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PubMed1993

The relationship between the number of loci and the statistical support for the topology of UPGMA trees obtained from genetic distance data.

An analysis of the relationship between the number of loci utilized in an electrophoretic study of genetic relationships and the statistical support for the topology of UPGMA trees is reported for two published data sets. These are Highton and Larson (Syst. Zool.28:579-599, 1979), an analysis of the relationships of 28 species of plethodonine salamanders, and Hedges (Syst. Zool., 35:1-21, 1986), a similar study of 30 taxa of Holarctic hylid frogs. As the number of loci increases, the statistical support for the topology at each node in UPGMA trees was determined by both the bootstrap and jackknife methods. The results show that the bootstrap and jackknife probabilities supporting the topology at some nodes of UPGMA trees increase as the number of loci utilized in a study is increased, as expected for nodes that have groupings that reflect phylogenetic relationships. The pattern of increase varies and is especially rapid in the case of groups with no close relatives. At nodes that likely do not represent correct phylogenetic relationships, the bootstrap probabilities do not increase and often decline with the addition of more loci.

Algorithms↗

PubMed2000

Molecular phylogenetic analysis of the Pneumoroidea (Orthoptera, Caelifera): molecular data resolve morphological character conflicts in the basal acridomorpha.

A key transition in the evolution of the insect suborder Caelifera (Orthoptera; Insecta) was from predominantly non-angiosperm-feeding basal lineages to the modern acridomorph fauna (grasshoppers and related insects). However, because of conflicts in the distribution of several complex morphological characters, the relationships of the presumed intermediates, and in particular of the superfamily Pneumoroidea, are presently unclear. We undertook a phylogenetic study of representatives of all of the transitional acridomorph families using mitochondrial and nuclear DNA sequences. No support for pneumoroid monophyly was obtained from nonparametric bootstrap analysis. Furthermore, adopting a maximum-likelihood approach, specific hypotheses of relationships within the Pneumoroidea were firmly rejected using parametric bootstrapping and Kishino-Hasegawa tests. The results indicate that the Pneumoroidea are at best a grade. This distinction implies that the evolution of the proposed pneumoroid synapomorphies, femoro-abdominal stridulation and simple male genital structure, might previously have been misinterpreted as cases of single character gains or losses within lineages. Reconstructions of character states for the femoro-abdominal stridulation indicate that, in fact, multiple losses or gains are equally likely. An important implication of our findings is that, in grasshoppers, auditory tympana may have evolved before stridulation, supporting the argument that the original function of tympana may have been related not to conspecific communication but to predator detection. Overall, the results of this study emphasize the high information content of these minor groups (in this case, the four intermediate families under consideration contain only 0.2% of extant orthopteran species diversity). Our analyses also demonstrate the advantages of model-based methods in analyzing systematic problems and, in particular, of the importance of testing specific phylogenetic hypotheses when a priori support for groupings (e.g., from nonparametric bootstrapping) is marginal.

Animals↗

PubMed2000

Resolution of phylogenetic relationships among recently evolved species as a function of amount of DNA sequence: an empirical study based on woodpeckers (Aves: Picidae).

Synonymous substitutions in the 13 mitochondrial encoded protein genes form a large pool of characters that should approach the ideal for phylogenetic analysis of being independently and identically distributed. Pooling sequences from multiple mitochondrial protein-coding genes should result in statistically more powerful estimates of relationships among species that diverged sufficiently recently that most nucleotide substitutions are synonymous. Cytochrome oxidase I (COI) was sequenced for woodpecker species for which cytochrome b (cyt b) sequences were available. A pairing-design test based on the normal distribution indicated that cyt b evolves more rapidly than COI when all nucleotides are compared but their rates are equal for synonymous substitutions. Nearly all of the phylogenetically informative substitutions among woodpeckers are synonymous. Statistical support for relationships, as measured by bootstrap proportions, increased as the number of nucleotides increased from 1047 (cyt b) to 1512 (COI) to 2559 nucleotides (aggregate data set). Pseudo-bootstrap replicates showed the same trend and increasing the amount of sequence beyond the actual length of 2559 nucleotides to 5120 (2x) resulted in stronger bootstrap support, even though the amount of phylogenetic information was the same. However, the amount of sequence required to resolve an internode depends on the length of the internode and its depth in the phylogeny.

Animals↗

PubMed2000

Ribosomal DNA and resolution of branching order among the ascomycota: how many nucleotides are enough?

