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PubMed2005

Evidence from small-subunit ribosomal RNA sequences for a fungal origin of Microsporidia.

The phylum Microsporidia comprises a species-rich group of minute, single-celled, and intra-cellular parasites. Lacking normal mitochondria and with unique cytology, microsporidians have sometimes been thought to be a lineage of ancient eukaryotes. Although phylogenetic analyses using small-subunit ribosomal RNA (SSU-rRNA) genes almost invariably place the Microsporidia among the earliest branches on the eukaryotic tree, many other molecules suggest instead a relationship with fungi. Using maximum likelihood methods and a diverse SSU-rRNA data set, we have re-evaluated the phylogenetic affiliations of Microsporidia. We demonstrate that tree topologies used to estimate likelihood model parameters can materially affect phylogenetic searches. We present a procedure for reducing this bias: "tree-based site partitioning," in which a comprehensive set of alternative topologies is used to estimate sequence data partitions based on inferred evolutionary rates. This hypothesis-driven approach appears to be capable of utilizing phylogenetic information that is not available to standard likelihood implementations (e.g., approximation to a gamma distribution); we have employed it in maximum likelihood and Bayesian analysis. Applying our method to a phylogenetically diverse SSU-rRNA data set revealed that the early diverging ("deep") placement of Microsporidia typically found in SSU-rRNA trees is no better than a fungal placement, and that the likeliest placement of Microsporidia among non-long-branch eukaryotic taxa is actually within fungi. These results illustrate the importance of hypothesis testing in parameter estimation, provide a way to address certain problems in difficult data sets, and support a fungal origin for the Microsporidia.

Animals↗

PubMed2005

Comparing alignment methods for inferring the history of the new world lizard genus Mabuya (Squamata: Scincidae).

The rapid increase in the ability to generate molecular data, and the focus on model-based methods for tree reconstruction have greatly advanced the use of phylogenetics in many fields. The recent flurry of new analytical techniques has focused almost solely on tree reconstruction, whereas alignment issues have received far less attention. In this paper, we use a diverse sampling of gene regions from lizards of the genus Mabuya to compare the impact, on phylogeny estimation, of new maximum likelihood alignment algorithms with more widely used methods. Sequences aligned under different optimality criteria are analyzed using partitioned Bayesian analysis with independent models and parameter settings for each gene region, and the most strongly supported phylogenetic hypothesis is then used to test the hypothesis of two colonizations of the New World by African scincid lizards. Our results show that the consistent use of model-based methods in both alignment and tree reconstruction leads to trees with more optimal likelihood scores than the use of independent criteria in alignment and tree reconstruction. We corroborate and extend earlier evidence for two independent colonizations of South America by scincid lizards. Relationships within South American Mabuya are found to be in need of taxonomic revision, specifically complexes under the names M. heathi, M. agilis, and M. bistriata (sensu, M.T. Rodrigues, Papeis Avulsos de Zoologia 41 (2000) 313).

Animals↗

PubMed2006

Phylogenetic relationships and convergence of helicosporous fungi inferred from ribosomal DNA sequences.

Helicosporous fungi form elegant, coiled, and multicellular mitotic spores (conidia). In this paper, we investigate the phylogenetic relationships among helicosporous fungi in the asexual genera Helicoma, Helicomyces, Helicosporium, Helicodendron, Helicoon, and in the sexual genus Tubeufia (Tubeufiaceae, Dothideomycetes, and Ascomycota). We generated ribosomal small subunit and partial large subunit sequences from 39 fungal cultures. These and related sequences from GenBank were analyzed using parsimony, likelihood, and Bayesian analysis. Results showed that helicosporous species arose convergently from six lineages of fungi in the Ascomycota. The Tubeufiaceae s. str. formed a strongly supported monophyletic lineage comprising most species from Helicoma, Helicomyces, and Helicosporium. However, within the Tubeufiaceae, none of the asexual genera were monophyletic. Traditional generic characters, such as whether conidiophores were conspicuous or reduced, the thickness of the conidial filament, and whether or not conidia were hygroscopic, were more useful for species delimitation than for predicting higher level relationships. In spite of their distinctive, barrel-shaped spores, Helicoon species were polyphyletic and had evolved in different ascomycete orders. Helicodendron appeared to be polyphyletic although most representatives occurred within Leotiomycetes. We speculate that some of the convergent spore forms may represent adaptation to dispersal in aquatic environments.

