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PubMed2001

Molecular phylogeny of butterflies Parnassius glacialis and P. stubbendorfii at various localities in East Asia.

The phylogeny of butterflies, Parnassius stubbendorfii and P. glacialis, collected at various localities in the Japan archipelago and the eastern part of the Asian continent was analyzed using mitochondrial DNA sequences coding for NADH dehydrogenase subunit 5 (805 bp). The molecular phylogenetic trees revealed that P. glacialis and P. stubbendorfii diverged from a common ancestor, and then the populations inhabiting the Japan archipelago and the Asian continent diverged in each species. The reliability of these divergences was supported by high bootstrap values. The divergences within the Japan archipelago and within the Asian continent in each species were unclear because of low bootstrap values. The genetic distance and a rough time-estimation in the UPGMA tree suggest that the both populations of P. glacialis and P. stubbendorfii may have been isolated in the Japan archipelago at the early time (about 1.7-2.0 Mya) of the glacial period in the Pleistocene. The genetic distance between the Japanese and the continental subspecies may be large enough that they can be classified as different species, in comparison with the genetic distances among some other parnassian species.

Animals↗

PubMed2000

Confidence intervals for hidden Markov model parameters.

Three methods for computing confidence intervals (CIs) of hidden Markov model parameters are compared in the context of 'long' time series, T > 100, namely likelihood profiling, bootstrapping and CIs based on a finite-differences approximation to the Hessian. First it is shown that with 'long' time series computing the exact Hessian is not feasible. In simulation studies quadratic and cubic interpolation polynomials for the likelihood profiles are compared. Likelihood profiling and bootstrapping produce similar CIs, whereas the CIs from the finite-differences approximation of the Hessian are mostly too small.

Humans↗

PubMed2000

A new ciprofloxacin stepdown program in the treatment of high-risk febrile neutropenia: a clinical and economic analysis.

STUDY OBJECTIVE: To determine treatment outcomes and economic impact of a ciprofloxacin stepdown program for high-risk febrile neutropenic adults from the hospital's perspective. DESIGN: Unblinded, two-phase, single-center study. SETTING: Adult leukemia and stem cell transplant unit. PATIENTS: High-risk adults with febrile neutropenia. INTERVENTION: Two conditions were analyzed: a multidisciplinary ciprofloxacin stepdown program involving a reduction in parenteral ciprofloxacin dose from 400 to 200 mg (i.v.-i.v.) and conversion to oral ciprofloxacin (i.v.-p.o.) when criteria were met; and no i.v.-i.v. stepdown program. MEASUREMENTS AND MAIN RESULTS: Forty-six sequential treatment courses were compared with 42 treatment course from 6-month periods in preintervention (P1) and postintervention (P2) phases. Assessed parameters were clinical and microbiologic outcomes, adverse drug reactions (ADRs), and direct medical resource use and costs (1998 $Canadian) for the episode of febrile neutropenia. A decision analytic model was used to map probabilities and costs and to conduct sensitivity analyses. To supplement standard statistical testing, 1,000 bootstrap samples were created, and the mean cost difference was calculated between phases for each sample. Patient demographics, percentage i.v.-p.o. stepdown, and duration of therapy were similar between phases. Clinical success (83% P1, 81% P2), microbiologic eradication (15% P1, 24% P2), and possible ADRs (6% P1, 9% P2) did not differ. Intravenous-to-intravenous dose stepdown occurred in 33% of P2 and no P1 treatment courses (p<0.001). Resource use and costs were similar between phases, although a reduction was seen in the drug's mean total cost/day ($58 P1, $52 P2, p=0.04). There was also a trend toward a decrease in mean total treatment costs ($4,843 P1, $3,493 P2, p=0.08). In 1,000 bootstrap samples, 99.8% showed a cost advantage for P2. The model was robust to sensitivity analyses. CONCLUSION: This intervention influenced administration of ciprofloxacin without apparent compromise of patient outcomes and resulted in a reduction in total costs of treating febrile neutropenia.

Administration, Oral↗

PubMed2006

Population pharmacokinetics of cyclosporine in chinese cardiac transplant recipients.

