orders. We reveal unexpected variation in patterns of DNA methylation across arthropods and examples of gene family and protein domain evolution coincident with the appearance of notable phenotypic and physiological adaptations such as flight, metamorphosis, sociality, and chemoperception. CONCLUSIONS: These analyses demonstrate how large-scale comparative genomics can provide broad new insights into the genotype to phenotype map and generate testable hypotheses about the evolution of animal diversity.

Impact of an educational intervention on residents' knowledge of pediatric disaster medicine.

BACKGROUND: Globally, natural and created events have underscored the vulnerability of children in disasters. There is an unmet need for a standardized pediatric disaster medicine (PDM) curriculum. OBJECTIVE: To create and implement a PDM course, measure course efficacy, and assess residents' attitudes toward and experience in disaster medicine. DESIGN/METHODS: An educational intervention was conducted for pediatric and emergency medicine residents at a tertiary care teaching hospital. Participants completed a precourse survey of PDM attitudes and experience. Paired t tests were used to compare pretest, immediate posttest, and delayed posttest scores. Test performance was assessed by resident type and postgraduate year. A postcourse survey gauged reaction to the course and interest in further PDM training. RESULTS: Among the participants, 11 residents (9.4%) have treated disaster victims, and 5 (4.3%) had formal disaster medicine education. Most (83%) felt PDM is an important part of their training. Seventy-five eligible residents (64.6%) completed the intervention. Pairwise comparison of scores showed a mean improvement in scores of 24.5% immediately after taking the course (95% confidence interval, 22.9%-30.1%; P < 0.001). Two months later, residents scored a mean of 69.0% for the delayed posttest, with a retained improvement in scores (18.3%; 95% confidence interval, 14.3%-22.3%; P < 0.001). Residents preferred future PDM exercises to additional didactic training (72.0% vs. 32.7%; P < 0.001%). CONCLUSIONS: Residents who complete this curriculum increase their knowledge of PDM with moderate retention of information. Most residents lack PDM training, believe it is important, and request disaster-training exercises.

Island Ancestors and New World Biogeography: A Case Study from the Scorpions (Buthidae: Centruroidinae).

Scorpions are an excellent system for understanding biogeographical patterns. Most major scorpion lineages predate modern landforms, making them suitable for testing hypotheses of vicariance and dispersal. The Caribbean islands are endowed with a rich and largely endemic scorpion fauna, the origins of which have not been previously investigated with modern biogeographical methods. Three sets of hypotheses have been proposed to explain present patterns of diversity in the Caribbean: (1) connections via land bridges, (2) vicariance events, and (3) overwater dispersal from continents and among islands. The present study investigates the biogeographical diversification of the New World buthid scorpion subfamily Centruroidinae Kraus, 1955, a clade of seven genera and more than 110 species; infers the ancestral distributions of these scorpions; and tests the relative roles of vicariance and dispersal in the formation of their present distributions. A fossil-calibrated molecular phylogeny was estimated with a Bayesian criterion to infer the dates of diversification events from which ancestral distributions were reconstructed, and the relative likelihood of models of vicariance vs. dispersal, calculated. Although both the timing of diversification and the ancestral distributions were congruent with the GAARlandia land-bridge hypothesis, there was no significant difference between distance-dependent models with or without the land-bridge. Heteroctenus Pocock, 1893, the Caribbean-endemic sister taxon of Centruroides Marx, 1890 provides evidence for a Caribbean ancestor, which subsequently colonized Central America and North America, and eventually re-colonized the Greater Antilles. This 'reverse colonization' event of a continent from an island demonstrates the importance of islands as a potential source of biodiversity.

Advancing mite phylogenomics: Designing ultraconserved elements for Acari phylogeny.

Mites (Acari) are one of the most diverse groups of life on Earth; yet, their evolutionary relationships are poorly understood. Also, the resolution of broader arachnid phylogeny has been hindered by an underrepresentation of mite diversity in phylogenomic analyses. To further our understanding of Acari evolution, we design targeted ultraconserved genomic elements (UCEs) probes, intended for resolving the complex relationships between mite lineages and closely related arachnids. We then test our Acari UCE baits in-silico by constructing a phylogeny using 13 existing Acari genomes, as well as 6 additional taxa from a variety of genomic sources. Our Acari-specific probe kit improves the recovery of loci within mites over an existing general arachnid UCE probe set. Our initial phylogeny recovers the major mite lineages, yet finds mites to be non-monophyletic overall, with Opiliones (harvestmen) and Ricinuleidae (hooded tickspiders) rendering Parasitiformes paraphyletic.

Evolutionary interpretations of mycobacteriophage biodiversity and host-range through the analysis of codon usage bias.

In an genomics course sponsored by the Howard Hughes Medical Institute (HHMI), undergraduate students have isolated and sequenced the genomes of more than 1,150 mycobacteriophages, creating the largest database of sequenced bacteriophages able to infect a single host, Mycobacterium smegmatis, a soil bacterium. Genomic analysis indicates that these mycobacteriophages can be grouped into 26 clusters based on genetic similarity. These clusters span a continuum of genetic diversity, with extensive genomic mosaicism among phages in different clusters. However, little is known regarding the primary hosts of these mycobacteriophages in their natural habitats, nor of their broader host ranges. As such, it is possible that the primary host of many newly isolated mycobacteriophages is not M. smegmatis, but instead a range of closely related bacterial species. However, determining mycobacteriophage host range presents difficulties associated with mycobacterial cultivability, pathogenicity and growth. Another way to gain insight into mycobacteriophage host range and ecology is through bioinformatic analysis of their genomic sequences. To this end, we examined the correlations between the codon usage biases of 199 different mycobacteriophages and those of several fully sequenced mycobacterial species in order to gain insight into the natural host range of these mycobacteriophages. We find that UPGMA clustering tends to match, but not consistently, clustering by shared nucleotide sequence identify. In addition, analysis of GC content, tRNA usage and correlations between mycobacteriophage and mycobacterial codon usage bias suggests that the preferred host of many clustered mycobacteriophages is not M. smegmatis but other, as yet unknown, members of the mycobacteria complex or closely allied bacterial species.