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Results for “Bayesian inference”

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At least 307 records · Page 17Linked to original sources
PubMed2004

Germination and growth from spores: variability and uncertainty in the assessment of food borne hazards.

We have developed a model for the variability of spore lag times and shown that variability has an important role in the quantitative assessment of risks associated with spore forming bacteria in food. The model includes two sequential independent delay times that contribute to the lag time for a single spore. We have shown that a population of variable spores also has a variable lag time, and we have emphasised the significance of this variability in quantitative representations of population dynamics for small populations. We have made a Bayesian estimate for the extent of the variability in spore lag times and made a comparison with direct microscopic observations of individual spores of nonproteolytic Clostridium botulinum. We conclude that Bayesian inference is a practical method for quantifying variability and hence a significant element in the development of quantitative risk assessments for hazards associated with spore forming bacteria.

Bacteria↗
PubMed2004

Phylogeny and paraphyly among tetrapod blood flukes (Digenea: Schistosomatidae and Spirorchiidae).

The blood flukes of turtles (Digenea: Spirorchiidae) and the blood flukes of crocodilians, birds and mammals (Digenea: Schistosomatidae) have long been considered as closely related, but distinct evolutionary lineages. Recent morphological and molecular studies have considered these families as sister taxa within the Schistosomatoidea. Representatives of both families have similar furcocercous cercariae and similar two-host life cycles, but have different definitive hosts, distinct reproductive patterns and different morphologies. Sequences including approximately 1800 bases of the small subunit ribosomal DNA and 1200 bases of the large subunit ribosomal DNA were generated from representatives of eight spirorchiid genera. These sequences were aligned with pre-existing sequences of Schistosomatidae and other representatives of the Diplostomida and analysed for phylogenetic signal using maximum parsimony and Bayesian inference. These analyses revealed that the Spirorchiidae is paraphyletic and that the turtle blood flukes are basal to the highly derived schistosomatids. Three genera of spirorchiids from marine turtles form a sister group to the Schistosomatidae and five genera of spirorchiids from freshwater turtles occupy basal positions in the phylogeny of tetrapod blood flukes. Marine turtles are considered to be derived from freshwater turtles and the results of the current study indicate that the spirorchiid parasites of marine turtles are similarly derived from a freshwater ancestor. The close relationship of the marine spirorchiids to schistosomatids and the basal position of the marine transmitted Austrobilharzia and Ornithobilharzia in the schistosomatid clade suggests that schistosomatids arose after a marine turtle blood fluke ancestor successfully colonised birds.

Alligators and Crocodiles↗
PubMed2006

The phylogeny of Myxosporea (Myxozoa) based on small subunit ribosomal RNA gene analysis.

The phylogeny of the Myxosporea was studied using the small-subunit ribosomal RNA gene sequences. Maximum parsimony and Bayesian inference were used to determine myxosporean phylogenetic relationships. The analysis included 120 myxosporean sequences retrieved from GenBank and 21 newly obtained sequences of myxosporeans representing nine genera. Members of the genera Palliatus and Auerbachia were sequenced for the first time. The phylogenetic analysis supported a split of myxosporeans into two main lineages separating most of freshwater species from marine ones as described by previous authors. In addition to the two main lineages, a third lineage consisting of three species was found (Sphaerospora truttae, Sphaerospora elegans and Leptotheca ranae) and additional exceptions to the marine/freshwater myxosporean split were recognised (Sphaeromyxa hellandi, Sphaeromyxa longa and Myxidium coryphaenoideum). All three myxosporean lineages were characterised by specific lengths of SSU rDNA sequences. The lineage of marine myxosporeans split into five well-defined clades. They consisted of species with a similar site of infection and spore morphology and were referred as the Parvicapsula clade, the Enteromyxum clade, the Ceratomyxa clade, the marine Myxidium clade and the Kudoa clade, respectively. The inner topology of the freshwater clade was more complex but the trend to branch according to site of infection was observed in this clade as well. Due to the number of sequences available, a histozoic (Myxobolus clade) predominated. Interestingly, five morphologically different species infecting urinary bladder clustered within the histozoic (Myxobolus) clade. The phylogenetic trees derived from this study differ in a number of respects from the current taxonomy of the myxosporeans, which suggests that several currently utilised characters may be homoplasious or that reliance on a single gene tree may not adequately reflect the phylogeny of the group.

