Phylogenetic systematic assessment of the Aspidobothrea (Platyhelminthes, Neodermata, Trematoda)

Phylogenetic systematic analysis of 20 aspidobothrean taxa using 33 transformation series based in comparative morphology yields three most parsimonious trees with a consistency index of 62%. The trees agree with familial-level relationships of (Rugogastridae (Stichocotylidae (Multicalycidae + Aspidogastridae))) supported by previous phylogenetic systematic assessments, which were based on only 10 transformation series. The analysis does not support completely the current subfamilial classification of the Aspidogastridae: both the Aspidobothriinae [as ( Aspidogaster + Lobatostoma )] and the Cotylaspinae [as Cotylogasteroides + Cotylogaster basiri (( Cotylaspis + Lissemysia ) ( Rohdella ( Lophotaspis ( Multicotyle + Sychnocotyle )))))] are supported as monophyletic groups. Recognizing Rohdellinae, however, would make the Cotylaspinae paraphyletic. The trees support a basal trichotomy of Cotylogaster michaelis + Aspidobothriinae + Cotylaspinae. Within the Aspidogastrinae, Aspidogaster conchicola , type species of the genus, is the sister group of all other species currently placed in the genus + Lobatosoma spp., rendering Aspidogaster paraphyletic.     

CLADISTIC REAPPRAISAL OF NEOTROPICAL STENODERMATINE BAT PHYLOGENY

Abstract— Several phylogenies have been proposed for neotropical stenodermatine fruit-eating bats (Phyllostomidae), based on detention, external morphology, osteology and chromosomes. However, these previous analyses did not incorporate fully the idea that relationships should be identified based solely on shared derived characteristics. A critique of past methodology and results, and an alternative phylogeny using a morphological data set supplemented with karyotypic information, is presented. In my analysis, there appear two main lineages. The eight genera of white-shouldered bats form a monophyletic clade based on three synapomorphies (white patch of fur on shoulders, lack of a palatial extension with varying degrees of emargination and modified upper incisors); previous work suggested a paraphyletic relationship for this group. Furthermore, the monophyly of the four genera endemic to the Antilles is supported by two synapomorphies, suggesting a common origin as opposed to a multiple invasion for these genera. The appearance of the derived 2n = 30 and FN = 56 standard karyotype suggests that the morphologically distinct Sturnira forms the sister taxon to the remaining genera which are united by the synapomorphy of white facial stripes. This supports the inclusion of Sturnira within the stendodermatines and not in its own monotypic higher-level taxon. My results do not refute the traditional systematic view of Artibeus (including Dermanura, Koopmania and Enchisthenes ) being monophyletic, and supports Mesophylla and Vampyressa being distinct non-sister genera.     

Bayesian Statistics-Based Procedure for Sampling of Contaminated Sites

A variable density sampling pattern based on Bayesian statistics is presented and compared to a uniform density statistical pattern and a judgmental approach in a real case study. The Bayesian statistics, supported by a software tool, supplied a soil sampling plan similar to the judgmental one, especially for the number of sampling points and their location. It allowed statistical goals to be set and expert judgment to be included in the sampling strategy in a transparent and systematic procedure. For these reasons, it appears quite suitable for inclusion into Quality Assurance Quality Control plans.     

Systematic positions of Lamiophiomis and Paraphlomis (Lamiaceae) based on nuclear and chloroplast sequences

Genera Lamiophlomis and Paraphlomis were originally separated from genus Phlomis s.l. on the basis of particular morphological characteristics. However, their relationship was highly contentious, as evidenced by the literature. In the present paper, the systematic positions of Lamiophlomis, Paraphlomis, and their related genera were assessed based on nuclear internal transcribed spacer (ITS) and chloroplast rpl16 and trnL-F sequence data using maximum parsimony (MP) and Bayesian methods. In total, 24 species representing six genera of the ingroup and outgroup were sampled. Analyses of both separate and combined sequence data were conducted to resolve the systematic relationships of these genera. The results reveal that Lamiophlomis is nested within Phlomis sect. Phlomoides and its genetic status is not supported. With the inclusion of Lamiophlomis rotata in sect. Phlomoides, sections Phlomis and Phlomoides of Phlomis were resolved as monophyletic. Paraphlomis was supported as an inde-pendent genus. However, the resolution of its monophyly conflicted between MP and Bayesian analyses, suggesting the need for expended sampling and further evidence.     