DNA, Ribosomal↗

PubMed2006

Basal relationships in the Drosophila melanogaster species group.

The Drosophila melanogaster species group is a popular model for evolutionary studies due to its morphological and ecological diversity and its inclusion of the model species D. melanogaster. However, phylogenetic relationships among major lineages within this species group remain controversial. In this report, the phylogeny of 10 species representing each of the well-supported monophyletic clades in the melanogaster group was studied using the sequences of 14 loci that together comprise 9493 nucleotide positions. Combined Bayesian analysis using gene-specific substitution models produced a 100% credible set of two trees. In the strict consensus of these trees, the ananassae subgroup branches first in the melanogaster species group, followed by the montium subgroup. The remaining lineages form a monophyletic clade in which D. ficusphila and D. elegans branch first, followed by D. biarmipes, D. eugracilis, and the melanogaster subgroup. This strongly supported phylogeny resolves most basal relationships in the melanogaster species group, and provides a framework that can be extended in the future to encompass more species.

Animals↗

PubMed2006

Round and pointed-head grenadier fishes (Actinopterygii: Gadiformes) represent a single sister group: evidence from the complete mitochondrial genome sequences.

The gene order of mitochondrial genomes (mitogenomes) has been employed as a useful phylogenetic marker in various metazoan animals, because it may represent uniquely derived characters shared by members of monophyletic groups. During the course of molecular phylogenetic studies of the order Gadiformes (cods and their relatives) based on whole mitogenome sequences, we found that two deep-sea grenadiers (Squalogadus modificatus and Trachyrincus murrayi: family Macrouridae) revealed a unusually identical gene order (translocation of the tRNA(Leu (UUR))). Both are members of the same family, although their external morphologies differed so greatly (e.g., round vs. pointed head) that they have been placed in different subfamilies Macrouroidinae and Trachyrincinae, respectively. Additionally, we determined the whole mitogenome sequences of two other species, Bathygadus antrodes and Ventrifossa garmani, representing a total of four subfamilies currently recognized within Macrouridae. The latter two species also exhibited gene rearrangements, resulting in a total of three different patterns of unique gene order being observed in the four subfamilies. Partitioned Bayesian analysis was conducted using available whole mitogenome sequences from five macrourids plus five outgroups. The resultant trees clearly indicated that S. modificatus and T. murrayi formed a monophyletic group, having a sister relationship to other macrourids. Thus, monophyly of the two species with disparate head morphologies was corroborated by two different lines of evidence (nucleotide sequences and gene order). The overall topology of the present tree differed from any of the previously proposed, morphology-based phylogenetic hypotheses.

Animals↗

PubMed2006

A molecular phylogeny of tortoises (Testudines: Testudinidae) based on mitochondrial and nuclear genes.

Although tortoises of the family Testudinidae represent a familiar and widely distributed group of turtles, their phylogenetic relationships have remained contentious. In this study, we included 32 testudinid species (all genera and subgenera, and all species of Geochelone, representing 65% of the total familial species diversity), and both mitochondrial (12S rRNA, 16S rRNA, and cytb) and nuclear (Cmos and Rag2) DNA data with a total of 3387 aligned characters. Using diverse phylogenetic methods (Maximum Parsimony, Maximum Likelihood, and Bayesian Analysis) congruent support is found for a well-resolved phylogeny. The most basal testudinid lineage includes a novel sister relationship between Asian Manouria and North American Gopherus. In addition, this phylogeny supports two other major testudinid clades: Indotestudo+Malacochersus+Testudo; and a diverse clade including Pyxis, Aldabrachelys, Homopus, Chersina, Psammobates, Kinixys, and Geochelone. However, we find Geochelone rampantly polyphyletic, with species distributed in at least four independent clades. Biogeographic analysis based on this phylogeny is consistent with an Asian origin for the family (as supported by the fossil record), but rejects the long-standing hypothesis of South American tortoises originating in North America. By contrast, and of special significance, our results support Africa as the ancestral continental area for all testudinids except Manouria and Gopherus. Based on our systematic findings, we also propose modifications concerning Testudinidae taxonomy.