Animals↗
PubMed2005

Bayesian estimation of Karplus parameters and torsion angles from three-bond scalar couplings constants.

We apply Bayesian inference to analyze three-bond scalar coupling constants in an objective and consistent way. The Karplus curve and a Gaussian error law are used to model scalar coupling measurements. By applying Bayes' theorem, we obtain a probability distribution for all unknowns, i.e., the torsion angles, the Karplus parameters, and the standard deviation of the Gaussian. We infer all these unknowns from scalar coupling data using Markov chain Monte Carlo sampling and analytically derive a probability distribution that only involves the torsion angles.

Algorithms↗
PubMed2006

Trial-by-trial estimation of amplitude and latency variability in neuronal spike trains.

The rate function underlying single-trial spike trains can vary from trial to trial. We propose to estimate the amplitude and latency variability in single-trial neuronal spike trains on a trial-by-trial basis. The firing rate over a trial is modeled by a family of rate profiles with trial-invariant waveform and trial-dependent amplitude scaling factors and latency shifts. Using a Bayesian inference framework we derive an iterative fixed-point algorithm from which the single-trial amplitude scaling factors and latency shifts are estimated. We test the performance of the algorithm on simulated data and then apply it to actual neuronal recordings from the sensorimotor cortex of the monkey.

Action Potentials↗
PubMed2006

Multilocus sequence analysis of Fusarium pseudograminearum reveals a single phylogenetic species.

Fusarium pseudograminearum causes crown rot of wheat in Australia and most other wheat growing regions, but its evolutionary history is largely unknown. We demonstrate for the first time that F. pseudograminearum is a single phylogenetic species without consistent lineage development across genes. Isolates of F. pseudograminearum, F. graminearum sensu lato, and F. cerealis, were collected from four countries and four single copy, nuclear genes were partially sequenced, aligned with previously published sequences of these and related species, and analysed by maximum parsimony and Bayesian inference. Evolutionary divergence varied between genes, with high phylogenetic incongruence occurring between the gene genealogies. The absence of geographic differentiation between isolates indicates that the introduction of new fungal strains to a region has the potential to introduce new pathogenic and toxigenic genes into the native population through sexual recombination.

Base Sequence↗
PubMed2004

Bayesian representation learning in the cortex regulated by acetylcholine.

A brain needs to detect an environmental change and to quickly learn internal representations necessary in a new environment. This paper presents a theoretical model of cortical representation learning that can adapt to dynamic environments, incorporating the results by previous studies on the functional role of acetylcholine (ACh). We adopt the probabilistic principal component analysis (PPCA) as a functional model of cortical representation learning, and present an on-line learning method for PPCA according to Bayesian inference, including a heuristic criterion for model selection. Our approach is examined in two types of simulations with synthesized and realistic data sets, in which our model is able to re-learn new representation bases after the environment changes. Our model implies the possibility that a higher-level recognition regulates the cortical ACh release in the lower-level, and that the ACh level alters the learning dynamics of a local circuit in order to continuously acquire appropriate representations in a dynamic environment.

Acetylcholine↗
PubMedDate not supplied

A comparative investigation on subspace dimension determination.

