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FIGURE 1 0 in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data

FIGURE 1 0 Typical habitat of C. dule, Arquia river

FIGURE 6 C. dule n in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data

FIGURE 6 C. dule n. sp. IMCN 8941, Holotype 37.4 mm LS. Scale bar = 1 cm

FIGURE 9 C. dule n in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data

FIGURE 9 C. dule n. sp. IMCN 8929, Paratype. Live specimen. Scale bar = 1 cm

FIGURE 5 in The unknown diversity of the genus Characidium (Characiformes: Crenuchidae) in the Chocó biogeographic region, Colombian Andes: Two new species supported by morphological and molecular data

FIGURE 5 Typical habitat of C. dule, Ingará River, San José Del Palmar, Chocó, Colombia

opencc-zeroSep 2020View details →

Data from: A virtual molecular tumor board platform to improve efficiency and scalability of delivering precision oncology to physicians and their patients

OBJECTIVES: Scalable informatics solutions that provide molecularly-tailored treatment recommendations to clinicians are needed to streamline Precision Oncology in care settings. MATERIALS AND METHODS: We developed a cloud-based virtual molecular tumor board (VMTB) platform that included a knowledgebase, scoring model, rules engine, an asynchronous virtual chat room and a reporting tool that generated a treatment plan for each of the 1725 patients based on their molecular profile, previous treatment history, structured trial eligibility criteria, clinically relevant cancer gene-variant assertions, biomarker-treatment associations, and current treatment guidelines. The VMTB systematically allows clinician users to combine expert-curated data and structured data from clinical charts along with molecular testing data to develop consensus on treatments, especially those that require off-label and clinical trial considerations. RESULTS: The VMTB was used as part of the cancer care process for a focused subset of 1725 patients referred by advocacy organizations wherein resultant personalized reports were successfully delivered to treating oncologists. Median turnaround time from data receipt to report delivery decreased from 14 days to 4 days over 4 years while the volume of cases increased nearly twofold each year. Using a novel scoring model for ranking therapy options, oncologists chose to implement the VMTB-derived therapies over others, except when pursuing immunotherapy options without molecular support. DISCUSSION: VMTBs will play an increasingly critical role in precision oncology as the compendium of biomarkers and associated therapy options available to a patient continues to expand. CONCLUSION: Further development of such clinical augmentation tools that systematically combine patient-derived molecular data, real world evidence from electronic health records, and expert curated knowledgebases on biomarkers with computational tools for ranking best treatments can support care pathways at point of care.

Fig. 9 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 9. Anaplecta bicolor Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Pronotum, dorsal view. D. Head, ventral view. E. Tegmina. F. Tegmina vein. G. Front femur, ventral view. H. Wings. I. Supra-anal plate, dorsal view. J. Subgenital plate, ventral view. K. Hook, ventral view. L. Left phallomere, ventral view. M. Right phallomere, ventral view. Scale bars: A–B, G–H = 1 mm; C–F, I–J = 0.5 mm; K–M = 0.25 mm.

Fig. 8 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 8. Anaplecta nigra Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Maxillary palp. F. Front femur, ventral view. G. Tegmina. H. Wings. I. Supra-anal plate, dorsal view. J. Subgenital plate, ventral view. K. Hook, ventral view. L. Left and right phallomeres, ventral view. M. L2d. Scale bars: A–D = 1 mm; E–J, M = 0.5 mm; K–L = 0.25 mm.

Fig. 2 in Eight new species of the genus Anaplecta Burmeister, 1838 (Blattodea: Blattoidea: Anaplectidae) from China based on molecular and morphological data

Fig. 2. Anaplecta corneola Deng & Che sp. nov., holotype, ♂ (SWU). A. Habitus, dorsal view. B. Habitus, ventral view. C. Head, ventral view. D. Pronotum, dorsal view. E. Tegmina. F. Tegmina vein. G. Maxillary palp. H. Front femur, ventral view. I. Wings. J. Supra-anal plate, dorsal view. K. Subgenital plate, ventral view. L. Hook, ventral view. M. Left phallomere, ventral view. N. Right phallomere, ventral view. Scale bars: A–B, E–F, I = 2 mm; C, G–H = 1 mm; D, J–K, M–N = 0.5 mm; L = 0.25 mm.