Animals↗

PubMed2006

Dissecting the ancient rapid radiation of microgastrine wasp genera using additional nuclear genes.

Previous estimates of a generic level phylogeny for the ubiquitous parasitoid wasp subfamily Microgastrinae (Hymenoptera) have been problematic due to short internal branches deep in the phylogeny. These short branches might be attributed to a rapid radiation among the taxa, the use of genes that are unsuitable for the levels of divergence being examined, or insufficient quantity of data. We added over 1200 nucleotides from four nuclear genes to a dataset derived from three genes to produce a dataset of over 3000 nucleotides per taxon. While the number of well-supported short branches in the phylogeny increased, we still did not obtain strong bootstrap support for every node. Parametric and nonparametric bootstrap simulations projected that an enormous, and likely unobtainable, amount of data would be required to get bootstrap support greater than 50% for every node. However, a marked increase in the number of well-supported nodes was seen when we conducted a Bayesian analysis of a combined dataset generated from morphological characters added to the seven gene dataset. Our results suggest that, in some cases, combining morphological and genetic characters may be the most practical way to increase support for short branches deep in a phylogeny.

Animals↗

PubMed2006

Molecular evidence for the monophyly of East Asian groups of Cyprinidae (Teleostei: Cypriniformes) derived from the nuclear recombination activating gene 2 sequences.

The family Cyprinidae is one of the largest families of fishes in the world and a well-known component of the East Asian freshwater fish fauna. However, the phylogenetic relationships among cyprinids are still poorly understood despite much effort paid on the cyprinid molecular phylogenetics. Original nucleotide sequence data of the nuclear recombination activating gene 2 were collected from 109 cyprinid species and four non-cyprinid cypriniform outgroup taxa and used to infer the cyprinid phylogenetic relationships and to estimate node divergence times. Phylogenetic reconstructions using maximum parsimony, maximum likelihood, and Bayesian analysis retrieved the same clades, only branching order within these clades varied slightly between trees. Although the morphological diversity is remarkable, the endemic cyprinid taxa in East Asia emerged as a monophyletic clade referred to as Xenocypridini. The monophyly for the subfamilies including Cyprininae and Leuciscinae, as well as the tribes including Labeonini, Gobionini, Acheilognathini, and Leuciscini, was also well resolved with high nodal support. Analysis of the RAG2 gene supported the following cyprinid molecular phylogeny: the Danioninae is the most basal subfamily within the family Cyprinidae and the Cyprininae is the sister group of the Leuciscinae. The divergence times were estimated for the nodes corresponding to the principal clades within the Cyprinidae. The family Cyprinidae appears to have originated in the mid-Eocene in Asia, with the cladogenic event of the key basal group Danioninae occurring in the early Oligocene (about 31-30 MYA), and the origins of the two subfamilies, Cyprininae and Leuciscinae, occurring in the mid-Oligocene (around 26 MYA).

Animals↗

PubMed2006

Lineage divergence of a freshwater snail clade associated with post-Tethys marine basin development.

The complex evolutionary history of the Eurasian gastropod lineage Theodoxus reflects the evolution of marine basins following the breakup of the Tethys Sea. Today, this clade inhabits the lakes, rivers, streams, and estuaries of Europe, southwestern Asia, and North Africa. Here we present the first phylogenetic hypothesis for this clade. Based upon extensive geographic and taxonomic sampling, portions of the mitochondrial genes for cytochrome c oxidase subunit I and 16S rRNA were sequenced and analysed using maximum likelihood and maximum parsimony methods. Results from bootstrap analyses, Bayesian analysis, and sensitivity analyses lend support to six deep phylogenetic subdivisions within Theodoxus. These major clades are geographically associated with the major post-Tethyan marine basins. Estimates of divergence times using a penalized likelihood approach indicate that divergence of these major lineages occurred during the Miocene, simultaneous with the breakup of the Mediterranean and Paratethys Seas. The resulting major subclades later diversified during the Pliocene, primarily within geographic regions associated with the eastern and western Mediterranean Sea, the Pannonian Basin, and the Black Sea, thus producing the extant species assemblages. Finally, these phylogenetic results imply that much of the current taxonomy is flawed, therefore we offer recommendations for revising the classification of Theodoxus species based on phylogenetic systematics.

