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At least 55 records · Page 3Linked to original sources
PubMed2006

Evolutionary history of Stratiomyidae (Insecta: Diptera): the molecular phylogeny of a diverse family of flies.

Stratiomyidae is a cosmopolitan family of Brachycera (Diptera) that contains over 2800 species. This study focused on the relationships of members of the subfamily Clitellariinae, which has had a complicated taxonomic history. To investigate the monophyly of the Clitellariinae, the relationships of its genera, and the ages of Stratiomyidae lineages, representatives for all 12 subfamilies of Stratiomyidae, totaling 68 taxa, were included in a phylogenetic reconstruction. A Xylomyidae representative, Solva sp., was used as an outgroup. Sequences of EF-1alpha and 28S rRNA genes were analyzed under maximum parsimony with bootstrapping, and Bayesian methods to recover the best estimate of phylogeny. A chronogram with estimated dates for all nodes in the phylogeny was generated with the program, r8s, and divergence dates and confidence intervals were further explored with the program, multidivtime. All subfamilies of Stratiomyidae with more than one representative were found to be monophyletic, except for Stratiomyinae and Clitellariinae. Clitellariinae were distributed among five separate clades in the phylogeny, and Raphiocerinae were nested within Stratiomyinae. Dating analysis suggested an early Cretaceous origin for the common ancestor of extant Stratiomyidae, and a radiation of several major Stratiomyidae lineages in the Late Cretaceous.

Animals↗
PubMed2006

Fossil-calibrated molecular phylogenies reveal that leaf-mining moths radiated millions of years after their host plants.

Coevolution has been hypothesized as the main driving force for the remarkable diversity of insect-plant associations. Dating of insect and plant phylogenies allows us to test coevolutionary hypotheses and distinguish between the contemporaneous radiation of interacting lineages vs. insect 'host tracking' of previously diversified plants. Here, we used nuclear DNA to reconstruct a molecular phylogeny for 100 species of Phyllonorycter leaf-mining moths and 36 outgroup taxa. Ages for nodes in the moth phylogeny were estimated using a combination of a penalized likelihood method and a Bayesian approach, which takes into account phylogenetic uncertainty. To convert the relative ages of the moths into dates, we used an absolute calibration point from the fossil record. The age estimates of (a selection of) moth clades were then compared with fossil-based age estimates of their host plants. Our results show that the principal radiation of Phyllonorycter leaf-mining moths occurred well after the main radiation of their host plants and may represent the dominant associational mode in the fossil record.

Animals↗
PubMed2004

The molecular population genetics of HIV-1 group O.

HIV-1 group O originated through cross-species transmission of SIV from chimpanzees to humans and has established a relatively low prevalence in Central Africa. Here, we infer the population genetics and epidemic history of HIV-1 group O from viral gene sequence data and evaluate the effect of variable evolutionary rates and recombination on our estimates. First, model selection tools were used to specify suitable evolutionary and coalescent models for HIV group O. Second, divergence times and population genetic parameters were estimated in a Bayesian framework using Markov chain Monte Carlo sampling, under both strict and relaxed molecular clock methods. Our results date the origin of the group O radiation to around 1920 (1890-1940), a time frame similar to that estimated for HIV-1 group M. However, group O infections, which remain almost wholly restricted to Cameroon, show a slower rate of exponential growth during the twentieth century, explaining their lower current prevalence. To explore the effect of recombination, the Bayesian framework is extended to incorporate multiple unlinked loci. Although recombination can bias estimates of the time to the most recent common ancestor, this effect does not appear to be important for HIV-1 group O. In addition, we show that evolutionary rate estimates for different HIV genes accurately reflect differential selective constraints along the HIV genome.

Bayes Theorem↗
PubMed2004

A molecular timeline for the origin of photosynthetic eukaryotes.

The appearance of photosynthetic eukaryotes (algae and plants) dramatically altered the Earth's ecosystem, making possible all vertebrate life on land, including humans. Dating algal origin is, however, frustrated by a meager fossil record. We generated a plastid multi-gene phylogeny with Bayesian inference and then used maximum likelihood molecular clock methods to estimate algal divergence times. The plastid tree was used as a surrogate for algal host evolution because of recent phylogenetic evidence supporting the vertical ancestry of the plastid in the red, green, and glaucophyte algae. Nodes in the plastid tree were constrained with six reliable fossil dates and a maximum age of 3,500 MYA based on the earliest known eubacterial fossil. Our analyses support an ancient (late Paleoproterozoic) origin of photosynthetic eukaryotes with the primary endosymbiosis that gave rise to the first alga having occurred after the split of the Plantae (i.e., red, green, and glaucophyte algae plus land plants) from the opisthokonts sometime before 1,558 MYA. The split of the red and green algae is calculated to have occurred about 1,500 MYA, and the putative single red algal secondary endosymbiosis that gave rise to the plastid in the cryptophyte, haptophyte, and stramenopile algae (chromists) occurred about 1,300 MYA. These dates, which are consistent with fossil evidence for putative marine algae (i.e., acritarchs) from the early Mesoproterozoic (1,500 MYA) and with a major eukaryotic diversification in the very late Mesoproterozoic and Neoproterozoic, provide a molecular timeline for understanding algal evolution.

