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At least 1,153 records · Page 64Linked to original sources
PubMed2006

Phylogeny of finescale shiners of the genus Lythrurus (Cypriniformes: Cyprinidae) inferred from four mitochondrial genes.

We infer the phylogenetic relationships of finescale shiners of the genus Lythrurus, a group of 11 species of freshwater minnows widely distributed in eastern North America, using DNA sequences from the ND2 (1047 bp), ATPase8 and 6 (823 bp), and ND3 (421 bp) mitochondrial protein-coding genes. The topologies resulting from maximum parsimony, Bayesian, and maximum likelihood tree building methods are broadly congruent, with two distinct clades within the genus: the L. umbratilis clade (L. umbratilis + L. lirus + (L. fasciolaris + (L. ardens, L. matutinus))) and the L. bellus clade (L. fumeus + L. snelsoni + (L. roseipinnis + (L. atrapiculus + (L. bellus, L. algenotus)))). Support is weak at the base of several clades, but strongly supported nodes differ significantly from prior investigations. In particular, our results confirm and extend earlier studies recovering two clades within Lythrurus corresponding to groups with largely "northern" and "southern" geographic distributions. Several species in this genus are listed in the United States as threatened or of special concern due to habitat degradation or limited geographic ranges. In this study, populations assigned to L. roseipinnis show significant genetic divergence suggesting that there is greater genetic diversity within this species than its current taxonomy reflects. A full accounting of the biodiversity of the genus awaits further study.

Animals↗
PubMed1999

A Bayesian approach to ordering gene markers.

A technique is presented whereby a marker map can be constructed using resource family data with an entire class of missing data. The focus is on a half-sib design where there is only information on a single parent and its progeny. A Bayesian approach is utilised with solutions obtained via a Markov chain Monte Carlo algorithm. Features of the approach include the capacity to determine parameters for the ungenotyped dam population, the ability to incorporate published information and its reliability, and the production of posterior densities and the consequent deduction of a wide range of inferences. These features are demonstrated through the analysis of simulated and experimental data.

Algorithms↗
PubMed2002

Ecological statistics of Gestalt laws for the perceptual organization of contours.

Although numerous studies have measured the strength of visual grouping cues for controlled psychophysical stimuli, little is known about the statistical utility of these various cues for natural images. In this study, we conducted experiments in which human participants trace perceived contours in natural images. These contours are automatically mapped to sequences of discrete tangent elements detected in the image. By examining relational properties between pairs of successive tangents on these traced curves, and between randomly selected pairs of tangents, we are able to estimate the likelihood distributions required to construct an optimal Bayesian model for contour grouping. We employed this novel methodology to investigate the inferential power of three classical Gestalt cues for contour grouping: proximity, good continuation, and luminance similarity. The study yielded a number of important results: (1) these cues, when appropriately defined, are approximately uncorrelated, suggesting a simple factorial model for statistical inference; (2) moderate image-to-image variation of the statistics indicates the utility of general probabilistic models for perceptual organization; (3) these cues differ greatly in their inferential power, proximity being by far the most powerful; and (4) statistical modeling of the proximity cue indicates a scale-invariant power law in close agreement with prior psychophysics.

Form Perception↗
PubMed2006

The phylogeny of the social Anelosimus spiders (Araneae: Theridiidae) inferred from six molecular loci and morphology.

We use fragments of three nuclear genes (Histone 3, 18SrDNA, and 28SrDNA) and three mitochondrial genes (16SrDNA, ND1, and COI) totalling approximately 4.5kb, in addition to morphological data, to estimate the phylogenetic relationships among Anelosimus spiders, well known for their sociality. The analysis includes 67 individuals representing 23 of the 53 currently recognized Anelosimus species and all species groups previously recognized by morphological evidence. We analyse the data using Bayesian, maximum likelihood, and parsimony methods, considering the genes individually as well as combined (mitochondrial, nuclear, and both combined) in addition to a 'total evidence' analysis including morphology. Most of the data partitions are congruent in agreeing on several fundamental aspects of the phylogeny, and the combined molecular data yield a tree broadly similar to an existing morphological hypothesis. We argue that such congruence among data partitions is an important indicator of support that may go undetected by standard robustness estimators. Our results strongly support Anelosimus monophyly, and the monophyly of the recently revised American 'eximius lineage', although slightly altered by excluding A. pacificus. There was consistent support for the scattering of American Anelosimus species in three clades suggesting intercontinental dispersal. Several recently described species are reconstructed as monophyletic, supporting taxonomic decisions based on morphology and behaviour in this taxonomically difficult group. Corroborating previous results from morphology, the molecular data suggest that social species are scattered across the genus and thus that sociality has evolved multiple times, a significant finding for exploring the causes and consequences of social evolution in this group of organisms.

