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At least 631 records · Page 35Linked to original sources
PubMed2005

Phylogenetic analyses reveal deeply divergent species lineages in the genus Sphaerobolus (Phallales: Basidiomycota).

Phylogenetic analyses of 27 artillery fungus (Sphaerobolus sp.) isolates were conducted to identify species boundaries in the genus Sphaerobolus. Multiple gene genealogies inferred from maximum likelihood, Bayesian, and maximum-parsimony analyses of sequence data from individual loci (mtSSU, ITS, EF 1-alpha, and LSU) and a combined dataset (mtSSU, ITS, and EF 1-alpha) concordantly indicate the existence of three deeply divergent lineages in the genus Sphaerobolus, each representing a phylogenetic species. These three phylogenetic species correspond to two known species: Sphaerobolus iowensis and Sphaerobolus stellatus, and a newly discovered species. Suprageneric phylogenetic analyses of the mtSSU and LSU datasets containing representatives of related genera of the gomphoid-phalloid clade of Homobasidiomycetes suggested that the undescribed taxon likely is more closely related to S. stellatus than to S. iowensis.

Base Sequence↗
PubMed2005

Molecular phylogenetics and evolution of host plant use in the Neotropical rolled leaf 'hispine' beetle genus Cephaloleia (Chevrolat) (Chrysomelidae: Cassidinae).

Here, we report the results of a species level phylogenetic study of Cephaloleia beetles designed to clarify relationships and patterns of host plant taxon and tissue use among species. Our study is based on up to 2088bp of mtDNA sequence data. Maximum parsimony, maximum likelihood, and Bayesian methods of phylogenetic inference consistently recover a monophyletic Cephaloleia outside of a basal clade of primarily palm feeding species (the 'Arecaceae-feeding clade'), and C. irregularis. In all three analyses, the 'Arecaceae-feeding clade' includes Cephaloleia spp. with unusual morphological features, and a few species currently placed in other cassidine genera and tribes. All three analyses also recover a clade that includes all Zingiberales feeding Cephaloleia and most Cephaloleia species (the 'Zingiberales-feeding clade'). Two notable clades are found within the 'Zingiberales-feeding clade.' One is comprised of beetles that normally feed only on the young rolled leaves of plants in the families Heliconiaceae and Marantaceae (the 'Heliconiaceae & Marantaceae-feeding clade'). The other is comprised of relative host tissue generalist, primarily Zingiberales feeding species (the 'generalist-feeding clade'). A few species in the 'generalist-feeding clade' utilize Cyperaceae or Poaceae as hosts. Overall, relatively basal Cephaloleia (e.g., the 'Arecaceae clade') feed on relatively basal monocots (e.g., Cyclanthaceae and Arecaceae), and relatively derived Cephaloleia (e.g., the 'Zingiberales-feeding clade') feed on relatively derived monocots (mostly in the order Zingiberales). Zingiberales feeding and specialization on young rolled Zingiberales leaves have each apparently evolved just once in Cephaloleia.

Adaptation, Biological↗
PubMed2003

Subunit sequences of the 4 x 6-mer hemocyanin from the golden orb-web spider, Nephila inaurata.

The transport of oxygen in the hemolymph of many arthropod and mollusc species is mediated by large copper-proteins that are referred to as hemocyanins. Arthropod hemocyanins are composed of hexamers and oligomers of hexamers. Arachnid hemocyanins usually form 4 x 6-mers consisting of seven distinct subunit types (termed a-g), although in some spider taxa deviations from this standard scheme have been observed. Applying immunological and electrophoretic methods, six distinct hemocyanin subunits were identified in the red-legged golden orb-web spider Nephila inaurata madagascariensis (Araneae: Tetragnathidae). The complete cDNA sequences of six subunits were obtained that corresponded to a-, b-, d-, e-, f- and g-type subunits. No evidence for a c-type subunit was found in this species. The inclusion of the N. inaurata hemocyanins in a multiple alignment of the arthropod hemocyanins and the application of the Bayesian method of phylogenetic inference allow, for the first time, a solid reconstruction of the intramolecular evolution of the chelicerate hemocyanin subunits. The branch leading to subunit a diverged first, followed by the common branch of the dimer-forming b and c subunits, while subunits d and f, as well as subunits e and g form common branches. Assuming a clock-like evolution of the chelicerate hemocyanins, a timescale for the evolution of the Chelicerata was obtained that agrees with the fossil record.