Phylogenetic position and generic differentiation of Epithemateae (Gesneriaceae) inferred from plastid DNA sequence data

The systematic position and generic differentiation of the morphologically and geographically outstanding tribe Epithemateae (Gesneriaceae) was analyzed using the rbcL/atpB-spacer and trnL-F intron-spacer regions of chloroplast DNA. In our analysis Epithemateae forms a strongly supported monophyletic clade (bootstrap [BS] = 100%; jackknife [JK] = 100%; decay index [DI] = 12) and appears as sister to the rest of the paleotropical Gesneriaceae (= subfamily Cyrtandroideae). The paleotropical Gesneriaceae form a monophyletic group (BS = 88%; JK = 85%; DI = 3) that is sister to the neotropical Gesneriaceae (subfamily Gesnerioideae) plus Austral Gesneriaceae (subfamily Coronantheroideae) (BS = 99%; JK = 98%; DI = 10). Within Epithemateae Rhynchoglossum is sister to the remaining Epithemateae (BS = 97%; JK = 96%; DI = 12), in which Epithema is sister to a clade of two genera: Loxonia/Stauranthera (BS = 68%; JK = 64%; DI = 1), which form, together with Epithema, a sister clade (BS = 85%; JK = 83%; DI = 2) to Whytockia and Monophyllaea. While the support for Loxonia and Stauranthera is moderate, the relationship of Whytockia and Monophyllaea is very strongly supported (BS = 100%; JK = 100%; DI = 13). Apart from the somewhat surprising (but well-substantiated) isolated position of Rhynchoglossum, the results are in perfect accordance with the relationships worked out earlier on grounds of architectural and floral characters. Especially remarkable is the predicted coherence between the morphologically and geographically different genera Whytockia and Monophyllaea.     

Studies on the Karyotype and Systematic Position of Larix Mill. (Pinaceae)

The present paper reports the karyotype of Larix potaninii Batal. endemic to China, and discuss classification of Larix and its systematic position in the Pinaceae based on karyotype and other data. The karyotypic formula of the species is K(2n)=24= 12m+ 8sm+4st, which belongs to Stebbins’2A type and the chromosome complement of relative length is 2n=24=4L+8M₂+8M₁+4S. The karyotype of the genus Larix (10 species) is composed of six pairs of longer metacentric chromosomes and six pairs of shorter submetacentric or subtelocentric chromosomes with arm ratio>2. This karyotype is an advanced one. It seems that Sect. Multiserales is more advanced than Sect. Larix. On the basis of the comparison among the karyotypes of pinaceous genera, the author finds that Larix and Pseudotsuga are much more closely related to each other than any of them to the others. Therefore, it may be more appropriate to group these two genera into Subfamily Laricoideae, which is a more advanced one. The conclusion is also supported by the data from morphology, anatomy, palynology,biochemistry, palaeobotany and so on.     

Developmental Stage Age Groups and African Population Structure: The Kusasi of the West African Savanna

African population structures based on censuses exhibit a distinctive pattern of distortion. It is often assumed that the cause for this distortion is systematic biases in age estimates by census enumerators and respondents influenced by perceptions of social and biological development. African developmental stage age groups are the cultural codification of such perceptions. I describe developmental stage age groups among the Kusasi of Bawku District in northeast Ghana, and analyze their age and sex structure for a sample of 1,132 individuals from the village of Zorse. I show that differences between men and women reflect differences in biological and social development, and that cultural concepts of developmental stages could influence age estimates to produce the pattern of distortions typical of those found in African population structures based on censuses. This is supported by a comparison of Bawku District population structure based on the Ghana census and an ethnographic sample census in Zorse which eliminated most age estimate biases.     

