Effects of phylogenetic reconstruction method on the robustness of species delimitation using single-locus data

1. Coalescent-based species delimitation methods combine population genetic and phylogenetic theory to provide an objective means for delineating evolutionarily significant units of diversity. The Generalized Mixed Yule Coalescent (GMYC) and the Poisson Tree Process (PTP) are methods that use ultrametric (GMYC or PTP) or non-ultrametric (PTP) gene trees as input, intended for use mostly with single-locus data such as DNA barcodes. 2. Here we assess how robust the GMYC and PTP are to different phylogenetic reconstruction and branch smoothing methods. We reconstruct over 400 ultrametric trees using up to 30 different combinations of phylogenetic and smoothing methods and perform over 2,000 separate species delimitation analyses across 16 empirical datasets. We then assess how variable diversity estimates are, in terms of richness and identity, with respect to species delimitation, phylogenetic and smoothing methods. 3. The PTP method generally generates diversity estimates that are more robust to different phylogenetic methods. The GMYC is more sensitive, but provides consistent estimates for BEAST trees. The lower consistency of GMYC estimates is likely a result of differences among gene trees introduced by the smoothing step. Unresolved nodes (real anomalies or methodological artefacts) affect both GMYC and PTP estimates, but have a greater effect on GMYC estimates. Branch smoothing is a difficult step and perhaps an underappreciated source of bias that may be widespread among studies of diversity and diversification. 4. Nevertheless, careful choice of phylogenetic method does produce equivalent PTP and GMYC diversity estimates. We recommend simultaneous use of the PTP model with any model-based gene tree (e.g. RAxML) and GMYC approaches with BEAST trees for obtaining species hypotheses

Sexual species are separated by larger genetic gaps than asexual species in rotifers.

Why organisms diversify into discrete species instead of showing a continuum of genotypic and phenotypic forms is an important yet rarely studied question in speciation biology. Does species discreteness come from adaptation to fill discrete niches or from interspecific gaps generated by reproductive isolation? We investigate the importance of reproductive isolation by comparing genetic discreteness, in terms of intra- and interspecific variation, between facultatively sexual monogonont rotifers and obligately asexual bdelloid rotifers. We calculated the age (phylogenetic distance) and average pairwise genetic distance (raw distance) within and among evolutionarily significant units of diversity in six bdelloid clades and seven monogonont clades sampled for 4211 individuals in total. We find that monogonont species are more discrete than bdelloid species with respect to divergence between species but exhibit similar levels of intraspecific variation (species cohesiveness). This pattern arises because bdelloids have diversified into discrete genetic clusters at a faster net rate than monogononts. Although sampling biases or differences in ecology that are independent of sexuality might also affect these patterns, the results are consistent with the hypothesis that bdelloids diversified at a faster rate into less discrete species because their diversification does not depend on the evolution of reproductive isolation

An improved method for discriminating ECG signals using typical nonlinear dynamic parameters and recurrence quantification analysis in cardiac disease therapy

The discrimination of ECG signals using nonlinear dynamic parameters is of crucial importance in the cardiac disease therapy and chaos control for arrhythmia defibrillation in the cardiac system. However, the discrimination results of previous studies using features such as maximal Lyapunov exponent (λ max) and correlation dimension (D 2) alone are somewhat limited in recognition rate. In this paper, improved methods for computing λ max and D 2 are purposed. Another parameter from recurrence quantification analysis is incorporated to the new multi-feature Bayesian classifier with λ max and D 2 so as to improve the discrimination power. Experimental results have verified the prediction using Fisher discriminant that the maximal vertical line length (V max) from recurrence quantification analysis is the best to distinguish different ECG classes. Experimental results using the MIT-BIH Arrhythmia Database show improved and excellent overall accuracy (96.3%), average sensitivity (96.3%) and average specificity (98.15%) for discriminating sinus, premature ventricular contraction and ventricular flutter signals. © 2005 IEEE.published_or_final_version27th Annual International Conference of the Engineering in Medicine and Biology Society (IEEE-EMBS 2005), Shanghai, 17-18 January 2006. In Conference Proceedings of IEEE Engineering in Medicine and Biology Society, 2005, p. 2459-246

Passive Prophylactic Administration with a Single Dose of Anti-Fel d 1 Monoclonal Antibodies REGN1908-1909 in Cat Allergen-Induced Allergic Rhinitis: A Randomized, Double-blind, Placebo Controlled Trial

RATIONALE: Sensitization to Felis domesticus allergen 1 (Fel d 1) contributes to persistent allergic rhinitis and asthma. Existing treatment options for cat allergy, including allergen immunotherapy (AIT) are only moderately effective, and AIT has limited use due to safety concerns. OBJECTIVES: To explore the relationship among the pharmaokinteic, clinical, and immunological effects of REGN1908-1909 (anti-Fel d 1 monoclonal antibodies) in patients after treatment. METHODS: Patients received REGN1908-1909 (n=36) or placebo (n=37) in a phase 1b study. Fel d 1-induced basophil and IgE-facilitated allergen binding responses were evaluated at baseline and days 8, 29 and 85. Cytokine and chemokine levels in nasal fluids were measured. REGN1908-1909 inhibition of allergen-IgE binding in patient serum was evaluated. MEASUREMENTS AND MAIN RESULTS: Peak serum drug concentrations were concordant with maximal observed clinical response. The anti-Fel d 1 IgE/cat-dander IgE ratio in pretreatment serum correlated with Total Nasal Symptom Score improvement. The allergen neutralizing capacity of REGN1908-1909 was observed in serum and nasal fluid, and was detected in an inhibition assay. Type-2 cytokines (IL-4, IL-5 and IL-13) and chemokines (CCL17/TARC, CCL5/RANTES) in nasal fluid were inhibited in REGN1908-1909-treated patients compared to placebo (all P < 0.05); IL-13 and IL-5 levels correlated with TNSS improvement. Ex vivo assays demonstrated that REGN1908 and REGN1909 combined was more potent than each alone for inhibiting FcεRI- and FcεRII (CD23)-mediated allergic responses and subsequent T-cell activation. CONCLUSION: Single passive dose administration of Fel d 1-neutralizing IgG antibodies improved nasal symptoms in cat-allergic patients, and was underscored by suppression of FcεRI-, FcεRII- and Th2-mediated allergic responses. Clinical trial registration available at www.clinicaltrials.gov, ID: NCT02127801