Data for figures in "Quantum spin-liquid states in an organic magnetic layer and molecular rotor hybrid"

Data used to produce the figures in the work entitled "Quantum spin-liquid states in an organic magnetic layer and molecular rotor hybrid"

opencc-by-4.0Apr 2020View details →

Molecular dynamics simulation data of designed cyclic peptide (ligand-binding)

Trajectories of ligand binding simulation and simulation set-up files of designed cyclic peptide as MDM2 binders.  The original paper of these designed cyclic peptide: Danelius, E., Pettersson, M., Bred, M., Min, J., Waddell, M. B., Guy, R. K., et al. (2016). Flexibility is important for inhibition of the MDM2/p53 protein–protein interaction by cyclic β-hairpins. Org. Biomol. Chem., 14(44), 10386–10393. http://doi.org/10.1039/C6OB01510G

opennotspecifiedOct 2020View details →

FIGURE 25 in Vietnamella chebalingensis, a new species of the family Vietnamellidae (Ephemeroptera) from China based on morphological and molecular data

FIGURE 25. Habitat of Vietnamella chebalingensis Tong, sp. nov.

opencc-zeroDec 2014View details →

Data from: Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function

Background: Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles. The lack of genetic, genomic and transcriptomic data for cartilaginous fish has hindered a more thorough understanding of the molecular-level functions of the chondrichthyan pancreas, particularly with respect to their "unusual" energy metabolism (where ketone bodies and amino acids are the main oxidative fuel source) and their paradoxical ability to both maintain stable blood glucose levels and tolerate extensive periods of hypoglycemia. In order to shed light on some of these processes, we carried out the first large-scale comparative transcriptomic survey of multiple cartilaginous fish tissues: the pancreas, brain and liver of the lesser spotted catshark, Scyliorhinus canicula. Results: We generated a mutli-tissue assembly comprising 86,006 contigs, of which 44,794 were assigned to a particular tissue or combination of tissues based on mapping of sequencing reads. We have characterised transcripts encoding genes involved in insulin regulation, glucose sensing, transcriptional regulation, signaling and digestion, as well as many peptide hormone precursors and their receptors for the first time. Comparisons to mammalian pancreas transcriptomes reveals that mechanisms of glucose sensing and insulin regulation used to establish and maintain a stable internal environment are conserved across jawed vertebrates and likely pre-date the vertebrate radiation. Conservation of pancreatic hormones and genes encoding digestive proteins support the single, early evolution of a distinct pancreatic gland with endocrine and exocrine functions in jawed vertebrates. In addition, we demonstrate that chondrichthyes lack pancreatic polypeptide (PP) and that reports of PP in the literature are likely due cross-reaction with PYY and/or NPY in the pancreas. A three hormone islet organ is therefore the ancestral jawed vertebrate condition, later elaborated upon only in the tetrapod lineage. Conclusions: The cartilaginous fish are a great untapped resource for the reconstruction of patterns and processes of vertebrate evolution and new approaches such as those described in this paper will greatly facilitate their incorporation into the rank of "model organism".

opencc-zeroDec 2014View details →

Data from: Molecular evolution of the neural crest regulatory network in ray-finned fish

Gene regulatory networks (GRN) are central to developmental processes. They are composed of transcription factors and signaling molecules orchestrating gene expression modules that tightly regulate the development of organisms. The neural crest (NC) is a multipotent cell population that is considered a key innovation of vertebrates. Its derivatives contribute to shaping the astounding morphological diversity of jaws, teeth, head skeleton or pigmentation. Here, we study the molecular evolution of the NC GRN by analyzing patterns of molecular divergence for a total of 36 genes in 16 species of bony fishes. Analyses of non-synonymous to synonymous substitution rate ratios (dN/dS) support patterns of variable selective pressures among genes deployed at different stages of NC development, consistent with the developmental hourglass model. Model-based clustering techniques of sequence features support the notion of extreme conservation of NC-genes across the entire network. Our data show that most genes are under strong purifying selection that is maintained throughout ray-finned fish evolution. Late NC development genes reveal a pattern of increased constraints in more recent lineages. Additionally, seven of the NC-genes showed signs of relaxation of purifying selection in the famously species-rich lineage of cichlid fishes. This suggests that NC genes might have played a role in the adaptive radiation of cichlids by granting flexibility in the development of NC-derived traits – suggesting an important role for NC network architecture during the diversification in vertebrates.