It is well-known that constrained Hebbian self-organization on multiple linear neural units leads to the same k-dimensional subspace spanned by the first k principal components. Not only the batch PCA algorithm has been widely applied in various fields since 1930s, but also a variety of adaptive algorithms have been proposed in the past two decades. However, most studies assume a known dimension k or determine it heuristically, though there exist a number of model selection criteria in the literature of statistics. Recently, criteria have also been obtained under the framework of Bayesian Ying-Yang (BYY) harmony learning. This paper further investigates the BYY criteria in comparison with existing typical criteria, including Akaike's information criterion (AIC), the consistent Akaike's information criterion (CAIC), the Bayesian inference criterion (BIC), and the cross-validation (CV) criterion. This comparative study is made via experiments not only on simulated data sets of different sample sizes, noise variances, data space dimensions, and subspace dimensions, but also on two real data sets from air pollution problem and sport track records, respectively. Experiments have shown that BIC outperforms AIC, CAIC, and CV while the BYY criteria are either comparable with or better than BIC. Therefore, BYY harmony learning is a more preferred tool for subspace dimension determination by further considering that the appropriate subspace dimension k can be automatically determined during implementing BYY harmony learning for the principal subspace while the selection of subspace dimension k by BIC, AIC, CAIC, and CV has to be made at the second stage based on a set of candidate subspaces with different dimensions which have to be obtained at the first stage of learning.

Air Pollution↗
PubMed2004

Seroprevalences for ovine enzootic abortion in Switzerland.

Our aim was to assess the seroprevalence of Chlamydophila (Cd) abortus (Chlamydia psittaci serotype 1), denoted ovine enzootic abortion (OEA), in the Swiss sheep population. A competitive enzyme-linked immunosorbent assay (cELISA) was adapted for the investigation of pooled serum samples (pool approach) and receiver-operator characteristic (ROC) analysis was applied to define the cut-off of the pool approach. At a cut-off value of 30% inhibition, the flock-level pooled sensitivity and specificity were 92.9% and 97.6% when compared to classifying the flock based on individual-animal samples. Subsequently, sera from 775 randomly selected flocks out of 11 cantons of Switzerland were investigated using the pool approach. The cantons included in the study represented 72% of the Swiss sheep flocks and 76% of Swiss sheep population. Antibodies against Cd. abortus were found in almost 19% (144) of the 775 examined sheep flocks. Test prevalences were adjusted for the imperfect test characteristics using the Rogan-Gladen estimator and Bayesian inference. Seroprevalence was highest (43%) in the canton Graubunden. In the remaining 10 cantons the seroprevalence ranged from 2 to 29%. The cELISA in combination with testing pooled sera and statistical methods for true prevalence estimation provided a good survey tool at lower costs and time when compared to other approaches.

Abortion, Veterinary↗
PubMed2006

Bayesian shadows of molecular mechanisms cast in the light of evolution.

A great many carefully designed experiments will be required to fully understand biological mechanisms in atomic detail. A complementary approach is to use powerful statistical procedures to rapidly test numerous scientific hypotheses using vast numbers of protein sequences--the cell's own blueprints for specifying biological mechanisms. Bayesian inference of the evolutionary constraints imposed on functionally divergent proteins can reveal key components of the molecular machinery and thereby suggest likely mechanisms to test experimentally. This approach is demonstrated by considering how DNA polymerase clamp-loader AAA+ ATPases couple DNA recognition to ATP hydrolysis and clamp loading.

Adenosine Triphosphatases↗
PubMed2006

Genetic distance of SARS coronavirus from the recent natural case.

Phylogenetic analysis of SARS coronavirus isolates based on the spike gene and protein sequence using Neighbor-Joining, maximum likelihood and Bayesian inference methods indicated that a recent human SARS-CoV isolate was closer to some human SARS-CoV isolates from earlier epidemic phase than to the SARS-CoV-like viruses isolated from wild animals during previous epidemic phase. A reasonable judgment based on phylogenetic relationship and sequence variations it is likely that the recent human SARS-CoV isolate is closer to an unknown SARS-CoV predecessor.

Amino Acid Sequence↗
PubMed2004

Phylogeny of elasmobranchs based on LSU and SSU ribosomal RNA genes.