Morphology of pollen and orbicules in some Dioscorea species and its systematic implications

Pollen and orbicule morphology of 35 Dioscorea L. species is described based on observations with light microscopy, and scanning and transmission electron microscopy. Pollen and orbicule characters are critically evaluated and discussed in the context of existing hypotheses of systematic relationships within the genus. Pollen is mostly bisulcate (sometimes monosulcate) with a perforate, microreticulate or striate sexine. Our results indicate that pollen data may be significant at sectional rank. The close relationship between sections Asterotricha and Enantiophyllum proposed by Burkill and Ayensu is supported by pollen morphology as all species investigated share bisulcate, perforate pollen with small perforations and a high perforation density. Macromorphological differences between the two compound-leaved sections Botryosicyos and Lasiophyton are also supported by pollen morphology; pollens of these two sections have very different perforation patterns. Orbicules in Dioscorea are mostly spherical and possess a smooth or spinulose surface. The latter is often correlated with a striate sexine.     

Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability

We are developing distance-restrained docking strategies for modeling macromolecular complexes that combine available high-resolution structures of the components and intercomponent distance restraints derived from systematic fluorescence resonance energy transfer (FRET) measurements. In this article, we consider the problem of docking small-molecule ligands within macromolecular complexes. Using simulated FRET data, we have generated a series of benchmarks that permit estimation of model accuracy based on the quantity and quality of FRET-derived distance restraints, including the number, random error, systematic error, distance distribution, and radial distribution of FRET-derived distance restraints. We find that expected model accuracy is 10 A or better for models based on: i), > or =20 restraints with up to 15% random error and no systematic error, or ii), > or =20 restraints with up to 15% random error, up to 10% systematic error, and a symmetric radial distribution of restraints. Model accuracies can be improved to 5 A or better by increasing the number of restraints to > or =40 and/or by optimizing the distance distribution of restraints. Using experimental FRET data, we have defined the positions of the binding sites within bacterial RNA polymerase of the small-molecule inhibitors rifampicin (Rif) and rifamycin SV (Rif SV). The inferred binding sites for Rif and Rif SV were located with accuracies of, respectively, 7 and 10 A relative to the crystallographically defined binding site for Rif. These accuracies agree with expectations from the benchmark simulations and suffice to indicate that the binding sites for Rif and Rif SV are located within the RNA polymerase active-center cleft, overlapping the binding site for the RNA-DNA hybrid.     

A three-genome phylogeny of malaria parasites (Plasmodium and closely related genera): evolution of life-history traits and host switches

Phylogenetic analysis of genomic data allows insights into the evolutionary history of pathogens, especially the events leading to host switching and diversification, as well as alterations of the life cycle (life-history traits). Hundreds, perhaps thousands, of malaria parasite species exploit squamate reptiles, birds, and mammals as vertebrate hosts as well as many genera of dipteran vectors, but the evolutionary and ecological events that led to this diversification and success remain unresolved. For a century, systematic parasitologists classified malaria parasites into genera based on morphology, life cycle, and vertebrate and insect host taxa. Molecular systematic studies based on single genes challenged the phylogenetic significance of these characters, but several significant nodes were not well supported. We recovered the first well resolved large phylogeny of Plasmodium and related haemosporidian parasites using sequence data for four genes from the parasites' three genomes by combining all data, correcting for variable rates of substitution by gene and site, and using both Bayesian and maximum parsimony analyses. Major clades are associated with vector shifts into different dipteran families, with other characters used in traditional parasitological studies, such as morphology and life-history traits, having variable phylogenetic significance. The common parasites of birds now placed into the genus Haemoproteus are found in two divergent clades, and the genus Plasmodium is paraphyletic with respect to Hepatocystis, a group of species with very different life history and morphology. The Plasmodium of mammal hosts form a well supported clade (including Plasmodium falciparum, the most important human malaria parasite), and this clade is associated with specialization to Anopheles mosquito vectors. The Plasmodium of birds and squamate reptiles all fall within a single clade, with evidence for repeated switching between birds and squamate hosts.     