Full-field 3D shape measurement of discontinuous specular objects by direct phase measuring deflectometry

With the advent of intelligent manufacturing, phase measuring deflectometry (PMD) has been widely studied for the measurement of the three-dimensional (3D) shape of specular objects. However, existing PMDs cannot measure objects having discontinuous specular surfaces. This paper presents a new direct PMD (DPMD) method that measures the full-field 3D shape of complicated specular objects. A mathematical model is derived to directly relate an absolute phase map to depth data, instead of the gradient. Two relevant parameters are calibrated using a machine vision-based method. On the basis of the derived model, a full-field 3D measuring system was developed. The accuracy of the system was evaluated using a mirror with known positions along an accurate translating stage. The 3D shape of a monolithic multi-mirror array having multiple specular surfaces was measured. Experimental results show that the proposed DPMD method can obtain the full-field 3D shape of specular objects having isolated and/or discontinuous surfaces accurately and effectively

Observation of a ppb mass threshoud enhancement in \psi^\prime\to\pi^+\pi^-J/\psi(J/\psi\to\gamma p\bar{p}) decay

The decay channel $\psi^\prime\to\pi^+\pi^-J/\psi(J/\psi\to\gamma p\bar{p})$ is studied using a sample of $1.06\times 10^8$ $\psi^\prime$ events collected by the BESIII experiment at BEPCII. A strong enhancement at threshold is observed in the $p\bar{p}$ invariant mass spectrum. The enhancement can be fit with an $S$-wave Breit-Wigner resonance function with a resulting peak mass of $M=1861^{+6}_{-13} {\rm (stat)}^{+7}_{-26} {\rm (syst)} {\rm MeV/}c^2$ and a narrow width that is $\Gamma<38 {\rm MeV/}c^2$ at the 90% confidence level. These results are consistent with published BESII results. These mass and width values do not match with those of any known meson resonance.Comment: 5 pages, 3 figures, submitted to Chinese Physics

Fifteen species in one: deciphering the Brachionus plicatilis species complex (Rotifera, Monogononta) through DNA taxonomy

Understanding patterns and processes in biological diversity is a critical task given current and rapid environmental change. Such knowledge is even more essential when the taxa under consideration are important ecological and evolutionary models. One of these cases is the monogonont rotifer cryptic species complex Brachionus plicatilis, which is by far the most extensively studied group of rotifers, is widely used in aquaculture, and is known to host a large amount of unresolved diversity. Here we collate a dataset of previously available and newly generated sequences of COI and ITS1 for 1273 isolates of the B. plicatilis complex and apply three approaches in DNA taxonomy (i.e. ABGD, PTP, and GMYC) to identify and provide support for the existence of 15 species within the complex. We used these results to explore phylogenetic signal in morphometric and ecological traits, and to understand correlation among the traits using phylogenetic comparative models. Our results support niche conservatism for some traits (e.g. body length) and phylogenetic plasticity for others (e.g. genome size)

Interactions of the Apolipoprotein A5 Gene Polymorphisms and Alcohol Consumption on Serum Lipid Levels

Little is known about the interactions of apolipoprotein (Apo) A5 gene polymorphisms and alcohol consumption on serum lipid profiles. The present study was undertaken to detect the interactions of ApoA5-1131T>C, c.553G>T and c.457G>A polymorphisms and alcohol consumption on serum lipid levels.A total of 516 nondrinkers and 514 drinkers were randomly selected from our previous stratified randomized cluster samples. Genotyping was performed by polymerase chain reaction and restriction fragment length polymorphism. The levels of serum total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), ApoA1 and ApoB were higher in drinkers than in nondrinkers (P<0.05-0.001). The genotypic and allelic frequencies of three loci were not different between the two groups. The interactions between -1131T>C genotypes and alcohol consumption on ApoB levels (P<0.05) and the ApoA1/ApoB ratio (P<0.01), between c.553G>T genotypes and alcohol consumption on low-density lipoprotein cholesterol (LDL-C) levels (P<0.05) and the ApoA1/ApoB ratio (P<0.05), and between c.457G>A genotypes and alcohol consumption on TG levels (P<0.001) were detected by factorial regression analysis after controlling for potential confounders. Four haplotypes (T-G-G, C-G-G, T-A-G and C-G-T) had frequencies ranging from 0.06 to 0.87. Three haplotypes (C-G-G, T-A-G, and C-G-T) were significantly associated with serum lipid parameters. The -1131T>C genotypes were correlated with TG, and c.553G>T and c.457G>A genotypes were associated with HDL-C levels in nondrinkers (P<0.05 for all). For drinkers, the -1131T>C genotypes were correlated with TC, TG, LDL-C, ApoB levels and the ApoA1/ApoB ratio (P<0.01 for all); c.553G>T genotypes were correlated with TC, TG, HDL-C and LDL-C levels (P<0.05-0.01); and c.457G>A genotypes were associated with TG, LDL-C, ApoA1 and ApoB levels (P<0.05-0.01).The differences in some serum lipid parameters between the drinkers and nondrinkers might partly result from different interactions of the ApoA5 gene polymorphisms and alcohol consumption