opencc-zeroDec 2015View details →

Data from: A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary

The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record. Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible-jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree-wide diversification-rate variation and mass-extinction events by specifying a biologically informed prior on the magnitude of mass-extinction events and empirical hyperpriors on the diversification-rate parameters. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events and provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e. <5%) false-discovery rate, even when background diversification rates vary. Finally, we provide an empirical demonstration of this approach, which reveals that conifers experienced a major episode of mass extinction ≈23 Ma. This new approach – the CPP on Mass-Extinction Times (CoMET) model – provides an effective tool for detecting the impact of mass-extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.

opencc-zeroDec 2015View details →

Data from: The impact of the tree prior on molecular dating of data sets containing a mixture of inter- and intraspecies sampling

In Bayesian phylogenetic analyses of genetic data, prior probability distributions need to be specified for the model parameters, including the tree. When Bayesian methods are used for molecular dating, available tree priors include those designed for species-level data, such as the pure-birth and birth-death priors, and coalescent-based priors designed for population-level data. However, molecular dating methods are frequently applied to data sets that include multiple individuals across multiple species. Such data sets violate the assumptions of both the speciation and coalescent-based tree priors, making it unclear which should be chosen and whether this choice can affect the estimation of node times. To investigate this problem, we used a simulation approach to produce data sets with different proportions of within- and between-species sampling under the multispecies coalescent model. These data sets were then analysed under pure-birth, birth-death, constant-size coalescent, and skyline coalescent tree priors. We also explored the ability of Bayesian model testing to select the best-performing priors. We confirmed the applicability of our results to empirical data sets from cetaceans, phocids, and coregonid whitefish. Estimates of node times were generally robust to the choice of tree prior, but some combinations of tree priors and sampling schemes led to large differences in the age estimates. In particular, the pure-birth tree prior frequently led to inaccurate estimates for data sets containing a mixture of inter- and intraspecific sampling, whereas the birth-death and skyline coalescent priors produced stable results across all scenarios. Model testing provided an adequate means of rejecting inappropriate tree priors. Our results suggest that tree priors do not strongly affect Bayesian molecular dating results in most cases, even when severely misspecified. However, the choice of tree prior can be significant for the accuracy of dating results in the case of data sets with mixed inter- and intraspecies sampling.

opencc-zeroDec 2012View details →

Data from: Molecular field analysis of trophic relationships in soil-dwelling invertebrates to identify mercury, lead and cadmium transmission through forest ecosystems

Contamination pathways in complex food chains in soil ecosystems can be difficult to elucidate. Molecular analysis of predator gut content can, however, rapidly reveal previously unidentified trophic interactions between invertebrates and thereby uncover pathways of pollutant spread. Here we measured concentrations of the toxic metals lead, cadmium and mercury in carabid beetle predators and their prey. Invertebrates were sampled at one control and four heavy metal polluted sites in order to reveal the impact of diet composition and seasonal variation in prey availability on metal burden in carabids and metal transfer pathways through forest ecosystems. This is the first report, to our knowledge, of carabid diet composition based on PCR analysis of gut contents at the forest community level, rather than in cultivated fields. Extensive screening using group- and species-specific primers revealed that carabids ate primarily earthworms and slugs, as well as smaller numbers of woodlice and springtails. Metal concentrations in carabids correlated with seasonal changes in diet. Mercury accumulated in beetle predators more than in their slug prey. Since earthworms, slugs and carabid beetles are the major prey of many birds and mammals, prey-predator transfer and associated toxicity are major risks at mercury-contaminated sites. Carabids may be useful bioindicators for assessing the impact of pollutants on soil ecosystems, as long as species and seasonal factors are taken into account.

opencc-zeroDec 2013View details →

Data from: Calibration uncertainty in molecular dating analyses: there is no substitute for the prior evaluation of time priors

Calibration is the rate-determining step in every molecular clock analysis and, hence, considerable effort has been expended in the development of approaches to distinguish good from bad calibrations. These can be categorized into a priori evaluation of the intrinsic fossil evidence, and a posteriori evaluation of congruence through cross-validation. We contrasted these competing approaches and explored the impact of different interpretations of the fossil evidence upon Bayesian divergence time estimation. The results demonstrate that a posteriori approaches can lead to the selection of erroneous calibrations. Bayesian posterior estimates are also shown to be extremely sensitive to the probabilistic interpretation of temporal constraints. Furthermore, the effective time priors implemented within an analysis differ for individual calibrations when employed alone and in differing combination with others. This compromises the implicit assumption of all calibration consistency methods, that the impact of an individual calibration is the same when used alone or in unison with others. Thus, the most effective means of establishing the quality of fossil-based calibrations is through a priori evaluation of the intrinsic palaeontological, stratigraphic, geochronological and phylogenetic data. However, effort expended in establishing calibrations will not be rewarded unless they are implemented faithfully in divergence time analyses.

opencc-zeroDec 2008View details →

Data from: Molecular and morphological phylogenetics of weevils (Coleoptera, Curculionoidea): do niche shifts accompany diversification?