Amino Acid Sequence↗
PubMed2002

Origin of plant glycerol transporters by horizontal gene transfer and functional recruitment.

Gene-family evolution mostly relies on gene duplication coupled with functional diversification of gene products. However, other evolutionary mechanisms may also be important in generating protein diversity. The ubiquitous membrane intrinsic protein (MIP) gene family is an excellent model system to search for such alternative evolutionary mechanisms. MIPs are proteins that transport water, glycerol, and small solutes across cell membranes in all living organisms. We reconstructed the molecular phylogeny of MIPs based on amino acid sequence data by using neighbor-joining, maximum-likelihood, and Bayesian methods of phylogenetic inference. The recovered trees show an early and distinct separation of water and glycerol transporters, i.e., aquaporins (AQPs), and aquaglyceroporins. The latter are absent from plants. As expected, gene duplication and functional diversification account for most of the diversity of animal and plant members of the family. However, in contrast to this model, we find that the sister group of plant glycerol transporters are bacterial AQPs. This relationship suggests first that plant glycerol transporters may resulted from a single event of horizontal gene transfer from bacteria, which we have estimated to have occurred approximately 1,200 million years ago, at the origin of plants, and second that bacterial AQPs were likely recruited to transport glycerol in plants because of their absence of aquaglyceroporins. This striking example of adaptive evolution at the molecular level was demonstrated further by finding convergent or parallel replacements at particular amino acid positions related to water- and glycerol-transporting specificity.

Amino Acid Sequence↗
PubMed2004

Calcium regulation of single ryanodine receptor channel gating analyzed using HMM/MCMC statistical methods.

Type-II ryanodine receptor channels (RYRs) play a fundamental role in intracellular Ca(2+) dynamics in heart. The processes of activation, inactivation, and regulation of these channels have been the subject of intensive research and the focus of recent debates. Typically, approaches to understand these processes involve statistical analysis of single RYRs, involving signal restoration, model estimation, and selection. These tasks are usually performed by following rather phenomenological criteria that turn models into self-fulfilling prophecies. Here, a thorough statistical treatment is applied by modeling single RYRs using aggregated hidden Markov models. Inferences are made using Bayesian statistics and stochastic search methods known as Markov chain Monte Carlo. These methods allow extension of the temporal resolution of the analysis far beyond the limits of previous approaches and provide a direct measure of the uncertainties associated with every estimation step, together with a direct assessment of why and where a particular model fails. Analyses of single RYRs at several Ca(2+) concentrations are made by considering 16 models, some of them previously reported in the literature. Results clearly show that single RYRs have Ca(2+)-dependent gating modes. Moreover, our results demonstrate that single RYRs responding to a sudden change in Ca(2+) display adaptation kinetics. Interestingly, best ranked models predict microscopic reversibility when monovalent cations are used as the main permeating species. Finally, the extended bandwidth revealed the existence of novel fast buzz-mode at low Ca(2+) concentrations.

Algorithms↗
PubMed2005

On the correlation between composition and site-specific evolutionary rate: implications for phylogenetic inference.