The dominant view of the phylogeny of living elasmobranchs, based on morphological characters, is that batoids (skates and rays) are derived sharks, joined with saw sharks, and angel sharks in the clade Hypnosqualea [S. Shirai, Squalean Phylogeny: A New Framework of 'Squaloid' Sharks and Related Taxa, Hokkaido University Press, Sapporo, 1992]. By contrast, a recent molecular-phylogenetic study based on mitochondrial genes for 12S and 16S rRNA and tRNA valine [C.J. Douady et al., Mol. Phylogenet. Evol., 26 (2003) 215-221] supported the older view that batoids and sharks are separate lineages. Here, we tested these two different views using combined, nuclear large-subunit and small-subunit rRNA gene sequences ( approximately 5.3kb) from 22 elasmobranchs, two chimeras, and two bony fishes. We used maximum likelihood, maximum parsimony, minimum evolution, and Bayesian inference for tree reconstruction, and found the large-subunit rRNA gene to contain far more signal than the small-subunit gene for resolving this mostly Mesozoic radiation. Our findings matched those of in separating batoids from sharks and in statistically rejecting Hypnosqualea. The angel shark (Squatina) was the sister group to squaliforms (dogfish sharks), and our findings are consistent with the idea that "orbitostylic" sharks form a monophyletic group (squaliforms+the hexanchiform Chlamydoselachus+Squatina+Pristiophorus). In the galeomorph sharks, however, lamniforms grouped with orectolobiforms, opposing the widely accepted 'lamniform+carcharhiniform' grouping. A tree based on the mitochondrial gene for cytochrome b also supported a separation of sharks and batoids, in contrast to Hypnosqualea. Among elasmobranchs, variation in the evolutionary rates of the nuclear rRNA genes was higher than that of cytochrome b genes, mainly due to the relatively rapid evolution of rRNA in some carcharhiniforms. In conclusion, several different molecular studies now refute the Hypnosqualea hypothesis of elasmobranch interrelationships.

Animals↗
PubMed2004

Phylogeny and evolution of basils and allies (Ocimeae, Labiatae) based on three plastid DNA regions.

A phylogeny of basils and allies (Lamiaceae, tribe Ocimeae) based on sequences of the trnL intron, trnL-trnF intergene spacer and rps 16 intron of the plastid genome is presented. Several methods were used to reconstruct phylogenies and to assess statistical support for clades: maximum parsimony with equally and successively weighted characters, bootstrap resampling, and Bayesian inference. The phylogeny is used to investigate the distribution of morphological, pericarp anatomy, chemical, and pollen characters as well as the geographical distribution of the clades. Tribe Ocimeae is monophyletic and easily diagnosable with morphological synapomorphies. There are monophyletic clades within Ocimeae that broadly correspond to currently recognised subtribes: Lavandulinae, Hyptidinae, Ociminae, and Plectranthinae. Only Lavandulinae has clear non-molecular synapomorphies. Several currently recognised genera are not monophyletic. Floral morphology consistent with sternotribic pollination is most common in Ocimeae, but there are independent departures from this model. Buzz pollination is likely in some species, the only postulated occurrence of this within Lamiaceae. Quinone diterpenoids and flavones in the leaf exudates differ in their distributions across the phylogeny and this could contribute to differences in the recorded medicinal as well as pesticidal uses of the species in the different clades. Mapping geographic distribution on to an ultrametric phylogenetic tree produced using non-parametric rate smoothing supports an Asiatic origin for Ocimeae. There are several secondary occurrences in Asia arising from the African Ociminae and Plectranthinae clades. Colonisation of Madagascar occurred at least five times, and New World colonisation occurred at least three times.

Bayes Theorem↗
PubMed2004

The phylogenetic history of Selaginellaceae based on DNA sequences from the plastid and nucleus: extreme substitution rates and rate heterogeneity.