Molecular phylogenies for the fungi in the Ascomycota rely heavily on 18S rRNA gene sequences but this gene alone does not answer all questions about relationships. Particularly problematical are the relationships among the first ascomycetes to diverge, the Archiascomycetes, and the branching order among the basal filamentous ascomycetes, the Euascomycetes. Would more data resolve branching order? We used the jackknife and bootstrapping resampling approach that constitutes the "pattern of resolved nodes" method to address the relationship between number of variable sites in a DNA sequence alignment and support for taxonomic clusters. We graphed the effect of increasing sizes of subsamples of the 18S rRNA gene sequences on bootstrap support for nodes in the Ascomycota tree. Nodes responded differently to increasing data. Some nodes, those uniting the filamentous ascomycetes for example, would still have been well supported with only two thirds of the 18S rRNA gene. Other nodes, like the one uniting the Archiascomycetes as a monophyletic group, would require about double the number of variable sites available in the 18S gene for 95% neighbor-joining bootstrap support. Of the several groups emerging at the base of the filamentous ascomycetes, the Pezizales receive the most support as the first to diverge. Our analysis suggests that we would also need almost three times as much sequence data as that provided by the 18S gene to confirm the basal position for the Pezizales and more than seven times as much data to resolve the next group to diverge. If more data from other genes show the same pattern, the lack of resolution for the filamentous ascomycetes may indicate rapid radiation within this clade.

Ascomycota↗

PubMed2002

Phylogenetic relationships of North American garter snakes (Thamnophis) based on four mitochondrial genes: how much DNA sequence is enough?

The clade of garter snakes (Thamnophis) includes some of the most abundant and well-studied snakes in North America. However, phylogenetic relationships within this group have been little studied. We used DNA sequences of four mitochondrial genes (cytochrome b and NADH dehydrogenase subunits 1, 2, and 4) to estimate relationships among 29 of the 31 recognized species of Thamnophis plus the related species Adelophis foxi. Both maximum parsimony (MP) and maximum-likelihood (ML) analyses of all these genes combined produced well-resolved trees with moderate (70-89%) to strong (90-100%) bootstrap support for most clades. MP and ML trees were very similar, with no strongly supported conflict between the two analyses. These analyses identify a clade of 12 species largely restricted to México (the "Mexican clade"), and a clade containing 15 species that collectively range from Central America to southern Canada (the "widespread clade"). These two groups are identified as sister taxa in both MP and ML analyses. A clade consisting of the ribbon snakes (T. sauritus and T. proximus) and the common garter snake (T. sirtalis) is placed as the sister group to all other Thamnophis (i.e., the Mexican + widespread clades) in our analyses. High bootstrap proportions at several levels in the tree support the inclusion of both Thamnophis validus, which has traditionally been placed in the genus Nerodia, and the poorly known species Adelophis foxi within Thamnophis. We used randomly sampled characters (i.e., standard bootstrapping) and randomly sampled contiguous blocks of characters to examine the effect of number of characters on resolution of and support for relationships within Thamnophis using MP. In general, these analyses indicate that we have reached a point of strongly diminishing returns with respect to the effect of adding mtDNA sequence characters for the current set of taxa; our sample of 3809 mtDNA characters is apparently "enough." The next steps to improve the phylogenetic estimate may be to add nuclear DNA sequences, morphology, or behavior, or to sequence additional mtDNA lineages within species.

Animals↗

PubMedDate not supplied

Circadian rhythm of cardiac responses to vagal stimulation tests.

To evaluate the existence of a circadian rhythm in cardiac responses to vagal stimulation tests, 10 children without neurologic or cardiopulmonary disease, were studied using a standardized procedure. A trigeminal airstream stimulation test (TAS) and an ocular compression test (OCT) were subsequently performed at 4 nonequidistant hours. These 2 vagal stimulation tests were performed according to well-established, previously published techniques. Prolongation of the RR-interval during TAS and OCT was calculated and compared to the mean control RR-interval preceding the stimulation period. Prolongation of the RR-interval during the stimulation period was obtained in all instances during TAS and OCT. Chronobiologic analysis was determined by the cosinor method and bootstrap analysis. A significant circadian rhythm was found in cardiac responses to vagal stimulation for both TAS and OCT. The maximal response hour for TAS was between 9:06 p.m. and 5:18 a.m. and for OCT between 10:18 p.m. and 4:24 a.m. The mean value and 95% intervals for the cardiac responses to both vagal stimulation tests revealed, when using the bootstrap analysis, an important overlap in the hour of appearance of the maximal responses to these procedures; the bootstrap analysis of the peak of the acrophase was at 2:50 a.m. for TAS and 1:15 a.m. for OCT. Our results indicate that there is a circadian rhythm in cardiac responses to vagal stimulation tests and demonstrate a preponderance of these responses during the early morning hours.

Arousal↗

PubMed2005

Support vector machines committee classification method for computer-aided polyp detection in CT colonography.