A systematic study of the genus hulsea (Asteraceae)

A systematic treatment based on genetic, biochemical, and morphological studies is presented for the 11 recognized taxa ofHulsea. A uniform diploid complement of 38 chromosomes was found in the 37 populations examined, including all species and representing first reports forH. brevifolia, H. californica, andH. mexicana. Thirteen flavonoid compounds, based on the aglycones quercetin, apigenin, cyanidin, and the 4′-O-methyl ether of luteolin, were detected inHulsea. Patterns of the flavonoid compounds are discussed with respect to the systematic treatment. The results of 595 synthetic crosses indicate thatHulsea species are self-incompatible, relatively cross-compatible, and that their F₁ hybrids are relatively fertile. Heterozygosity for one or two translocations is reported for 11 interspecific and intersubspecific hybrid combinations.     

Assessment of methodological quality of primary studies by systematic reviews: results of the metaquality cross sectional study

Objectives To describe how the methodological quality of primary studies is assessed in systematic reviews and whether the quality assessment is taken into account in the interpretation of results.Data sources Cochrane systematic reviews and systematic reviews in paper based journals.Study selection 965 systematic reviews (809 Cochrane reviews and 156 paper based reviews) published between 1995 and 2002.Data synthesis The methodological quality of primary studies was assessed in 854 of the 965 systematic reviews (88.5%). This occurred more often in Cochrane reviews than in paper based reviews (93.9% v 60.3%, P < 0.0001). Overall, only 496 (51.4%) used the quality assessment in the analysis and interpretation of the results or in their discussion, with no significant differences between Cochrane reviews and paper based reviews (52% v 49%, P = 0.58). The tools and methods used for quality assessment varied widely.Conclusions Cochrane reviews fared better than systematic reviews published in paper based journals in terms of assessment of methodological quality of primary studies, although they both largely failed to take it into account in the interpretation of results. Methods for assessment of methodological quality by systematic reviews are still in their infancy and there is substantial room for improvement.     

Evolution of insular Pacific Pittosporum (Pittosporaceae): origin of the Hawaiian radiation.

We investigated the origin of Hawaiian Pittosporum and their relationship to other South Pacific Pittosporum species using internal transcribed spacer sequences of nuclear ribosomal DNA. We performed both maximum-parsimony and maximum-likelihood analyses, which produced congruent results. Sequence divergence was 0.0% between Hawaiian members of Pittosporum. These taxa formed a strongly supported clade, suggesting a single colonization event followed by phyletic radiation. Sister to the Hawaiian clade were two South Pacific species, P. yunckeri from Tonga and P. rhytidocarpum from Fiji. This result presents convincing evidence for a South Pacific origin of Hawaiian Pittosporum. Our results also identify a monophyletic group comprising three species representing the Fijian Province and East Polynesia, two introductions onto New Caledonia, and at least one (but possibly two) introduction(s) onto New Zealand. Whether the New Zealand taxa form a monophyletic group is unclear from these data. Previous morphologically based hypotheses, however, suggest the presence of four different lineages occupying New Zealand. The nonmonophyly of the New Caledonian species was not surprising based on the extent of their morphological diversity. Although this latter result is not strongly supported, these species are morphologically complex and are currently the subject of taxonomic revision and molecular systematic analyses.     