Animals↗
PubMed2003

Bayesian model choice and search strategies for mapping interacting quantitative trait Loci.

Most complex traits of animals, plants, and humans are influenced by multiple genetic and environmental factors. Interactions among multiple genes play fundamental roles in the genetic control and evolution of complex traits. Statistical modeling of interaction effects in quantitative trait loci (QTL) analysis must accommodate a very large number of potential genetic effects, which presents a major challenge to determining the genetic model with respect to the number of QTL, their positions, and their genetic effects. In this study, we use the methodology of Bayesian model and variable selection to develop strategies for identifying multiple QTL with complex epistatic patterns in experimental designs with two segregating genotypes. Specifically, we develop a reversible jump Markov chain Monte Carlo algorithm to determine the number of QTL and to select main and epistatic effects. With the proposed method, we can jointly infer the genetic model of a complex trait and the associated genetic parameters, including the number, positions, and main and epistatic effects of the identified QTL. Our method can map a large number of QTL with any combination of main and epistatic effects. Utility and flexibility of the method are demonstrated using both simulated data and a real data set. Sensitivity of posterior inference to prior specifications of the number and genetic effects of QTL is investigated.

Bayes Theorem↗
PubMed2007

Genetic connectivity in the Florida reef system: comparative phylogeography of commensal invertebrates with contrasting reproductive strategies.

Effective spatial management of coral reefs including design of marine protected areas requires an understanding of interpopulation genetic connectivity. We assessed gene flow along 355 km of the Florida reef system and between Florida and Belize in three commensal invertebrates occupying the same host sponge (Callyspongia vaginalis) but displaying contrasting reproductive dispersal strategies: the broadcast-spawning brittle star Ophiothrix lineata and two brooding amphipods Leucothoe kensleyi and Leucothoe ashleyae. Multiple analytical approaches to sequence variation in the mitochondrial COI gene demonstrated a high degree of overall connectivity for all three species along the Florida reef system. Ophiothrix lineata showed significant genetic structuring between Florida and Belize, and a pattern of isolation by distance but no significant genetic structuring along the Florida coastline. Bayesian estimates of migration detected a strong southerly dispersal bias for O. lineata along the Florida reef system, contrary to the general assumption of northerly gene flow in this region based on the direction of the Florida Current. Both amphipods, despite direct development, also showed high gene flow along the Florida reef system. Multiple inferences of long-distance dispersal from a nested clade analysis support the hypothesis that amphipod transport, possibly in detached sponge fragments, could generate the high levels of overall gene flow observed. However, this transport mechanism appears much less effective across deep water as connectivity between Florida and Belize (1072 km) is highly restricted.

Amphipoda↗
PubMed2006

Estimating receiver operating characteristic curves with covariates when there is no perfect reference test for diagnosis of Johne's disease.

Paratuberculosis (Johne's disease) is a significant animal health problem. Evaluation of diagnostic tests for Johne's disease has been difficult due to lack of a gold standard test. In recent years, there has been interest in receiver operating characteristic (ROC) curve estimation without any gold standard test. Typically, either Bayesian or maximum likelihood methods are proposed. Although these methods overcome the lack of a gold standard test in ROC curve estimation, little work has been done to incorporate covariates in the analysis. In this paper, we propose a method for estimation of ROC curves based on statistical models to adjust for covariate effects when the true disease states of test animals are unknown. The covariates may be correlated with the disease process or with the diagnostic testing procedure, or both. We propose a 2-part Bayesian model: first, a logistic regression model for disease prevalence is used to fit the covariates; second, a linear model is used to fit the covariates to the distribution of test scores. We used Markov chain Monte Carlo methods to compute the posterior estimates of the sensitivities and specificities that provide the groundwork for inference concerning the diagnostic procedure's accuracy. We applied the methodology to milk ELISA scores from several dairy-cow herds for the diagnostic testing of paratuberculosis. We found that both milk yield and its interaction with age had significant effects on the disease process whereas only milk yield was significant on the testing procedure.

Animals↗
PubMed2003

A phylogeny of Chinese species in the genus Phrynocephalus (Agamidae) inferred from mitochondrial DNA sequences.