Model-based phylogenetic reconstruction methods traditionally assume homogeneity of nucleotide frequencies among sequence sites and lineages. Yet, heterogeneity in base composition is a characteristic shared by most biological sequences. Compositional variation in time, reflected in the compositional biases among contemporary sequences, has already been extensively studied, and its detrimental effects on phylogenetic estimates are known. However, fewer studies have focused on the effects of spatial compositional heterogeneity within genes. We show here that different sites in an alignment do not always share a unique compositional pattern, and we provide examples where nucleotide frequency trends are correlated with the site-specific rate of evolution in RNA genes. Spatial compositional heterogeneity is shown to affect the estimation of evolutionary parameters. With standard phylogenetic methods, estimates of equilibrium frequencies are found to be biased towards the composition observed at fast-evolving sites. Conversely, the ancestral composition estimates of some time-heterogeneous but spatially homogeneous methods are found to be biased towards frequencies observed at invariant and slow-evolving sites. The latter finding challenges the result of a previous study arguing against a hyperthermophilic last universal ancestor from the low apparent G + C content of its rRNA sequences. We propose a new model to account for compositional variation across sites. A Gaussian process prior is used to allow for a smooth change in composition with evolutionary rate. The model has been implemented in the phylogenetic inference software PHASE, and Bayesian methods can be used to obtain the model parameters. The results suggest that this model can accurately capture the observed trends in present-day RNA sequences.

Evolution, Molecular↗
PubMed2006

Bayesian semiparametric dynamic frailty models for multiple event time data.

Many biomedical studies collect data on times of occurrence for a health event that can occur repeatedly, such as infection, hospitalization, recurrence of disease, or tumor onset. To analyze such data, it is necessary to account for within-subject dependency in the multiple event times. Motivated by data from studies of palpable tumors, this article proposes a dynamic frailty model and Bayesian semiparametric approach to inference. The widely used shared frailty proportional hazards model is generalized to allow subject-specific frailties to change dynamically with age while also accommodating nonproportional hazards. Parametric assumptions on the frailty distribution are avoided by using Dirichlet process priors for a shared frailty and for multiplicative innovations on this frailty. By centering the semiparametric model on a conditionally conjugate dynamic gamma model, we facilitate posterior computation and lack-of-fit assessments of the parametric model. Our proposed method is demonstrated using data from a cancer chemoprevention study.

Algorithms↗
PubMed2006

Comparing phylogenetic codivergence between polyomaviruses and their hosts.

Seventy-two full genomes corresponding to nine mammalian (67 strains) and two avian (5 strains) polyomavirus species were analyzed using maximum likelihood and Bayesian methods of phylogenetic inference. Our fully resolved and well-supported (bootstrap proportions > 90%; posterior probabilities = 1.0) trees separate the bird polyomaviruses (avian polyomavirus and goose hemorrhagic polyomavirus) from the mammalian polyomaviruses, which supports the idea of spitting the genus into two subgenera. Such a split is also consistent with the different viral life strategies of each group. Simian (simian virus 40, simian agent 12 [Sa12], and lymphotropic polyomavirus) and rodent (hamster polyomavirus, mouse polyomavirus, and murine pneumotropic polyomavirus [MPtV]) polyomaviruses did not form monophyletic groups. Using our best hypothesis of polyomavirus evolutionary relationships and established host phylogenies, we performed a cophylogenetic reconciliation analysis of codivergence. Our analyses generated six optimal cophylogenetic scenarios of coevolution, including 12 codivergence events (P < 0.01), suggesting that Polyomaviridae coevolved with their avian and mammal hosts. As individual lineages, our analyses showed evidence of host switching in four terminal branches leading to MPtV, bovine polyomavirus, Sa12, and BK virus, suggesting a combination of vertical and horizontal transfer in the evolutionary history of the polyomaviruses.

Animals↗
PubMed2006

Shape recognition alters sensitivity in stereoscopic depth discrimination.

A fundamental question in visual perception is to characterize how information from sensory input is integrated with prior probabilities. The role of prior probabilities is controversial for elementary visual processes, which are often believed to be immune from higher-level influences. In this paper, we demonstrate such influences. We tested human observers' abilities to discriminate stereoscopic depth defined by points embedded in a biological pattern--a human figure. Our results indicate that the internal representation of a walking human figure imposed constraints on depth discrimination of a static stimulus. This constraint was manifested when the stimulus was recognized as a human figure. When the expected human figure configuration (forearms having equal length) was inconsistent with the sensory input information, discrimination of forearm lengths was impaired. In contrast, when there was no inconsistency (the hand-hip distance on the left was not expected to be equal to that on the right), discrimination between the two distances was improved, presumably because the human figure configuration provided a more accurate frame of reference for stereoscopic depth. Both the impairment and improvement were due to changes of discrimination sensitivity rather than decision bias. Our findings support the view that visual perception is an inference process constrained by Bayesian prior probabilities.