The efficacy of app‐supported smartphone interventions for mental health problems: a meta‐analysis of randomized controlled trials

Although impressive progress has been made toward developing empirically‐supported psychological treatments, the reality remains that a significant proportion of people with mental health problems do not receive these treatments. Finding ways to reduce this treatment gap is crucial. Since app‐supported smartphone interventions are touted as a possible solution, access to up‐to‐date guidance around the evidence base and clinical utility of these interventions is needed. We conducted a meta‐analysis of 66 randomized controlled trials of app‐supported smartphone interventions for mental health problems. Smartphone interventions significantly outperformed control conditions in improving depressive (g=0.28, n=54) and generalized anxiety (g=0.30, n=39) symptoms, stress levels (g=0.35, n=27), quality of life (g=0.35, n=43), general psychiatric distress (g=0.40, n=12), social anxiety symptoms (g=0.58, n=6), and positive affect (g=0.44, n=6), with most effects being robust even after adjusting for various possible biasing factors (type of control condition, risk of bias rating). Smartphone interventions conferred no significant benefit over control conditions on panic symptoms (g=–0.05, n=3), post‐traumatic stress symptoms (g=0.18, n=4), and negative affect (g=–0.08, n=5). Studies that delivered a cognitive behavior therapy (CBT)‐based app and offered professional guidance and reminders to engage produced larger effects on multiple outcomes. Smartphone interventions did not differ significantly from active interventions (face‐to‐face, computerized treatment), although the number of studies was low (n≤13). The efficacy of app‐supported smartphone interventions for common mental health problems was thus confirmed. Although mental health apps are not intended to replace professional clinical services, the present findings highlight the potential of apps to serve as a cost‐effective, easily accessible, and low intensity intervention for those who cannot receive standard psychological treatment.     

Molecular phylogenetic convergence within Elasmobranchii revealed by cytochrome oxidase subunits

The phylogenetic relationships within the subclass of Elasmobranchii are under question within the academic community and their systematic classification based on morphological, or physiological characteristics has not yet been fully justified. Modern cladistic studies suggested that batoids are derived sharks, a taxonomic status known as the Hypnosqualean hypothesis. The main purpose of this study was to address this issue using a data set of aligned, directly sequenced, mitochondrial cytochrome oxidase subunits I and II. Maximum Likelihood, Maximum Parsimony, Minimum Evolution and Bayesian inference were implemented for tree reconstructions. The results provided evidence that supported the rejection of the above hypothesis, in accordance with other recent molecular phylogenetic studies. More specifically Rajiformes species were presented as separate lineages from sharks. Prionace species on the other hand was grouped within Carcharhinoformes, which was clustered as sister group to Lamniformes. COI and COII regions supported, monophylies of Squaliformes and paraphylies of Carchariniformes.     

The hyo-laryngeal complex of Tarsius bancanus (Mammalia, Primates): a developmental and phylogenetic aspect

The present approach reconstructed the hyo-laryngeal complex of fetal Tarsius bancanus by using the AMIRA 3.1.1 software. Our work fills a gap of ontogenetic research as this region has only been superficially described for an adult specimen representing the same genus. Furthermore, based on 51 characters we conducted several cladistic analyses considering the "Prosimii"/Haplorrhini-debate. Some anatomical information has been taken from the literature. MacClade 4.06 was used in order to measure TL-, CI-, and RC-values of these two competing hypotheses, however, resulting in equal support. A PAUP 4.02b parsimony analysis based on the Haplorrhini-hypothesis showed a significant bootstrap-value: the Pan and Alouatta-clade was supported with 90 % in spite of the highly derived morphology of the howler monkey. This fact reflects the importance of fetal data for systematic research. The study might serve as a morphological basement for further experimental studies of vocal communication.     