Molecular phylogenetic research on Selaginellaceae has focused on the plastid gene rbcL, which in this family has unusually high substitution rates. Here we develop a molecular data set from the nuclear 26S ribosomal DNA gene with the aim of evaluating and extending the results of previous phylogenetic research. The 26S rDNA and the rbcL regions were sequenced for a sample of 23 species, which represent the main elements of species diversity in the family. The data were analysed independently and in combination using both maximum parsimony and Bayesian inference. Although several between genome differences were found, the general pattern of relationships uncovered by all analyses was very similar. Results corroborate the previous study supporting new groupings not previously recognised on morphological grounds. Substitution rates in the 26S rDNA were also found to be high (26% informative) for the region analysed, but lower than for rbcL (37% informative). These data indicate that high substitution rates might be widespread in all three genomes (i.e., plastid, mitochondrion, and nucleus).

Bayes Theorem↗
PubMed2004

Phylogeny and host-specificity of European seed beetles (Coleoptera, Bruchidae), new insights from molecular and ecological data.

We used partial sequences of three mitochondrial genes (12S rRNA, cytochrome b, and cytochrome c oxidase subunit I) to reconstruct the phylogeny of European seed beetles (Bruchidae) belonging to the genera Bruchus Linnaeus and Bruchidius Schilsky. Adult beetles examined in this study were obtained from larvae bred from seeds directly collected in the field. Parsimony, maximum likelihood, and Bayesian inference were used to infer phylogenetic relationships among species. Both genera, Bruchidius and Bruchus, formed monophyletic groups in all analyses. Our results were partially in discrepancy with existing taxonomic groups (Borowiec, 1987). Critical analysis of relationships among taxa, and exhaustive review of host-plants data highlight the very high level of specialization of these seed beetles. Phylogenetically related insects were associated with host-plants belonging to the same botanical tribes.

Animals↗
PubMed2004

Molecular phylogeny and character evolution in the Western Palaearctic Helicidae s.l. (Gastropoda: Stylommatophora).

In this study, we present a molecular phylogeny for the west Palaearctic Helicidae sensu lato based on sequence data from two mitochondrial (COI, 16S rDNA) and two nuclear (ITS-1, 18S rDNA) genes. Maximum likelihood analysis and Bayesian inference revealed well supported monophyletic clades partly conflicting traditional classifications. Based on these results, we propose the following system. The Western Palaearctic Helicidae s.l. consist of two families, Helicidae and Hygromiidae. Within the Helicidae, three well supported subfamilies can be recognised: the Helicinae, Ariantinae, and Helicodontinae. The Hygromiidae consist of three clades: the Hygromiinae, the Helicellinae, and a yet unnamed clade comprising the genera Sphincterochila and Cochlicella. We then used the phylogeny to study the evolution of anatomical, and ecological characters traditionally used for systematic classification. In the Helicidae s.l., two independent evolutionary transitions to life in xeric environments occurred, which allowed the occupation of new niches with a subsequent radiation of the Helicellinae-Cochlicella/Sphincterochila clade and the Helicinae. Whereas, the multiplication of the Glandulae mucosae is a synapomorphy of the Hygromiidae, the lovedart sac apparatus is present in all groups and thus, the trait cannot provide a synapomorphy for either families or subfamilies. Additionally, we evaluated the use of structural molecular genetic characters for taxonomic assessment. The presence of an unique loop region of the 16S rDNA gene and a short tandem repeat in the ITS-1 region provide independent evidence for the monophyly of these major two groups, and can be used for preliminary classification.

Animals↗
PubMed2004

Morphological convergence characterizes the evolution of Xanthophyceae (Heterokontophyta): evidence from nuclear SSU rDNA and plastidial rbcL genes.