Animals↗

PubMed2006

Molecular and morphological incongruence in European species of Isothecium (Bryophyta).

During the identification of Moroccan samples a plant belonging to Isothecium with characteristics of I. alopecuroides (Dubois) Isov. and, to a smaller degree, I. algarvicum W.E. Nicholson and Dixon was found. Problems with attributing the plant to any of the European Isothecium species and the known large morphological variation in I. alopecuroides suggested that molecular studies were needed to evaluate patterns of relationships in this complex. We investigated one nuclear and one chloroplast marker from 66 samples (gametophytes) of Isothecium alopecuroides and from 18 samples of other Isothecium species. Parsimony and likelihood (via Bayesian analysis) were used as optimality criteria to compute phylogenetic trees. Bootstrapping and posterior probabilities were used, not only to quantify support, but also to evaluate competing phylogenetic alternatives in consensus networks. Finally, split decomposition and neighbour net analysis were used to compute distance based split networks, in order to avoid systematic error. The observed discrepancy among morphological and molecular data suggests that none of the European species Isothecium alopecuroides, I. holtii and I. myosuroides are monophyletic as defined by traditional morphological characters. Convergent morphological evolution cannot explain the discrepancy in this particular case; instead exchange of genetic material among Isothecium species is considered a potential explanation for the molecular diversity within morphospecies.

Base Sequence↗

PubMed2006

Molecular phylogenetics of Caenogastropoda (Gastropoda: Mollusca).

Caenogastropoda is the dominant group of marine gastropods in terms of species numbers, diversity of habit and habitat and ecological importance. This paper reports the first comprehensive multi-gene phylogenetic study of the group. Data were collected from up to six genes comprising parts of 18S rRNA, 28S rRNA (five segments), 12S rRNA, cytochrome c oxidase subunit I, histone H3 and elongation factor 1alpha. The alignment has a combined length of 3995 base positions for 36 taxa, comprising 29 Caenogastropoda representing all of its major lineages and seven outgroups. Maximum parsimony, maximum likelihood and Bayesian analyses were conducted. The results generally support monophyly of Caenogastropoda and Hypsogastropoda (Caenogastropoda excepting Architaenioglossa, Cerithioidea and Campanilioidea). Within Hypsogastropoda, maximum likelihood and Bayesian analyses identified a near basal clade of nine or 10 families lacking an anterior inhalant siphon, and Cerithiopsidae s.l. (representing Triphoroidea), where the siphon is probably derived independently from other Hypsogastropoda. The asiphonate family Eatoniellidae was usually included in the clade but was removed in one Bayesian analysis. Of the two other studied families lacking a siphon, the limpet-shaped Calyptraeidae was associated with this group in some analyses, but the tent-shaped Xenophoridae was generally associated with the siphonate Strombidae. The other studied hypsogastropods with an anterior inhalant siphon include nine families, six of which are Neogastropoda, the only traditional caenogastropod group above the superfamily-level with strong morphological support. The hypotheses that Neogastropoda are monophyletic and that the group occupies a derived position within Hypsogastropoda are both contradicted, but weakly, by the molecular analyses. Despite the addition of large amounts of new molecular data, many caenogastropod lineages remain poorly resolved or unresolved in the present analyses, possibly due to a rapid radiation of the Hypsogastropoda following the Permian-Triassic extinction during the early Mesozoic.

Animals↗

PubMed1998

Predicting the future and reconstructing the past: a Bayesian characterization of the utility of subjective fluency.

The subjective sense of fluency with which an item can be perceived or remembered is proposed to be a vital cue in making decisions about the future memorability and the nature of our past experience with that stimulus. We first outline a number of cases in which such perceptual or retrieval fluency influences judgments both about our own future performance and our likely past experience, and then present a Bayesian analysis of how judgments of recognition--deciding whether or not a currently viewed item was studied at a particular point in the past--may incorporate information about the perceptual fluency of that item. Using a simple mathematical model, we then provide an interpretation of certain enigmatic phenomena in recognition memory.

Bayes Theorem↗

PubMed1997

Coronary artery bypass risk prediction using neural networks.