Bayes Theorem↗
PubMed2001

Random effects models for HIV marker data: practical approaches with currently available software.

The analysis of marker data from HIV positive patients has been the motivation for many new developments in applied statistics. As well as reviewing these methods, this paper considers the extent to which programs to implement them are available in current software. Particular areas of development have been the joint modelling of markers and survival outcomes, non-linear random effects models that are of particular relevance for studying the efficacy of treatments and the use of Bayesian computational methods for inference from marker data. The package WinBUGS is recommended as being particularly well suited to the analysis of marker data.

Biomarkers↗
PubMedDate not supplied

A Bayesian approach for constructing genetic maps when markers are miscoded.

The advent of molecular markers has created opportunities for a better understanding of quantitative inheritance and for developing novel strategies for genetic improvement of agricultural species, using information on quantitative trait loci (QTL). A QTL analysis relies on accurate genetic marker maps. At present, most statistical methods used for map construction ignore the fact that molecular data may be read with error. Often, however, there is ambiguity about some marker genotypes. A Bayesian MCMC approach for inferences about a genetic marker map when random miscoding of genotypes occurs is presented, and simulated and real data sets are analyzed. The results suggest that unless there is strong reason to believe that genotypes are ascertained without error, the proposed approach provides more reliable inference on the genetic map.

Bayes Theorem↗
PubMed2006

Analysis of rabbit doe longevity using a semiparametric log-Normal animal frailty model with time-dependent covariates.

Data on doe longevity in a rabbit population were analysed using a semiparametric log-Normal animal frailty model. Longevity was defined as the time from the first positive pregnancy test to death or culling due to pathological problems. Does culled for other reasons had right censored records of longevity. The model included time dependent covariates associated with year by season, the interaction between physiological state and the number of young born alive, and between order of positive pregnancy test and physiological state. The model also included an additive genetic effect and a residual in log frailty. Properties of marginal posterior distributions of specific parameters were inferred from a full Bayesian analysis using Gibbs sampling. All of the fully conditional posterior distributions defining a Gibbs sampler were easy to sample from, either directly or using adaptive rejection sampling. The marginal posterior mean estimates of the additive genetic variance and of the residual variance in log frailty were 0.247 and 0.690.

Animals↗
PubMed2004

Comparative evaluation of a new effective population size estimator based on approximate bayesian computation.

We describe and evaluate a new estimator of the effective population size (N(e)), a critical parameter in evolutionary and conservation biology. This new "SummStat" N(e) estimator is based upon the use of summary statistics in an approximate Bayesian computation framework to infer N(e). Simulations of a Wright-Fisher population with known N(e) show that the SummStat estimator is useful across a realistic range of individuals and loci sampled, generations between samples, and N(e) values. We also address the paucity of information about the relative performance of N(e) estimators by comparing the SummStat estimator to two recently developed likelihood-based estimators and a traditional moment-based estimator. The SummStat estimator is the least biased of the four estimators compared. In 32 of 36 parameter combinations investigated using initial allele frequencies drawn from a Dirichlet distribution, it has the lowest bias. The relative mean square error (RMSE) of the SummStat estimator was generally intermediate to the others. All of the estimators had RMSE > 1 when small samples (n = 20, five loci) were collected a generation apart. In contrast, when samples were separated by three or more generations and N(e) < or = 50, the SummStat and likelihood-based estimators all had greatly reduced RMSE. Under the conditions simulated, SummStat confidence intervals were more conservative than the likelihood-based estimators and more likely to include true N(e). The greatest strength of the SummStat estimator is its flexible structure. This flexibility allows it to incorporate any potentially informative summary statistic from population genetic data.

Bayes Theorem↗
PubMed2004

Inference of gene regulatory networks by means of dynamic differential Bayesian networks and nonparametric regression.