Bayes Theorem↗
PubMed2006

The hepatitis C virus epidemic in Cameroon: genetic evidence for rapid transmission between 1920 and 1960.

Hepatitis C virus (HCV) infection in Cameroon is characterized by widespread seropositivity and great virus genetic diversity (3 genotypes and over 10 subtypes). A total of 244 HCV NS5B sequences of 382-405 bp long (95 type 1, 58 type 2, and 91 type 4) were phylogenetically analyzed to estimate the history of the HCV epidemic in Cameroon. The newly developed Bayesian coalescent approach was used to infer the history of each HCV type. The estimated dates of the most recent common ancestors (MRCA) for genotypes 1 (1500; 95% confidence interval (95% CI): 1300-1650) and 4 (1500; 95% CI: 1350-1700) were in the same range, while the date for genotype 2 MRCA (1600; 95% CI: 1400-1750) was slightly more recent. The mean genetic distance between HCV genotype 1 sequences was greater than that of HCV type 4 sequences, itself greater than that of HCV type 2 sequences. The initial infected populations of all three genotypes did not grow until recently, when they grew exponentially. The growth rate has now begun to slow, with a less steep exponential growth curve. The period of exponential growth of all the three genotypes was between 1920 and 1960. These results (i) confirm that HCV genotypes 1 and 4 have produced long-term endemics, (ii) suggest that genotype 2 was introduced into Cameroon more recently, and (iii) indicate that the exponential spread of the three genotypes between 1920 and 1960 coincided with the mass campaign against trypanosomiasis and mass vaccinations in Cameroon.

Bayes Theorem↗
PubMed2004

Mosaic evolution of the severe acute respiratory syndrome coronavirus.

Severe acute respiratory syndrome (SARS) is a deadly form of pneumonia caused by a novel coronavirus, a viral family responsible for mild respiratory tract infections in a wide variety of animals including humans, pigs, cows, mice, cats, and birds. Analyses to date have been unable to identify the precise origin of the SARS coronavirus. We used Bayesian, neighbor-joining, and split decomposition phylogenetic techniques on the SARS virus replicase, surface spike, matrix, and nucleocapsid proteins to reveal the evolutionary origin of this recently emerging infectious agent. The analyses support a mammalian-like origin for the replicase protein, an avian-like origin for the matrix and nucleocapsid proteins, and a mammalian-avian mosaic origin for the host-determining spike protein. A bootscan recombination analysis of the spike gene revealed high nucleotide identity between the SARS virus and a feline infectious peritonitis virus throughout the gene, except for a 200- base-pair region of high identity to an avian sequence. These data support the phylogenetic analyses and suggest a possible past recombination event between mammalian-like and avian-like parent viruses. This event occurred near a region that has been implicated to be the human receptor binding site and may have been directly responsible for the switch of host of the SARS coronavirus from animals to humans.

Animals↗
PubMed2005

Diversification of the forest beetle genus Tarphius on the Canary Islands, and the evolutionary origins of island endemics.

The flightless beetle genus Tarphius Erichson (Coleoptera: Colydiidae) is a distinctive element of the beetle fauna of the Canary Islands with 29 species distributed across the five western islands. The majority of Tarphius species are rare and intimately associated with the monteverde forest and only two species occur on more than one island. In this study we investigate the phylogeography of the Canary Island Tarphius, and their relationship to Tarphius from the more northerly archipelagos of Madeira and the Azores using maximum parsimony and Bayesian inference analysis of mitochondrial cytochrome oxidase I and II sequence data. We use geological datings for the Canary Islands, Azores, and Madeira to calibrate specific nodes of the tree for the estimation of divergence times using a penalized likelihood method. Data suggest that the Canary Island species assemblage is of some antiquity, however, much of this species diversity is relatively recent in origin. The phylogenetic relationships of species inhabiting the younger islands of El Hierro and La Palma indicate that colonization events between islands have probably been a significant factor in the evolutionary history of the Canary Island species assemblage. A comparison of molecular phylogenetic studies of arthropods on the Canary Islands suggests that, in the evolution of the arthropod species community of an island, the origin of endemic species is initially the result of colonizing lineages differentiating from their source populations. However, as an island matures a greater proportion of endemic species originate from intra-island speciation.