New contributions to the phylogeny of the ciliate class Heterotrichea (Protista,Ciliophora): analyses at family-genus level and new evolutionary hypotheses

Heterotrichous ciliates play an important role in aquatic ecosystem energy flow processes and many are model organisms for research in cytology, regenerative biology, and toxicology. In the present study, we combine both morphological and molecular data to infer phylogenetic relationships at family-genus level and propose new evolutionary hypotheses for the class Heterotrichea. The main results include:(1) 96 new ribosomal DNA sequences from 36 populations, representing eight families and 13 genera, including three poorly annotated genera, Folliculinopsis, Ampullofolliculina and Linostomella;(2) the earliest-branching families are Spirostomidae in single-gene trees and Peritromidae in the concatenated tree, but the family Peritromidae probably represents the basal lineage based on its possession of many "primitive" morphological characters;(3) some findings in molecular trees are not supported by morphological evidence, such as the family Blepharismidae is one of the most recent branches and the relationship between Fabreidae and Folliculinidae is very close;(4) the systematic positions of Condylostomatidae, Climacostomidae, and Gruberiidae remain uncertain based either on morphological or molecular data; and(5)the monophyly of each genus included in the present study is supported by the molecular phylogenetic trees, except for Blepharisma in the SSU r DNA tree and Folliculina in the ITS1-5.8 S-ITS2 tree.     

A Statistical Framework for Improving Genomic Annotations of Prokaryotic Essential Genes

Large-scale systematic analysis of gene essentiality is an important step closer toward unraveling the complex relationship between genotypes and phenotypes. Such analysis cannot be accomplished without unbiased and accurate annotations of essential genes. In current genomic databases, most of the essential gene annotations are derived from whole-genome transposon mutagenesis (TM), the most frequently used experimental approach for determining essential genes in microorganisms under defined conditions. However, there are substantial systematic biases associated with TM experiments. In this study, we developed a novel Poisson model–based statistical framework to simulate the TM insertion process and subsequently correct the experimental biases. We first quantitatively assessed the effects of major factors that potentially influence the accuracy of TM and subsequently incorporated relevant factors into the framework. Through iteratively optimizing parameters, we inferred the actual insertion events occurred and described each gene’s essentiality on probability measure. Evaluated by the definite mapping of essential gene profile in Escherichia coli, our model significantly improved the accuracy of original TM datasets, resulting in more accurate annotations of essential genes. Our method also showed encouraging results in improving subsaturation level TM datasets. To test our model’s broad applicability to other bacteria, we applied it to Pseudomonas aeruginosa PAO1 and Francisella tularensis novicida TM datasets. We validated our predictions by literature as well as allelic exchange experiments in PAO1. Our model was correct on six of the seven tested genes. Remarkably, among all three cases that our predictions contradicted the TM assignments, experimental validations supported our predictions. In summary, our method will be a promising tool in improving genomic annotations of essential genes and enabling large-scale explorations of gene essentiality. Our contribution is timely considering the rapidly increasing essential gene sets. A Webserver has been set up to provide convenient access to this tool. All results and source codes are available for download upon publication at http://research.cchmc.org/essentialgene/.     

The Williams' legacy: A critical reappraisal of his nine predictions about the evolution of senescence

Williams' evolutionary theory of senescence based on antagonistic pleiotropy has become a landmark in evolutionary biology, and more recently in biogerontology and evolutionary medicine. In his original article, Williams launched a set of nine “testable deductions” from his theory. Although some of these predictions have been repeatedly discussed, most have been overlooked and no systematic evaluation of the whole set of Williams' original predictions has been performed. For the sixtieth anniversary of the publication of the Williams' article, we provide an updated evaluation of all these predictions. We present the pros and cons of each prediction based on recent accumulation of both theoretical and empirical studies performed in the laboratory and in the wild. From our viewpoint, six predictions are mostly supported by our current knowledge at least under some conditions (although Williams' theory cannot thoroughly explain why for some of them). Three predictions, all involving the timing of senescence, are not supported. Our critical review of Williams' predictions highlights the importance of William's contribution and clearly demonstrates that, 60 years after its publication, his article does not show any sign of senescence.