STUDY OBJECTIVE: To characterize the population pharmacokinetics of cyclosporine in Chinese patients undergoing cardiac transplantation and to identify the demographic and clinical covariates affecting cyclosporine clearance. DESIGN: Population pharmacokinetic analysis using data from a retrospective chart review. SETTING: Specialty hospital in Hong Kong for treatment of cardiac and pulmonary diseases. PATIENTS: Thirty-eight Chinese adult patients (mean age 46 yrs) who had undergone routine cyclosporine therapeutic drug monitoring after cardiac transplantation between January 1, 1991, and December 31, 2003. MEASUREMENTS AND MAIN RESULTS: Data regarding dosing, demographics, clinical laboratory values, and concurrent drugs were collected retrospectively. Data were included if patients had blood cyclosporine concentrations determined for at least 12 weeks after transplantation; an average of 18 blood samples/patient were collected. Population modeling was performed using a one-compartment linear model with first-order absorption and elimination. Various demographic and clinical covariates were tested for their significant effects on the apparent oral clearance (Cl/F) of cyclosporine. The stability of the final population model was evaluated by using the bootstrap resampling method. Statistically significant associations were observed between Cl/F and each of the following covariates: body weight (BW), use of diltiazem (DIL), and hematocrit value (HCT). The final model was Cl/F=5.00*(1-DIL)+365/HCT+(0.144*BW). The interindividual variabilities of Cl/F and apparent volume of distribution were 14.5% and 40.2%, respectively. The mean parameter estimates obtained from bootstrap analyses were highly consistent with those obtained with the original data set. CONCLUSION: The estimated Cl/F values of cyclosporine in our Chinese cardiac transplant recipients appeared to be similar to those reported for Caucasian cardiac transplant recipients. Thus, our data provide support that a cyclosporine dosage regimen similar to that in Caucasian patients may be needed in Chinese cardiac transplant recipients. However, further studies are required to determine the optimum cyclosporine dosage regimen in the Chinese population.

Adult↗

PubMed2006

Population pharmacokinetics of pranlukast hydrate dry syrup in children with allergic rhinitis and bronchial asthma.

This study aimed to assess the steady-state pharmacokinetics of pranlukast, a leukotriene receptor antagonist, in children with allergic rhinitis and bronchial asthma, and to clarify factors affecting apparent clearance (CL/F). A total of 192 plasma samples were obtained from 98 children (rhinitis 64, asthma 13, complications 21), aged 3-14 years in 2 clinical trials. Plasma concentration of pranlukast was determined by liquid chromatography connected with a tandem mass spectrometer and analyzed by a population approach using NONMEM program. The plasma concentration-time course of pranlukast was described by using a one-compartment model with the first-order absorption and lag time. The robustness of the population pharmacokinetic model was evaluated by using 200 bootstrap samples. The results of population pharmacokinetic analysis showed that only age was a factor affecting the CL/F per body weight, with CL/F decreasing with increasing age. No significant variation was seen in the CL/F between rhinitis and asthma. The interindividual variability in the CL/F and the residual variability were 19.7% and 48.4%, respectively. All the parameters fell within 10% of the bootstrapped mean. In conclusion, the results show that age is the most influential factor for explaining interindividual variability in CL/F, and the difference in diseases does not affect CL/F.

Adolescent↗

PubMed1998

The economics of TRACE. A cost-effectiveness analysis of trandolapril in postinfarction patients with left ventricular dysfunction.