Animals↗
PubMed2003

Bayesian deconvolution analysis of pulsatile hormone concentration profiles.

Many hormones are secreted into the circulatory system in a pulsatile manner and are cleared exponentially. The most common method of analyzing these systems is to deconvolve the hormone concentration into a secretion function and a clearance function. Accurate estimation of the model parameters depends on the number and location of the secretion pulses. To date, deconvolution analysis assumes the number and approximate location of these pulses are known a priori. In this article, we present a novel Bayesian approach to deconvolution that jointly models the number of pulses along with all other model parameters. Our method stochastically searches for the secretion pulses. This is accomplished by viewing the set of parameters that define the pulses as a point process. Pulses are determined by a birth-death process which is embedded in Markov chain Monte Carlo algorithm. This idea originated with Stephens (2000, Annals of Statistics 28, 40-74) in the context of finite mixture model density estimation, where the number of mixture components is unknown. There are several advantages that our model enjoys over the traditional frequentist approaches. These advantages are highlighted with four datasets consisting of serum concentration levels of luteinizing hormone obtained from ovariectomized ewes.

Animals↗
PubMed2005

Cytochrome b and Bayesian inference of whale phylogeny.

In the mid 1990s cytochrome b and other mitochondrial DNA data reinvigorated cetacean phylogenetics by proposing many novel and provocative hypotheses of cetacean relationships. These results sparked a revision and reanalysis of morphological datasets, and the collection of new nuclear DNA data from numerous loci. Some of the most controversial mitochondrial hypotheses have now become benchmark clades, corroborated with nuclear DNA and morphological data; others have been resolved in favor of more traditional views. That major conflicts in cetacean phylogeny are disappearing is encouraging. However, most recent papers aim specifically to resolve higher-level conflicts by adding characters, at the cost of densely sampling taxa to resolve lower-level relationships. No molecular study to date has included more than 33 cetaceans. More detailed molecular phylogenies will provide better tools for evolutionary studies. Until more genes are available for a high number of taxa, can we rely on readily available single gene mitochondrial data? Here, we estimate the phylogeny of 66 cetacean taxa and 24 outgroups based on Cytb sequences. We judge the reliability of our phylogeny based on the recovery of several deep-level benchmark clades. A Bayesian phylogenetic analysis recovered all benchmark clades and for the first time supported Odontoceti monophyly based exclusively on analysis of a single mitochondrial gene. The results recover the monophyly of all but one family level taxa within Cetacea, and most recently proposed super- and subfamilies. In contrast, parsimony never recovered all benchmark clades and was sensitive to a priori weighting decisions. These results provide the most detailed phylogeny of Cetacea to date and highlight the utility of both Bayesian methodology in general, and of Cytb in cetacean phylogenetics. They furthermore suggest that dense taxon sampling, like dense character sampling, can overcome problems in phylogenetic reconstruction.

Animals↗
PubMedDate not supplied

Bayesian communication of research results over the World Wide Web.

The World Wide Web provides a unique opportunity to reconsider how the results of scientific studies can best be presented to clinicians. For decades statisticians, philosophers, medical investigators, and others interested in data analysis have assumed that the Bayesian paradigm is the proper approach for reporting the findings of scientific analyses for use by client computers and readers. At the heart of that approach is the inclusion of the reader's preexisting knowledge and beliefs. Yet, to date, the methods for inclusion have been too complicated for non-statisticians to use. We believe that the World Wide Web provides an ideal environment for putting the Bayesian paradigm into practice: the author publishes the data from the server side, the reader uses the client to represent her or his prior belief, a downloaded program (a Java applet) combines the two. This article describes a prototype implementation for two-arm clinical trials with normally distributed outcomes.

Bayes Theorem↗
PubMed2004

Bayesian inference of the metazoan phylogeny; a combined molecular and morphological approach.