BACKGROUND: Neural networks are nonparametric, robust, pattern recognition techniques that can be used to model complex relationships. METHODS: The applicability of multilayer perceptron neural networks (MLP) to coronary artery bypass grafting risk prediction was assessed using The Society of Thoracic Surgeons database of 80,606 patients who underwent coronary artery bypass grafting in 1993. The results of traditional logistic regression and Bayesian analysis were compared with single-layer (no hidden layer), two-layer (one hidden layer), and three-layer (two hidden layer) MLP neural networks. These networks were trained using stochastic gradient descent with early stopping. All prediction models used the same variables and were evaluated by training on 40,480 patients and cross-validation testing on a separate group of 40,126 patients. Techniques were also developed to calculate effective odds ratios for MLP networks and to generate confidence intervals for MLP risk predictions using an auxiliary "confidence MLP." RESULTS: Receiver operating characteristic curve areas for predicting mortality were approximately 76% for all classifiers, including neural networks. Calibration (accuracy of posterior probability prediction) was slightly better with a two-member committee classifier that averaged the outputs of a MLP network and a logistic regression model. Unlike the individual methods, the committee classifier did not overestimate or underestimate risk for high-risk patients. CONCLUSIONS: A committee classifier combining the best neural network and logistic regression provided the best model calibration, but the receiver operating characteristic curve area was only 76% irrespective of which predictive model was used.

Bayes Theorem↗

PubMed1998

Site-specific thermodynamics and kinetics of a coiled-coil transition by spin inversion transfer NMR.

A 33-residue pseudo-wild-type GCN4 leucine zipper peptide is used to probe the equilibrium conformational population in proteins. 13Calpha-NMR shows that chain sites differ in structural content at a given temperature, and that two dimeric folded forms are evident at many sites. Spin inversion transfer experiments are reported bearing on the thermodynamics and kinetics of interconversion of the two dimeric folded forms (Fa <--> Fb) at the 13Calpha-labeled position L13. At each temperature, at conditions wherein the population of unfolded chains is quite small, inversion of the Fa spins via a tuned Gaussian pi-pulse is followed by a time interval (tau), interrogation, and recording of the free induction decay. Fifteen such inversions, with varying tau, provide the time course for recovery of equilibrium magnetization after inversion. Similar experiments follow inversion of the Fb spins. Re-equilibration is known to be modulated by four first-order rate constants: two (T1a(-1) and T1b(-1)) for spin-lattice relaxation intrinsic to the respective sites, and two (kab and kba) for the conformational change. All four follow from joint, Bayesian analysis of all the data at each temperature. The equilibrium constant at each temperature for this local transition, determined simply from the equilibrium relative magnetizations at Fa and Fb sites, agrees well with the kinetic ratio kab/kba. The standard Gibbs energies, enthalpy, and entropy follow. Activation parameters, both ways, are accessible from the rate constants and suggest a transition state with high Gibbs energy and enthalpy, but with entropy between those of Fa and Fb.

Amino Acid Sequence↗

PubMed1999

Thermodynamics and kinetics of a folded-folded' transition at valine-9 of a GCN4-like leucine zipper.

Spin inversion transfer (SIT) NMR experiments are reported probing the thermodynamics and kinetics of interconversion of two folded forms of a GCN4-like leucine zipper near room temperature. The peptide is 13Calpha-labeled at position V9(a) and results are compared with prior findings for position L13(e). The SIT data are interpreted via a Bayesian analysis, yielding local values of T1a, T1b, kab, kba, and Keq as functions of temperature for the transition FaV9 right arrow over left arrow FbV9 between locally folded dimeric forms. Equilibrium constants, determined from relative spin counts at spin equilibrium, agree well with the ratios kab/kba from the dynamic SIT experiments. Thermodynamic and kinetic parameters are similar for V9(a) and L13(e), but not the same, confirming that the molecular conformational population is not two-state. The energetic parameters determined for both sites are examined, yielding conclusions that apply to both and are robust to uncertainties in the preexponential factor (kT/h) of the Eyring equation. These conclusions are 1) the activation free energy is substantial, requiring a sparsely populated transition state; 2) the transition state's enthalpy far exceeds that of either Fa or Fb; 3) the transition state's entropy far exceeds that of Fa, but is comparable to that of Fb; 4) "Arrhenius kinetics" characterize the temperature dependence of both kab and kba, indicating that the temperatures of slow interconversion are not below that of the glass transition. Any postulated free energy surface for these coiled coils must satisfy these constraints.