OBJECTIVE: The objective of the study was to compute a cost-effectiveness ratio relating the economic cost of trandolapril to the number of effectiveness units (i.e. life-years) gained. DESIGN AND SETTING: The trandolapril cardiac evaluation (TRACE) study was a prospective placebo-controlled clinical trial designed to determine the long term effect of the oral angiotensin-converting enzyme (ACE) inhibitor trandolapril in postinfarction patients with left ventricular dysfunction. We used the individual data of the TRACE trial to compute a cost-effectiveness ratio relating the economic cost of trandolapril to the number of life-years saved. The analysis was differential and was conducted from a payer perspective in a French setting. Costs were computed from individual data related to the use of resources during the TRACE trial. For drug treatments, we chose French public prices, and for hospitalisations, we used the mean cost as determined by the diagnosis related group (DRG) from the 1996 Programme de Médicalisation des Systémes d'Information (PMSI) database from the French Ministry of Health. Life expectancy was estimated through an accelerated failure-time model with an exponential distribution specification; we made the conservative hypothesis that the effect of trandolapril on mortality after the end of the trial was nil. We assessed the standard deviation and the 95% confidence interval (CI) of the ratio through its bootstrap distribution. RESULTS: The incremental cost-effectiveness ratio of treating patients with trandolapril rather than with placebo was estimated as 4910 French francs (FF) per life-year saved. Discounting both costs and health effects led to ratio of FF6950 per life-year saved. The bootstrap estimate of the ratio reached FF5950 and the 95% CI was FF5650 to FF6250 per life-year saved. CONCLUSIONS: These results could be considered as highly cost effective, even though our estimation was very close to the design and the conditions of the TRACE trial. Nevertheless, we showed that this trial constitutes a favourable case for economic evaluation.

Aged↗

PubMed2004

Cost effectiveness of ibutilide with prophylactic magnesium in the treatment of atrial fibrillation.

BACKGROUND: In the Treatment with Ibutilide and Magnesium Evaluation (TIME) study, a retrospective multicentre cohort trial, prophylactic magnesium was found to improve the antiarrhythmic efficacy of ibutilide as demonstrated by an increase in the rate of successful chemical conversion and reduction in the need for direct current cardioversion (DCC). OBJECTIVE: The primary objective of this piggyback cost-effectiveness analysis of the TIME study was to compare the cost per successful conversion of atrial fibrillation (AF) for ibutilide in the presence and absence of magnesium prophylaxis. A secondary objective was to determine whether specific factors predict costs in the conversion of AF. METHOD: The study was conducted from the US hospital-payer perspective. Direct medical costs (USD, 2002 values) including drugs, intravenous admixture and administration, DCC, electrocardiographs and physicians' fees were obtained directly from the provider. Nonparametric bootstrapping was conducted to calculate confidence intervals for the incremental cost-effectiveness ratios. One-way sensitivity analysis was conducted varying efficacy, and drug, hospital and physician costs. Multivariate analysis was conducted to determine whether specific baseline factors were predictors of total cost. RESULTS: Total costs per patient were lower in the ibutilide plus magnesium group compared with ibutilide alone (USD1075 vs USD1201); however, the difference was not statistically significant (p = 0.116). Patients receiving ibutilide plus magnesium had lower DCC costs compared with those receiving ibutilide alone (USD261 vs USD399; p = 0.036), but higher magnesium-associated costs (USD0.50 vs USD0; p < 0.001). Bootstrapping revealed that the ibutilide plus magnesium strategy would result in lower costs and greater efficacy 93.4% of the time. These results remained robust to changes in both cost and efficacy. No baseline factors were found to be independent predictors of total costs. CONCLUSION: Our data suggest that adding prophylactic magnesium to ibutilide may be cost effective, from a US hospital-payer perspective, for the acute conversion of patients in AF or flutter compared with ibutilide alone.

Aged↗

PubMed2004

Multiple testing. Part I. Single-step procedures for control of general type I error rates.

The present article proposes general single-step multiple testing procedures for controlling Type I error rates defined as arbitrary parameters of the distribution of the number of Type I errors, such as the generalized family-wise error rate. A key feature of our approach is the test statistics null distribution (rather than data generating null distribution) used to derive cut-offs (i.e., rejection regions) for these test statistics and the resulting adjusted p-values. For general null hypotheses, corresponding to submodels for the data generating distribution, we identify an asymptotic domination condition for a null distribution under which single-step common-quantile and common-cut-off procedures asymptotically control the Type I error rate, for arbitrary data generating distributions, without the need for conditions such as subset pivotality. Inspired by this general characterization of a null distribution, we then propose as an explicit null distribution the asymptotic distribution of the vector of null value shifted and scaled test statistics. In the special case of family-wise error rate (FWER) control, our method yields the single-step minP and maxT procedures, based on minima of unadjusted p-values and maxima of test statistics, respectively, with the important distinction in the choice of null distribution. Single-step procedures based on consistent estimators of the null distribution are shown to also provide asymptotic control of the Type I error rate. A general bootstrap algorithm is supplied to conveniently obtain consistent estimators of the null distribution. The special cases of t- and F-statistics are discussed in detail. The companion articles focus on step-down multiple testing procedures for control of the FWER (van der Laan et al., 2004b) and on augmentations of FWER-controlling methods to control error rates such as tail probabilities for the number of false positives and for the proportion of false positives among the rejected hypotheses (van der Laan et al., 2004a). The proposed bootstrap multiple testing procedures are evaluated by a simulation study and applied to genomic data in the fourth article of the series (Pollard et al., 2004).