Metazoan phylogeny remains one of evolutionary biology's major unsolved problems. Molecular and morphological data, as well as different analytical approaches, have produced highly conflicting results due to homoplasy resulting from more than 570 million years of evolution. To date, parsimony has been the only feasible combined approach but is highly sensitive to long-branch attraction. Recent development of stochastic models for discrete morphological characters and computationally efficient methods for Bayesian inference has enabled combined molecular and morphological data analysis with rigorous statistical approaches less prone to such inconsistencies. We present the first statistically founded analysis of a metazoan data set based on a combination of morphological and molecular data and compare the results with a traditional parsimony analysis. Interestingly, the Bayesian analyses demonstrate a high degree of congruence between morphological and molecular data, and both data sets contribute to the result of the combined analysis. Additionally, they resolve several irregularities obtained in previous studies and show high credibility values for controversial groups such as the ecdysozoans and lophotrochozoans. Parsimony, on the contrary, shows conflicting results, with morphology being congruent to the Bayesian results and the molecular data set producing peculiarities that are largely reflected in the combined analysis.

Animals↗
PubMed2001

Predicting analysis times in randomized clinical trials.

Randomized clinical trial designs commonly include one or more planned interim analyses. At these times an external monitoring committee reviews the accumulated data and determines whether it is scientifically and ethically appropriate for the study to continue. With failure-time endpoints, it is common to schedule analyses at the times of occurrence of specified landmark events, such as the 50th event, the 100th event, and so on. Because interim analyses can impose considerable logistical burdens, it is worthwhile predicting their timing as accurately as possible. We describe two model-based methods for making such predictions during the course of a trial. First, we obtain a point prediction by extrapolating the cumulative mortality into the future and selecting the date when the expected number of deaths is equal to the landmark number. Second, we use a Bayesian simulation scheme to generate a predictive distribution of milestone times; prediction intervals are quantiles of this distribution. We illustrate our method with an analysis of data from a trial of immunotherapy in the treatment of chronic granulomatous disease.

Bayes Theorem↗
PubMed2005

Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary.

Tertiary macrofossils of the flowering plant family Leguminosae (legumes) were used as time constraints to estimate ages of the earliest branching clades identified in separate plastid matK and rbcL gene phylogenies. Penalized likelihood rate smoothing was performed on sets of Bayesian likelihood trees generated with the AIC-selected GTR+ Gamma +I substitution model. Unequivocal legume fossils dating from the Recent continuously back to about 56 million years ago were used to fix the family stem clade at 60 million years (Ma), and at 1-Ma intervals back to 70 Ma. Specific fossils that showed distinctive combinations of apomorphic traits were used to constrain the minimum age of 12 specific internal nodes. These constraints were placed on stem rather than respective crown clades in order to bias for younger age estimates. Regardless, the mean age of the legume crown clade differs by only 1.0 to 2.5 Ma from the fixed age of the legume stem clade. Additionally, the oldest caesalpinioid, mimosoid, and papilionoid crown clades show approximately the same age range of 39 to 59 Ma. These findings all point to a rapid family-wide diversification, and predict few if any legume fossils prior to the Cenozoic. The range of the matK substitution rate, 2.1-24.6 x 10(-10) substitutions per site per year, is higher than that of rbcL, 1.6- 8.6 x 10(-10), and is accompanied by more uniform rate variation among codon positions. The matK and rbcL substitution rates are highly correlated across the legume family. For example, both loci have the slowest substitution rates among the mimosoids and the fastest rates among the millettioid legumes. This explains why groups such as the millettioids are amenable to species-level phylogenetic analysis with these loci, whereas other legume groups are not.

Bayes Theorem↗
PubMed1991

An updated comparison of drug dosing methods. Part I: Phenytoin.

The relationship between a dose of phenytoin and the resultant serum concentration is difficult to predict, and numerous dosing methods have been developed to quantify the dose required to achieve a specific concentration. This review brings up to date the earlier article in the Journal regarding predictive algorithms, various pharmacokinetics-based dosing techniques and Bayesian feedback methods for phenytoin dosing. The latest data support the original conclusions that dosing methods for phenytoin which incorporate an individualised approach or Bayesian principles tend to offer results superior to those from predictive algorithms. Bayesian methods have the additional advantage of using only 1 serum concentration, obtained under either steady-state or non-steady-state conditions. There is still a need for future investigations that include prospective evaluations of predictive performance and cost-effectiveness data.

Aging↗
PubMed2000

The proof of the pudding: an illustration of the relative strengths of null hypothesis, meta-analysis, and Bayesian analysis.

Some methodologists have recently suggested that scientific psychology's over-reliance on null hypothesis significance testing (NHST) impedes the progress of the discipline. In response, a number of defenders have maintained that NHST continues to play a vital role in psychological research. Both sides of the argument to date have been presented abstractly. The authors take a different approach to this issue by illustrating the use of NHST along with 2 possible alternatives (meta-analysis as a primary data analysis strategy and Bayesian approaches) in a series of 3 studies. Comparing and contrasting the approaches on actual data brings out the strengths and weaknesses of each approach. The exercise demonstrates that the approaches are not mutually exclusive but instead can be used to complement one another.