We investigated the phylogenetic relationships among most Chinese species of lizards in the genus Phrynocephalus (118 individuals collected from 56 populations of 14 well-defined species and several unidentified specimens) using four mitochondrial gene fragments (12S rRNA, 16S rRNA, cytochrome b, and ND4-tRNA(LEU)). The partition-homogeneity tests indicated that the combined dataset was homogeneous, and maximum-parsimony (MP), neighbor-joining (NJ), maximum-likelihood (ML) and Bayesian (BI) analyses were performed on this combined dataset (49 haplotypes including outgroups for 2058bp in total). The maximum-parsimony analysis resulted in 24 equally parsimonious trees, and their strict consensus tree shows that there are two major clades representing the Chinese Phrynocephalus species: the viviparous group (Clade A) and the oviparous group (Clade B). The trees derived from Bayesian, ML, and NJ analyses were topologically identical to the MP analysis except for the position of P. mystaceus. All analyses left the nodes for the oviparous group, the most basal clade within the oviparous group, and P. mystaceus unresolved. The phylogenies further suggest that the monophyly of the viviparous species may have resulted from vicariance, while recent dispersal may have been important in generating the pattern of variation among the oviparous species.

Animals↗
PubMed2005

Methods for incorporating covariate adjustment, subgroup analysis and between-centre differences into cost-effectiveness evaluations.

BACKGROUND: Overall assessments of cost-effectiveness are now commonplace in informing medical policy decision making. It is often important, however, also to investigate how cost-effectiveness varies between patient subgroups. Yet such analyses are rarely undertaken, because appropriate methods have not been sufficiently developed. METHODS: We propose a coherent set of Bayesian methods to extend cost-effectiveness analyses to adjust for baseline covariates, to investigate differences between subgroups, and to allow for differences between centres in a multicentre study using a hierarchical model. These methods consider costs and effects jointly, and allow for the typically skewed distribution of cost data. The results are presented as inferences on the cost-effectiveness plane, and as cost-effectiveness acceptability curves. RESULTS: In applying these methods to a randomised trial of case management of psychotic patients, we show that overall cost-effectiveness can be affected by ignoring the skewness of cost data, but that it may be difficult to gain substantial precision by adjusting for baseline covariates. While analyses of overall cost-effectiveness can mask important subgroup differences, crude differences between centres may provide an unrealistic indication of the true differences between them. CONCLUSIONS: The methods developed allow a flexible choice for the distributions used for cost data, and have a wide range of applicability--to both randomised trials and observational studies. Experience needs to be gained in applying these methods in practice, and using their results in decision making.

Bayes Theorem↗
PubMed1992

A semi-Bayes approach to the analysis of correlated multiple associations, with an application to an occupational cancer-mortality study.

Thomas et al. presented the application of empirical-Bayes methods to the problem of multiple inference in epidemiologic studies. One limitation of their approach, which they noted, was the need to assume exchangeable log relative-risk parameters, and independent relative-risk estimates. Numerical integration was also required. Here I generalize their approach to allow for non-exchangeable parameters and non-independent estimates. The resulting method is Bayesian in so far as some feature of the prior distribution are specified from prior information, but is empirical Bayes in so far as some explicit parameters in the prior distribution are estimated from the data. Estimation is based on approximations to the posterior distribution; this allows one to implement the approach with standard software packages for matrix algebra. The method is illustrated in an occupational mortality study of 84 exposure-cancer associations.

Bayes Theorem↗
PubMed2006

Identifying sites under positive selection with uncertain parameter estimates.

Codon-based substitution models are routinely used to measure selective pressures acting on protein-coding genes. To this effect, the nonsynonymous to synonymous rate ratio (dN/dS = omega) is estimated. The proportion of amino-acid sites potentially under positive selection, as indicated by omega > 1, is inferred by fitting a probability distribution where some sites are permitted to have omega > 1. These sites are then inferred by means of an empirical Bayes or by a Bayes empirical Bayes approach that, respectively, ignores or accounts for sampling errors in maximum-likelihood estimates of the distribution used to infer the proportion of sites with omega > 1. Here, we extend a previous full-Bayes approach to include models with high power and low false-positive rates when inferring sites under positive selection. We propose some heuristics to alleviate the computational burden, and show that (i) full Bayes can be superior to empirical Bayes when analyzing a small data set or small simulated data, (ii) full Bayes has only a small advantage over Bayes empirical Bayes with our small test data, and (iii) Bayesian methods appear relatively insensitive to mild misspecifications of the random process generating adaptive evolution in our simulations, but in practice can prove extremely sensitive to model specification. We suggest that the codon model used to detect amino acids under selection should be carefully selected, for instance using Akaike information criterion (AIC).