Journal Article↗

PubMed1997

Phylogenetic relationships of the helical-shaped bacteria in the alpha Proteobacteria inferred from 16S rDNA sequences.

16S ribosomal RNA gene sequences from seven strains of Aquaspirillum peregrinum, Aqu. itersonii, Aqu. polymorphum, and Oceanospirillum pusillum were compared with homologous sequences from other members of helical-shaped bacteria. The bootstrapped neighbor-joining tree, inferred from 887 aligned sites, placed the spirillum taxa assigned to Aquaspirillum, Oceanospirillum, Azospirillum, Magnetospirillum, Rhodospirillum, and Rhodocista of the Proteobacteria in seven clusters of alpha Proteobacteria separately from other shapes of bacteria. Aqu. peregrinum and Aqu. itersonii grouped together in 88% bootstrap support. They were more related to Rhodospirillum rubrum and Rsp. photometricum than Aqu. polymorphum. Aqu. polymorphum was close to Magnetospirillum gryphiswaldense, Mag. magnetotacticum, Rsp. fulvum, and Rsp. molischianum, and more close to Mag. gryphiswaldense. Oce. pusillum was not related to other spirillum taxa and was placed in a separate branch. Rhodocista was very closely related to Azospirillum. Photosynthesis and magnetotaxis, as phenotypic characters, were not important in the classification of helical bacteria.

Journal Article↗

PubMed2005

Estimation of genetic effects in the presence of multicollinearity in multibreed beef cattle evaluation.

Breed additive, dominance, and epistatic loss effects are of concern in the genetic evaluation of a multibreed population. Multiple regression equations used for fitting these effects may show a high degree of multicollinearity among predictor variables. Typically, when strong linear relationships exist, the regression coefficients have large SE and are sensitive to changes in the data file and to the addition or deletion of variables in the model. Generalized ridge regression methods were applied to obtain stable estimates of direct and maternal breed additive, dominance, and epistatic loss effects in the presence of multicollinearity among predictor variables. Preweaning weight gains of beef calves in Ontario, Canada, from 1986 to 1999 were analyzed. The genetic model included fixed direct and maternal breed additive, dominance, and epistatic loss effects, fixed environmental effects of age of the calf, contemporary group, and age of the dam x sex of the calf, random additive direct and maternal genetic effects, and random maternal permanent environment effect. The degree and the nature of the multicollinearity were identified and ridge regression methods were used as an alternative to ordinary least squares (LS). Ridge parameters were obtained using two different objective methods: 1) generalized ridge estimator of Hoerl and Kennard (R1); and 2) bootstrap in combination with cross-validation (R2). Both ridge regression methods outperformed the LS estimator with respect to mean squared error of predictions (MSEP) and variance inflation factors (VIF) computed over 100 bootstrap samples. The MSEP of R1 and R2 were similar, and they were 3% less than the MSEP of LS. The average VIF of LS, R1, and R2 were equal to 26.81, 6.10, and 4.18, respectively. Ridge regression methods were particularly effective in decreasing the multicollinearity involving predictor variables of breed additive effects. Because of a high degree of confounding between estimates of maternal dominance and direct epistatic loss effects, it was not possible to compare the relative importance of these effects with a high level of confidence. The inclusion of epistatic loss effects in the additive-dominance model did not cause noticeable reranking of sires, dams, and calves based on across-breed EBV. More precise estimates of breed effects as a result of this study may result in more stable across-breed estimated breeding values over the years.