We propose a dynamic differential Bayesian networks (DDBNs) and nonparametric regression model. This model is an extended model of traditional dynamic Bayesian networks (DBNs), which can incorporate temporal information in a natural way and directly handle real-valued data obtained from microarrays without any transformation. In addition, it can cope with differential information between gene expression levels, without any loss to the traditional advantage, i.e., the capability of estimating non-linear relationships between genes. We apply DDBNs to analyze simulated data and real data, i.e., Saccharomyces cerevisiae cell cycle gene expression data. We have confirmed the effectiveness of our approach in the sense that some edges have been successfully detected only by DDBNs, not by DBNs.

Algorithms↗
PubMed1988

Segregation analysis with uncertain ascertainment: application to Fanconi anemia.

A Bayesian solution for making inferences about segregation parameters with no information about the ascertainment is presented. Inferences about the segregation probability and the probability of being sporadic are made through the posterior marginal distribution of these parameters after integrating out the ascertainment probability, the nuisance parameter. The method was tested with real and simulated data and performed well. Original Fanconi anemia data, for which no information about the ascertainment was available, were then analyzed, with results that confirmed a monogenic autosomal recessive mode of inheritance.

Anemia, Aplastic↗
PubMed1982

Jerome Cornfield's contributions to the conduct of clinical trials.

Jerome Cornfield's important contributions to the conduct of clinical trials are summarized here. They include consultative advice in the planning of many national trials, active collaboration in the conduct of many others, discussions of the role of classical and Bayesian methods of statistical inference in clinical trials, recommendations on data monitoring, contributions to the analysis of results of the University Group Diabetes Project, and efforts to assist the planning of coronary intervention trials with quantitative assessments of possible reductions in disease rates due to intervention on smoking and diet. An attempt is made to evaluate the impact of Cornfield's contributions to clinical trials.

Bayes Theorem↗
PubMed2006

Phylogenetic analysis of honey bee behavioral evolution.

DNA sequences from three mitochondrial (rrnL, cox2, nad2) and one nuclear gene (itpr) from all 9 known honey bee species (Apis), a 10th possible species, Apis dorsata binghami, and three outgroup species (Bombus terrestris, Melipona bicolor and Trigona fimbriata) were used to infer Apis phylogenetic relationships using Bayesian analysis. The dwarf honey bees were confirmed as basal, and the giant and cavity-nesting species to be monophyletic. All nodes were strongly supported except that grouping Apis cerana with A. nigrocincta. Two thousand post-burnin trees from the phylogenetic analysis were used in a Bayesian comparative analysis to explore the evolution of dance type, nest structure, comb structure and dance sound within Apis. The ancestral honey bee species was inferred with high support to have nested in the open, and to have more likely than not had a silent vertical waggle dance and a single comb. The common ancestor of the giant and cavity-dwelling bees is strongly inferred to have had a buzzing vertical directional dance. All pairwise combinations of characters showed strong association, but the multiple comparisons problem reduces the ability to infer associations between states between characters. Nevertheless, a buzzing dance is significantly associated with cavity-nesting, several vertical combs, and dancing vertically, a horizontal dance is significantly associated with a nest with a single comb wrapped around the support, and open nesting with a single pendant comb and a silent waggle dance.

Animals↗
PubMed2004

Bayesian models for the analysis of genetic structure when populations are correlated.

MOTIVATION: Population allele frequencies are correlated when populations have a shared history or when they exchange genes. Unfortunately, most models for allele frequency and inference about population structure ignore this correlation. Recent analytical results show that among populations, correlations can be very high, which could affect estimates of population genetic structure. In this study, we propose a mixture beta model to characterize the allele frequency distribution among populations. This formulation incorporates the correlation among populations as well as extending the model to data with different clusters of populations. RESULTS: Using simulated data, we show that in general, the mixture model provides a good approximation of the among-population allele frequency distribution and a good estimate of correlation among populations. Results from fitting the mixture model to a dataset of genotypes at 377 autosomal microsatellite loci from human populations indicate high correlation among populations, which may not be appropriate to neglect. Traditional measures of population structure tend to overestimate the amount of genetic differentiation when correlation is neglected. Inference is performed in a Bayesian framework. CONTACT: fur@ohsu.edu.

Bayes Theorem↗