Amino Acids↗
PubMed2007

A haplotype-linkage analysis method for estimating recombination rates using dense SNP trio data.

Meiotic recombination is an important evolution force in shaping human genomes and creating human diversity. Recent explorations suggest that meiotic recombination events tend to happen in certain regions of the genome, leading to the hypothesis of recombination hot spots. To identify such hot spots, we describe an empirical method for estimating the recombination rate, which reflects both historical and current meiotic events, using unphased genotypes from nuclear families, in particular, parents-child trios. The key idea is that use of the haplotypic polymorphisms with multiple adjacent SNPs will increase the number of informative meioses and hence would improve the power of linkage analysis. Since haplotypes of individuals are not directly observed, e.g., in HapMap data, we infer the haplotypes simultaneously while estimating recombination rate. We refer this described method as haplotype-linkage (HALIN) method. Our simulation results show that HALIN gives unbiased estimates of recombination rate. We apply HALIN to analyze the genotype data of chromosome 20 from HapMap data and compare the results to the results using two existing methods, Bayesian coalescent method described by McVean et al. [2004] science 304:581-584 and empirical method by Clarke and Cardon ([2005] Genetics). Results suggest that HALIN identified 75 hot spots on chromosome 20, and 85% of them are also identified by the method by McVean et al. ([2004] science 304:581-584), in addition to a few new hot spots. In comparison with Clarke and Cardon's result, estimated recombination rates (RRs) under these 75 hot spots are significantly greater than those outside of hot spots, which support the general consistency in discovering recombination hot spots between two methods.

Child↗
PubMed2002

Bayesian estimation, simulation and uncertainty analysis: the cost-effectiveness of ganciclovir prophylaxis in liver transplantation.

This paper demonstrates the usefulness of combining simulation with Bayesian estimation methods in analysis of cost-effectiveness data collected alongside a clinical trial. Specifically, we use Markov Chain Monte Carlo (MCMC) to estimate a system of generalized linear models relating costs and outcomes to a disease process affected by treatment under alternative therapies. The MCMC draws are used as parameters in simulations which yield inference about the relative cost-effectiveness of the novel therapy under a variety of scenarios. Total parametric uncertainty is assessed directly by examining the joint distribution of simulated average incremental cost and effectiveness. The approach allows flexibility in assessing treatment in various counterfactual premises and quantifies the global effect of parametric uncertainty on a decision-maker's confidence in adopting one therapy over the other.

Antiviral Agents↗
PubMed2002

A Bayesian analysis of a proportion under non-ignorable non-response.

The National Health Interview Survey (NHIS) is one of the surveys used to assess one aspect of the health status of the U.S. population. One indicator of the nation's health is the total number of doctor visits made by the household members in the past year. We study the binary variable of at least one doctor visit versus no doctor visit by all household members to each of the 50 states and the District of Columbia. The proportion of households with at least one doctor visit is an indicator of the status of health of the U.S. population. There is a substantial number of non-respondents among the sampled households. The main issue we address here is that the non-response mechanism should not be ignored because respondents and non-respondents differ. The purpose of this work is to estimate the proportion of households with at least one doctor visit, and to investigate what adjustment needs to be made for non-ignorable non-response. We consider a non-ignorable non-response model that expresses uncertainty about ignorability through the ratio of odds of a household doctor visit among respondents to the odds of doctor visit among all households, and this ratio varies from state to state. We use a hierarchical Bayesian selection model to accommodate this non-response mechanism. Because of the weak identifiability of the parameters, it is necessary to 'borrow strength' across states as in small area estimation. We also perform a simulation study to compare the expansion model with an alternative expansion model, an ignorable model and a non-ignorable model. Inference for the probability of a doctor visit is generally similar across the models. Our main result is that for some of the states the non-response mechanism can be considered non-ignorable, and that 95 per cent credible intervals of the probability for a household doctor visit and the probability that a household responds shed important light on the NHIS data.

Bayes Theorem↗
PubMed2006

Molecular phylogeny of Clupeiformes (Actinopterygii) inferred from nuclear and mitochondrial DNA sequences.