Animals↗

PubMed1997

Genetic comparison between Spirometra erinacei and S. mansonoides using PCR-RFLP analysis.

The only observed morphological difference between Spirometra erinacei and S. mansonoides is the uterine shape of the mature proglottid. Two species of worms are thought to be evolutionarily closely related. Biomolecular comparison of the two worms by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis was conducted to observe the genetic distance. The 28s rDNA, mitochondrial cytochrome c oxidase subunit I (mCOI), and ribosomal internal transcribed spacer 1 (ITS1) fragments were obtained from the worms by PCR. The PCR products were cleaved by 5 four-base pair restriction enzyme combinations (Msp I, Hae III, Alu I, Cfo I, Rsa I), electrophoresed and analyzed with PAUP 3.1.1. The fragment patterns of 28S rDNA and ITS1 demonstrated that two worms were in identical systematic tree with bootstrap number 94 and 100, respectively. As for mCOI, bootstrap number was 74 in a different tree. Above results are indicative of recent common ancestry between S. erinacei and S. mansonoides.

Animals↗

PubMed2026

Genome analysis and antagonistic activity of Streptomyces sp. strain J36 against Phytophthora cactorum.

The Phytophthora blight of Panax notoginseng, caused by Phytophthora cactorum, is a devastating oomycete disease. Biocontrol strategies hold immense potential for inhibiting the spread of P. cactorum. We isolated 72 actinobacteria from soil and screened their antagonistic activity against P. cactorum. Both strain J36 and its cell-free filtrate exhibited strong antagonistic activity against P. cactorum and were therefore selected. Based on the 16S rRNA gene phylogenetic tree, strain J36 formed a well supported subclade with Streptomyces zaomyceticus NRRL B-2038 (bootstrap value 100%). However, because 16S rRNA sequences often lack sufficient resolution for species-level discrimination, we performed multilocus sequence analysis (MLSA) using three housekeeping genes (rpoB, recA, and atpD). The MLSA results consistently placed strain J36 within the same cluster as S. zaomyceticus NRRL B-2038, with a bootstrap support of 99%, indicating a close phylogenetic relationship. To further clarify the taxonomic status, we calculated the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain J36 and the type strain of S. zaomyceticus NBC-00415T. The ANI value was 90.91% and the dDDH value was 39.30%, both well below the accepted thresholds for species demarcation (ANI < 95%, dDDH < 70%). These genomic indices therefore strongly support that strain J36 represents a novel species within the genus Streptomyces. Through whole-genome sequencing and CAZymes analysis, a total of 98 carbohydrate-active enzymes (CAZymes) were detected, including 2 cellulase and 2 β-1,3-glucanases. The cell-free filtrate, which exhibited strong antagonistic activity against P. cactorum, also showed high activities of cellulase and β-1,3-glucanase, suggesting that these enzymes may be involved in its anti-oomycete activity. These findings suggest that J36 has potential as a biocontrol candidate, although further in vivo evaluation is needed to confirm its efficacy against Phytophthora blight of P. notoginseng.

Panax notoginseng↗

PubMed2004

Population-based pharmacokinetics of the soluble TNFr etanercept: a clinical study in 43 patients with ankylosing spondylitis compared with post hoc data from patients with rheumatoid arthritis.