Xanthophyceae are a group of heterokontophyte algae. Few molecular studies have investigated the evolutionary history and phylogenetic relationships of this class. We sequenced the nuclear-encoded SSU rDNA and chloroplast-encoded rbcL genes of several xanthophycean species from different orders, families, and genera. Neither SSU rDNA nor rbcL genes show intraspecific sequence variation and are good diagnostic markers for characterization of problematic species. New sequences, combined with those previously available, were used to create different multiple alignments. Analyses included sequences from 26 species of Xanthophyceae plus three Phaeothamniophyceae and two Phaeophyceae taxa used as outgroups. Phylogenetic analyses were performed according to Bayesian inference, maximum likelihood, and maximum parsimony methods. We explored effects produced on the phylogenetic outcomes by both taxon sampling as well as selected genes. Congruent results were obtained from analyses performed on single gene multiple alignments as well as on a data set including both SSU rDNA and rbcL sequences. Trees obtained in this study show that several currently recognized xanthophycean taxa do not form monophyletic groups. The order Mischococcales is paraphyletic, while Tribonematales and Botrydiales are polyphyletic even if evidence for the second order is not conclusive. Botrydiales and Vaucheriales, both including siphonous taxa, do not form a clade. The families Botrydiopsidaceae, Botryochloridaceae, and Pleurochloridaceae as well as the genera Botrydiopsis and Chlorellidium are polyphyletic. The Centritractaceae and the genus Bumilleriopsis also appear to be polyphyletic but their monophyly cannot be completely rejected with current evidence. Our results support morphological convergence at any taxonomic rank in the evolution of the Xanthophyceae. Finally, our phylogenetic analyses exclude an origin of the Xanthophyceae from a Vaucheria-like ancestor and favor a single early origin of the coccoid cell form.

Base Composition↗
PubMed2004

Phylogeny of caecilian amphibians (Gymnophiona) based on complete mitochondrial genomes and nuclear RAG1.

We determined the complete nucleotide sequence of the mitochondrial (mt) genome of five individual caecilians (Amphibia: Gymnophiona) representing five of the six recognized families: Rhinatrema bivittatum (Rhinatrematidae), Ichthyophis glutinosus (Ichthyophiidae), Uraeotyphlus cf. oxyurus (Uraeotyphlidae), Scolecomorphus vittatus (Scolecomorphidae), and Gegeneophis ramaswamii (Caeciliidae). The organization and size of these newly determined mitogenomes are similar to those previously reported for the caecilian Typhlonectes natans (Typhlonectidae), and for other vertebrates. Nucleotide sequences of the nuclear RAG1 gene were also determined for these six species of caecilians, and the salamander Mertensiella luschani atifi. RAG1 (both at the amino acid and nucleotide level) shows slower rates of evolution than almost all mt protein-coding genes (at the amino acid level). The new mt and nuclear sequences were compared with data for other amphibians and subjected to separate and combined phylogenetic analyses (Maximum Parsimony, Minimum Evolution, Maximum Likelihood, and Bayesian Inference). All analyses strongly support the monophyly of the three amphibian Orders. The Batrachia hypothesis (Gymnophiona, (Anura, Caudata) receives moderate or good support depending on the method of analysis. Within Gymnophiona, the optimal tree (Rhinatrema, (Ichthyophis, Uraeotyphlus), (Scolecomorphus, (Gegeneophis Typhlonectes) agrees with the most recent morphological and molecular studies. The sister group relationship between Rhinatrematidae and all other caecilians, that between Ichthyophiidae and Uraeotyphlidae, and the monophyly of the higher caecilians Scolecomorphidae+Caeciliidae+Typhlonectidae, are strongly supported, whereas the relationships among the higher caecilians are less unambiguously resolved. Analysis of RAG1 is affected by a spurious local rooting problem and associated low support that is ameliorated when outgroups are excluded. Comparisons of trees using the non-parametric Templeton, Kishino-Hasegawa, Approximately Unbiased, and Shimodaira-Hasegawa tests suggest that the latter may be too conservative.

Amphibians↗