The taxonomy of clupeiforms has been extensively studied, yet phylogenetic relationships among component taxa remain controversial or unresolved. Here we test current and new hypotheses of relationships among clupeiforms using mitochondrial rRNA genes (12S and 16S) and nuclear RAG1 and RAG2 sequences (total of 4749bp) for 37 clupeiform taxa representing all five extant families and all subfamilies of Clupeiformes, except Pristigasterinae, plus seven outgroups. Our results, based on maximum parsimony, maximum likelihood, and Bayesian analyses of these data, show that some traditional hypotheses are supported. These include the monophyly of the families Engraulidae, consisting of two monophyletic subfamilies, Engraulinae (Engraulis and Anchoa) and Coilinae (Coilia and Setipinna), and Pristigasteridae (here represented only by Ilisha and Pellona). The basal position of Denticeps among clupeiforms is consistent with the molecular data when base compositional biases are accounted for. However, the monophyly of Clupeidae was not supported. Some clupeids were more closely related to taxa assigned to Pristigasteridae and Chirocentridae (Chirocentrus). These results suggest that a major revision in the classification of clupeiform fishes may be necessary, but should await a more complete taxonomic sampling and additional data.

Animals↗
PubMed2006

Noise characteristics and prior expectations in human visual speed perception.

Human visual speed perception is qualitatively consistent with a Bayesian observer that optimally combines noisy measurements with a prior preference for lower speeds. Quantitative validation of this model, however, is difficult because the precise noise characteristics and prior expectations are unknown. Here, we present an augmented observer model that accounts for the variability of subjective responses in a speed discrimination task. This allowed us to infer the shape of the prior probability as well as the internal noise characteristics directly from psychophysical data. For all subjects, we found that the fitted model provides an accurate description of the data across a wide range of stimulus parameters. The inferred prior distribution shows significantly heavier tails than a Gaussian, and the amplitude of the internal noise is approximately proportional to stimulus speed and depends inversely on stimulus contrast. The framework is general and should prove applicable to other experiments and perceptual modalities.

Bayes Theorem↗
PubMed2004

Molecular phylogeny, historical biogeography, and divergence time estimates for swallowtail butterflies of the genus Papilio (Lepidoptera: Papilionidae).

Swallowtail butterflies are recognized as model organisms in ecology, evolutionary biology, genetics, and conservation biology but present numerous unresolved phylogenetic problems. We inferred phylogenetic relationships for 51 of about 205 species of the genus Papilio (sensu lato) from 3.3-Kilobase (kb) sequences of mitochondrial and nuclear DNA (2.3 kb of cytochrome oxidases I and II and 1.0 kb of elongation factor 1 alpha). Congruent phylogenetic trees were recovered within Papilio from analyses of combined data using maximum likelihood, Bayesian analysis, and maximum parsimony bootstrap consensus. Several disagreements with the traditional classification of Papilio were found. Five major previously hypothesized subdivisions within Papilio were well supported: Heraclides, Pterourus, Chilasa, Papilio (sensu stricto), and Eleppone. Further studies are required to clarify relationships within traditional "Princeps," which was paraphyletic. Several biologically interesting characteristics of Papilio appear to have polyphyletic origins, including mimetic adults, larval host associations, and larval morphology. Early diversification within Papilio is estimated at 55-65 million years ago based on a combination of biogeographic time constraints rather than fossils. This divergence time suggests that Papilio has slower apparent substitution rates than do Drosophila and fig-pollinating wasps and/or divergences corrected using best-fit substitution models are still being consistently underestimated. The amount of sequence divergence between Papilio subdivisions is equivalent to divergences between genera in other tribes of the Papilionidae, and between genera of moths of the noctuid subfamily Heliothinae.

Animals↗
PubMed2006

Molecular evolution and functionally important structures of molluscan Dermatopontin: implications for the origins of molluscan shell matrix proteins.

A major shell matrix protein originally obtained from a freshwater snail is a molluscan homologue of Dermatopontins, a group of Metazoan proteins also called TRAMP (tyrosine-rich acidic matrix protein). We sequenced and identified 14 molluscan homologues of Dermatopontin from eight snail species belonging to the order Basommatophora and Stylommatophora. The bassommatophoran Dermatopontins fell into three types, one is suggested to be a shell matrix protein and the others are proteins having more general functions based on gene expression analyses. N-glycosylation is inferred to be important for the function involved in shell calcification, because potential N-glycosylation sites were found exclusively in the Dermatopontins considered as shell matrix proteins. The stylommatophoran Dermatopontins fell into two types, also suggested to comprise a shell matrix protein and a protein having a more general function. Phylogenetic analyses using maximum likelihood and Bayesian methods revealed that gene duplication events occurred independently in both basommatophoran and stylommatophoran lineages. These results suggest that the dermatopontin genes were co-opted for molluscan calcification at least twice independently after the divergence of basommatophoran and stylommatophoran lineages, or more recently than we have expected.

Amino Acid Sequence↗