OBJECTIVE: The purpose of this study was to evaluate the pharmacokinetics of etanercept in patients with ankylosing spondylitis (AS) in a phase 3 study. METHODS: Serum etanercept concentrations were analyzed from samples obtained at weeks 4 and 12 from 43 patients with AS (median age: 45 years; median body weight: 75 kg; white/non-white: 40/3; male/female: 34/9) receiving 25 mg subcutaneously twice weekly for 12 weeks. A population pharmacokinetics analysis using NONMEM was conducted to estimate individual etanercept pharmacokinetic parameters. Initially, appropriate base and covariate population pharmacokinetic models were built based on data from 10 prior clinical studies of etanercept administered subcutaneously or intravenously to healthy subjects (n = 53) and to patients with rheumatoid arthritis (RA) (n = 212). The influence of demographic characteristics on the pharmacokinetics of etanercept was thoroughly evaluated. The stability of the final model was evaluated using both internal (bootstrapping) and external (data splitting) validation approaches. Finally, the selected final population covariate model was used to estimate the Bayesian pharmacokinetic parameters for the patients with AS. RESULTS: The data from the 10 prior clinical studies were optimally fitted to a 2-compartment linear population covariate model. Both age (< 17 years) and body weight (< 60 kg) were found to be important covariates on clearance. Both bootstrapping and data splitting validated the population model. The mean Bayesian-predicted etanercept clearance and steady-state trough concentration were 0.072 l/h and 2,004 ng/ml, respectively. The pharmacokinetic parameters of etanercept in the patients with AS were similar to those observed in the patients with RA. CONCLUSIONS: The pharmacokinetics of etanercept in patients with AS were similar to those in patients with RA. The AS disease state does not appear to alter the disposition of etanercept.

Adult↗

PubMed2026

Phylogenomic subsampling and upsampling for efficient evolutionary analyses of big data.

Long runtimes, high memory demands, and reliance on high-performance computing impede phylogenomic analyses. We review a scalable phylogenomic subsampling with upsampling (PSU) framework, in which small subsamples of sites from a concatenated alignment are expanded by upsampling before inference, and the resulting analyses are then aggregated to obtain evolutionary estimates. PSU harnesses the fact that the computational cost of maximum likelihood analysis is strongly influenced by the number of distinct site patterns in the concatenated alignment, whereas statistical power depends primarily on the amount of evolutionary information represented by the total number of sites and substitutions. By reducing the former while restoring the latter through upsampling, PSU can approximate many full-data analyses at substantially lower computational cost. Analysis of simulated and empirical datasets shows that PSU can accurately estimate bootstrap support values, select the optimal substitution model, test evolutionary hypotheses, and infer branch lengths, divergence times, and associated uncertainty measures, while reducing runtime and memory requirements by orders of magnitude. PSU also provides distributions of inferred clade support across independent subsamples, enabling detection of conflicting phylogenetic signals that may remain hidden in conventional bootstrap analysis. Automated tuning of subsample size, the number of subsamples, and the number of upsampling replicates make PSU practical across diverse datasets. We suggest that PSU is a general strategy for scalable phylogenomic inference using a broad range of statistical methods. By enabling analyses of genome-scale alignments on commodity hardware, PSU broadens research access and reduces environmental and infrastructural costs of big-data phylogenomics.

confidence limits↗

PubMed2004

Cost-effectiveness of rhythm versus rate control in atrial fibrillation.

BACKGROUND: Atrial fibrillation is the most common type of sustained cardiac arrhythmia, but recent trials have identified no clear advantage of rhythm control over rate control. Consequently, economic factors often play a role in guiding treatment selection. OBJECTIVE: To estimate the cost-effectiveness of rhythm-control versus rate-control strategies for atrial fibrillation in the Atrial Fibrillation Follow-up Investigation of Rhythm Management (AFFIRM). DESIGN: Retrospective economic evaluation. Nonparametric bootstrapping was used to estimate the distribution of incremental costs and effects on the cost-effectiveness plane. DATA SOURCES: Data on survival and use of health care resources were obtained for all 4060 AFFIRM participants. Unit costs were estimated from various U.S. databases. TARGET POPULATION: Patients with atrial fibrillation who were 65 years of age or who had other risk factors for stroke or death, similar to those enrolled in AFFIRM. TIME HORIZON: Mean follow-up of 3.5 years. PERSPECTIVE: Third-party payer. INTERVENTIONS: Management of patients with atrial fibrillation with antiarrhythmic drugs (rhythm control) compared with drugs that control heart rate (rate control). OUTCOME MEASURES: Mean survival, resource use, costs, and cost-effectiveness. RESULTS OF BASE-CASE ANALYSIS: A mean survival gain of 0.08 year (P = 0.10) was observed for rate control. Patients in the rate-control group used fewer resources (hospital days, pacemaker procedures, cardioversions, and short-stay and emergency department visits). Rate control costs 5077 dollars less per person than rhythm control. RESULTS OF SENSITIVITY ANALYSIS: Cost savings ranged from 2189 dollars o 5481 dollars per person. Rhythm control was more costly and less effective than rate control in 95% of the bootstrap replicates over a wide range of cost assumptions. LIMITATIONS: Resource use was limited to key items collected in AFFIRM, and the results are generalizable only to similar patient populations with atrial fibrillation. CONCLUSION: Rate control is a cost-effective approach to the management of atrial fibrillation compared with maintenance of sinus rhythm in patients with atrial fibrillation similar to those enrolled in AFFIRM.