The main goals of this study were to provide a robust phylogeny for the families of the superfamily Curculionoidea, to discover relationships and major natural groups within the family Curculionidae, and to clarify the evolution of larval habits and host-plant associations in weevils to analyze their role in weevil diversification. Phylogenetic relationships among the weevils (Curculionoidea) were inferred from analysis of nucleotide sequences of 18S ribosomal DNA (rDNA; ~2,000 bases) and 115 morphological characters of larval and adult stages. A worldwide sample of 100 species was compiled to maximize representation of weevil morphological and ecological diversity. All families and the main subfamilies of Curculionoidea were represented. The family Curculionidae sensu lato was represented by about 80 species in 30 "subfamilies" of traditional classifications. Phylogenetic reconstruction was accomplished by parsimony analysis of separate and combined molecular and morphological data matrices and Bayesian analysis of the molecular data; tree topology support was evaluated. Results of the combined analysis of 18S rDNA and morphological data indicate that monophyly of and relationships among each of the weevil families are well supported with the topology ((Nemonychidae, Anthribidae) (Belidae (Attelabidae (Caridae (Brentidae, Curculionidae))))). Within the clade Curculionidae sensu lato, the basal positions are occupied by mostly monocot-associated taxa with the primitive type of male genitalia followed by the Curculionidae sensu stricto, which is made up of groups with the derived type of male genitalia. High support values were found for the monophyly of some distinct curculionid groups such as Dryophthorinae (several tribes represented) and Platypodinae (Tesserocerini plus Platypodini), among others. However, the subfamilial relationships in Curculionidae are unresolved or weakly supported. The phylogeny estimate based on combined 18S rDNA and morphological data suggests that diversification in weevils was accompanied by niche shifts in host-plant associations and larval habits. Pronounced conservatism is evident in larval feeding habits, particularly in the host tissue consumed. Multiple shifts to use of angiosperms in Curculionoidea were identified, each time associated with increases in weevil diversity and subsequent shifts back to gymnosperms, particularly in the Curculionidae.

opencc-zeroDec 2008View details →

Data from: Combined molecular phylogenetic analysis of the Orthoptera (Arthropoda, Insecta) and implications for their higher systematics

A phylogenetic analysis of mitochondrial and nuclear rDNA sequences from species of all the superfamilies of the insect order Orthoptera (grasshoppers, crickets and relatives) confirmed that although mitochondrial sequences provided good resolution of the youngest superfamilies, nuclear rDNA sequences were necessary to separate the basal groups. To try to reconcile these data sets into a single fully resolved orthopteran phylogeny, we adopted consensus and combined data strategies. The consensus analysis produced a partially resolved tree, lacking several well-supported features of the individual analyses. However, this lack of resolution was explained by an examination of resampled data sets that identified the likely source of error as the relatively short length of the individual mitochondrial data partitions. In a subsequent comparison in which the mitochondrial sequences were initially combined, we observed less conflict. We then used two approaches to examine the validity of combining all of the data in a single analysis; comparative analysis of trees recovered from resampled data sets and the application of a randomization test. The results did not point to significant levels of heterogeneity in phylogenetic signal between the mitochondrial and nuclear data sets, and we therefore proceeded with a combined analysis. Reconstructing phylogenies under the minimum evolution and maximum likelihood optimality criteria, we examined monophyly of the major orthopteran groups using nonparametric and parametric bootstrap analysis and Kishino-Hasegawa tests. Our analysis suggests that phylogeny reconstruction under the ML criteria is the most discriminating approach for the combined sequences. The results indicate that the caeliferan Pneumoroidea and Pamphagoidea (as previously suggested) are polyphyletic. The Acridoidea is redefined to include all pamphagoid families other than the Pyrgomorphidae, which we propose should be accorded superfamily status.