Bayes Theorem↗
PubMed2000

Risk of HIV infection as a function of the duration of intravenous drug use: a non-parametric Bayesian approach.

We analyse the elapsed time between intravenous (IV) drug initiation and HIV infection in a cohort of 972 injecting drug users attending a hospital detoxification unit. We use the time of seroconversion instead of the time of HIV infection because the date of HIV infection is rarely known and the gap between these two times is negligible (around one to three months). Although seroconversion time cannot be determined exactly, it can be inferred at least to within an interval. This seroconversion interval is determined from the dates of HIV antibody tests, if available. The data is consequently interval-censored. We estimate the distribution function of the elapsed time from IV drug initiation to seroconversion as well as the risk of seroconversion by means of a non-parametric Bayesian approach. The analysis is conducted according to the following four calendar periods: before or at 1980; between 1981 and 1985; between 1986 and 1991; after or at 1992 where the IV drug use was initiated. The methodology used is based on an alternating conditional sampling algorithm. The Bayesian approach allows not only the incorporation of prior beliefs about the distribution function, but also the analysis of the risk of seroconversion without assuming restrictive parametric models. Furthermore, the estimator for the distribution function is smooth and thus differences between groups can be easily interpreted.

Adolescent↗
PubMed1996

Statistical analysis of zidovudine (AZT) effect on CD4 cell counts in HIV disease.

We fit a class of random effects linear growth curve models for the square root of CD4 count to serial marker data from 164 HIV-positive individuals with known (or accurately estimated) dates of seroconversion and at least 10 CD4 measurements each (median 16). We do so by adopting a Bayesian viewpoint and using the Markov chain Monte Carlo technique Gibbs sampling. In particular, we examine the effect of the antiretroviral treatment zidovudine on the square root of CD4 series for the 136 patients who took the drug. Treatment effects are modelled by positing recoveries in square root of CD4 level proportional to current immuno-competence and changes in slope proportional to current rate of square root of CD4 loss. Both fixed and random treatment effects are considered and models are criticized and compared using Bayesian predictive methodology and checking data which comprise 424 new observations. Results indicate re-elevation of square root of CD4 level is associated with treatment but the effect, though significant, is mostly of small magnitude and is possibly transient; models neglecting consideration of treatment fit the checking data almost as well. Best overall model estimates mean rate of square root of CD4 loss per annum to be 2.1 (standard error 0.12); mean seroconversion value of square root of CD4 is 28.4 (SE 0.65). The estimated variance of individual slopes is 1.9 (SE 0.28), there being considerable individual variation in rate of CD4 loss, and a recovery in level of 0.047 (SE 0.014) times current square root of CD4 level is estimated at treatment uptake.

Antiviral Agents↗
PubMed1986

Carrier detection and prenatal diagnosis in X linked muscular dystrophy using restriction fragment length polymorphisms.

With the aim of offering carrier detection, genetic counselling, and prenatal diagnosis to as many families with Duchenne (DMD) and Becker (BMD) muscular dystrophy as possible, we used available DNA probes to determine the usefulness of the RFLP approach. We report in detail the risks calculated using Bayesian theory and combining pedigree and creatine kinase (CK) data with information derived from the RFLP studies. To date we have analysed members of 28 DMD families (10 familial, 18 sporadic) and six BMD families (four familial, two sporadic) with the closely linked pERT probes 87-1, 87-8, and 87-15 (DXS164). In addition, key members of all families were analysed with probes D2 (DXS43), C7 (DXS28), 754 (DXS84), and L1 X 28 (DXS7). Of the 97 females at risk of being carriers (not including 26 obligate carriers), the RFLP results were compatible with carriership in 22 and not in 51. In 24 females (including 17 mothers of sporadic cases), no information regarding carriership was derived from the RFLP studies. There was no disagreement between pedigree information, clearly raised CK values, and DNA studies. Of 52 obligate or possible carriers under the age of 45, prenatal diagnosis is possible in 49. Prenatal diagnostic RFLP studies have so far been done in three women. In one sporadic DMD family and one BMD family with three affected males the probands showed a deletion involving the three pERT87 subclones used. Experience derived from these families indicates that in our society genetic counselling in X linked muscular dystrophy is received with approval or even enthusiasm in spite of the 5% error estimate that we have quoted for pERT87 derived results.

Female↗