Anti-Arrhythmia Agents↗

PubMed1999

Phylogeny and taxonomy of the family Arthrodermataceae (dermatophytes) using sequence analysis of the ribosomal ITS region.

The internal transcribed spacer (ITS) region, covering the ITS1, ITS2 and 5.8S ribosomal DNA was used to evaluate phylogenetic relationships within the fungal family Arthrodermataceae. Sequences of variable length, ranging between 522 and 684 base pairs were aligned. An unrooted consensus tree based on parsimony analysis showed Trichophyton to be polyphyletic, and Microsporum to be paraphyletic. Non-monophyly of these two genera is in conflict with traditional classification. But this relation is not strongly supported by bootstrap analysis. Phylogenetic analysis showed that the two known members of the genus Epidermophyton grouped widely apart from each other. Within Trichophyton, our results suggest a separation of human pathogenic species and primarily geophilic species. Bootstrap support for these two groups is fairly high and both groups are recognized by current taxonomy. Three lineages were revealed within the T. mentagrophytes species complex. Microsporum canis, M. audouinii and M. equinum were found to be closely related. The topology of the tree was robust to various methods of analysis (parsimony and distance) and a different weighting scheme. Weighting of transversions over transitions did not improve the status of poorly supported branches of the tree.

Animals↗

PubMed2001

Coding and noncoding plastid DNA in palm systematics.

Plastid DNA sequences evolve slowly in palms but show that the family is monophyletic and highly divergent relative to other major monocot clades. It is therefore difficult to place the root within the palms because faster evolving, length-variable sequences cannot be aligned with outgroup monocots, and length-conserved regions have been thought to give too few characters to resolve basal nodes. To solve this problem, we combined 94 ingroup and 24 outgroup sequences from the length-conserved rbcL gene with ingroup and alignable outgroup sequences from noncoding rps16 intron and trnL-trnF regions. The separate rps16 intron and trnL-trnF region contained about the same number of variable sites (autapomorphies not included) as rbcL, but gave higher retention indices and more clades with bootstrap support. In general, the strict consensus tree based on combined rbcL, rps16 intron, and trnL-trnF data showed more resolution towards the base of the palm family than previous hypotheses of relationships of the Arecaceae. An important result was the position of subfamily Calamoideae as sister to the rest of the palms, but this received <50% bootstrap support. Another result of systematic significance was the indication that subfamily Phytelephantoideae is related to two tribes from subfamily Ceroxyloideae, Cyclospatheae and Ceroxyleae.

Journal Article↗

PubMed2001

Model selection and parameterization of the concentration-response functions for population-level effects.

As concentration response functions for chronic population-level effects of pollutant chemicals, three mathematical models were presented and examined for goodness of fit to published toxicological data that estimated the population-level effects of chemicals in terms of the intrinsic rate of population growth (r). Among the examined concentration-r functions, the power function model, that is, r(x) = r(0)[1 - (x/alpha)beta], in which x is the exposure concentration and alpha and beta are parameters, performed with the best fit to each data set. The power function model is characterized by two parameters representing the absolute value of toxicity, alpha, and the curvature of responses, beta. The bootstrap simulation, conducted on the entire data set consisting of all published data that we collected, indicated that the observed variance of beta among actual data sets could be mostly explained by the random error variation generated from the bootstrap resamplings. The generic beta value, determined from the entire data set and expected to denote the best estimate of beta if the variability of beta was completely due to random sampling error, was estimated as 1.84. It was implied that the response of the intrinsic rate of natural increase (r) to chemical exposure was nearly quadratic in many cases.

Animals↗