Amino Acid Sequence↗

PubMed1997

Genetic polymorphism of the CYP2C subfamily and its effect on the pharmacokinetics of phenytoin in Japanese patients with epilepsy.

OBJECTIVE: To examine the genetic polymorphism of CYP2C9 and CYP2C19 and its effect on the pharmacokinetics of phenytoin among 44 Japanese patients with epilepsy. METHODS: Polymerase chain reaction tests with leukocyte deoxyribonucleic acid were used to detect the mutations for the amino acid substitution (Arg144-->Cys and Ile359-->Leu) in CgammaP2C9 and for the defective allele (m1 and m2) in CgammaP2C19. The pharmacokinetic parameters of phenytoin in individual patients were estimated by means of empirical bayesian analysis, in which the prior information was the population parameters for Japanese patients with epilepsy. RESULTS: Of the 44 patients, none had the CgammaP2C9 mutation for the Cys144 allele, whereas six patients were heterozygous for the wild-type (wt) and Leu359 allele (wt/Leu359) in cgammaP2C9. The maximal elimination rate (Vmax) of phenytoin among patients with heterozygous wt/Leu359 in CgammaP2C9 was 33% lower than that among patients with normal CgammaP2C9. A total of 21 patients were heterozygous for the CgammaP2C19 mutation (wt/m1 or wt/m2), and five patients had the homozygous or heterozygous mutations in CgammaP2C19 (m1/m1 or m1/m2). The Vmax values of phenytoin were slightly decreased (up to 14%) among patients with CgammaP2C19 mutations compared with patients with normal CgammaP2C19. CONCLUSION: The findings indicated that the genetic polymorphisms of CYP2C isozymes play an important role in the pharmacokinetic variability of phenytoin and that the mutation in CYP2C9 proteins (Ile359-->Leu) is a determinant of impaired metabolism of the drug among Japanese persons.

Adolescent↗

PubMed2003

Eutrophication risk assessment in coastal embayments using simple statistical models.

A statistical methodology is proposed for assessing the risk of eutrophication in marine coastal embayments. The procedure followed was the development of regression models relating the levels of chlorophyll a (Chl) with the concentration of the limiting nutrient--usually nitrogen--and the renewal rate of the systems. The method was applied in the Gulf of Gera, Island of Lesvos, Aegean Sea and a surrogate for renewal rate was created using the Canberra metric as a measure of the resemblance between the Gulf and the oligotrophic waters of the open sea in terms of their physical, chemical and biological properties. The Chl-total dissolved nitrogen-renewal rate regression model was the most significant, accounting for 60% of the variation observed in Chl. Predicted distributions of Chl for various combinations of the independent variables, based on Bayesian analysis of the models, enabled comparison of the outcomes of specific scenarios of interest as well as further analysis of the system dynamics. The present statistical approach can be used as a methodological tool for testing the resilience of coastal ecosystems under alternative managerial schemes and levels of exogenous nutrient loading.

Bayes Theorem↗

PubMed2003

Mixture models and the probabilistic structure of depth cues.

Monocular cues to depth derive their informativeness from a combination of perspective projection and prior constraints on the way scenes in the world are structured. For many cues, the appropriate priors are best described as mixture models, each of which characterizes a different category of objects, surfaces, or scenes. This paper provides a Bayesian analysis of the resulting model selection problem, showing how the mixed structure of priors creates the potential for non-linear, cooperative interactions between cues and how the information provided by a single cue can effectively determine the appropriate constraint to apply to a given image. The analysis also leads to a number of psychophysically testable predictions. We test these predictions by applying the framework to the problem of perceiving planar surface orientation from texture. A number of psychophysical experiments are described that show that the visual system is biased to interpret textures as isotropic, but that when sufficient image data is available, the system effectively turns off the isotropy constraint and interprets texture information using only a homogeneity assumption. Human performance is qualitatively similar to an optimal estimator that assumes a mixed prior on surface textures--some proportion being isotropic and homogeneous and some proportion being anisotropic and homogeneous.

Adult↗