RATIONALE AND OBJECTIVES: A new classification scheme for the computer-aided detection of colonic polyps in computed tomographic colonography is proposed. MATERIALS AND METHODS: The scheme involves an ensemble of support vector machines (SVMs) for classification, a smoothed leave-one-out (SLOO) cross-validation method for obtaining error estimates, and use of a bootstrap aggregation method for training and model selection. Our use of an ensemble of SVM classifiers with bagging (bootstrap aggregation), built on different feature subsets, is intended to improve classification performance compared with single SVMs and reduce the number of false-positive detections. The bootstrap-based model-selection technique is used for tuning SVM parameters. In our first experiment, two independent data sets were used: the first, for feature and model selection, and the second, for testing to evaluate the generalizability of our model. In the second experiment, the test set that contained higher resolution data was used for training and testing (using the SLOO method) to compare SVM committee and single SVM performance. RESULTS: The overall sensitivity on independent test set was 75%, with 1.5 false-positive detections/study, compared with 76%-78% sensitivity and 4.5 false-positive detections/study estimated using the SLOO method on the training set. The sensitivity of the SVM ensemble retrained on the former test set estimated using the SLOO method was 81%, which is 7%-10% greater than the sensitivity of a single SVM. The number of false-positive detections per study was 2.6, a 1.5 times reduction compared with a single SVM. CONCLUSION: Training an SVM ensemble on one data set and testing it on the independent data has shown that the SVM committee classification method has good generalizability and achieves high sensitivity and a low false-positive rate. The model selection and improved error estimation method are effective for computer-aided polyp detection.

Algorithms↗

PubMed2006

Estimated incidence of hepatitis A virus infection in Catalonia.

PURPOSE: Hepatitis A normally is underreported by statutory disease reporting systems. The objective of this study is to estimate the incidence of hepatitis A virus (HAV) infection from prevalence surveys of infection carried out in representative samples of the population in 1989, 1996, and 2002 and the reported disease incidence during 1991 to 2003 in Catalonia. METHODS: The real incidence of the infection was estimated from the reported incidence adjusted by the prevalence of susceptible individuals and the probability of presenting clinical manifestations. The bootstrap resampling technique was used to calculate 95% confidence intervals (CIs) of reported, clinical, and all infection cases. RESULTS: The infection rate estimated by the bootstrap method was 31.1/100,000 person-years (bootstrap studentized 95% CI, 19.4-56.0), and the rate of clinical hepatitis was 20.0/100,000 person-years (95% CI, 11.8-39.9), rates that were 6.3 and 4.1 times greater than the reported rate during the same period, respectively. CONCLUSIONS: In children younger than 5 years, the estimated infection rate was 13.8 times greater than the reported rate. Combined use of reported cases and results of seroprevalence surveys suggest that underreporting of HAV infection is substantial in Catalonia, especially in children younger than 5 years.

Adolescent↗

PubMed2005

Economic evaluation of a randomized trial comparing Helicobacter pylori test-and-treat and prompt endoscopy strategies for managing dyspepsia in a primary-care setting.

BACKGROUND: In western European countries, most dyspeptic patients are initially managed by their general practitioners (GPs), who use a range of strategies to manage dyspepsia. We performed an economic analysis of a Helicobacter pylori test-and-treat strategy versus a prompt endoscopy approach in a primary care setting. METHODS: Data were used from the Strategy: Endoscopy versus Serology (SENSE) study, performed in The Netherlands from 1998 to 2001. Patients were randomized to a prompt endoscopy (n = 105) or test-and-treat (n = 118) group. Follow-up lasted 1 year. Adverse events were not recorded in the SENSE study. Health care costs were based on the total amount of dyspepsia-related drugs used, the number of dyspepsia-related GP visits, the number of diagnostic tests, and the number of dyspepsia-related referrals to specialists. The use of medical resources was calculated as standardized costs for 1999, recorded as euros. (On December 31, 1999, 1.00 Euro = 1.00 US dollar.) Quality of life was measured at inclusion and 1 year later, using the RAND-36 questionnaire. To calculate quality-adjusted life-years (QALYs), we transformed the individual scores of the RAND-36 into 1 overall score, the Health Utilities Index Mark 2, which introduced a limitation to the study. An incremental cost-effectiveness ratio (ICER) was calculated. The 95% confidence limits were calculated using a parametric bootstrap method with angular transformation. All cost data were analyzed from a third-party payer perspective. RESULTS: The total costs per patient were 511 Euros, with 0.037 QALY gained per patient, in the test-and-treat group, and 748 Euros, with 0.032 QALY gained per patient, in the endoscopy group (between groups, P < 0.001 and P = NS, respectively). The point estimate of the ICER indicated that the test-and-treat strategy yielded cost savings and QALYs gained. Parametric bootstrap confidence limits indicated cost savings per QALY gained in 75.7% of the bootstrap simulations. CONCLUSION: This analysis of data from the SENSE1026 study suggests that the H pylori test-and-treat strategy was more cost-effective than prompt endoscopy in the initial management of dyspepsia in general practice, from the perspective of a third-party payer.

Adult↗

PubMed2006

Effectiveness and cost-effectiveness of facilitated percutaneous coronary intervention compared with primary percutaneous coronary intervention in patients with ST-segment elevation myocardial infarction transferred from community hospitals.

BACKGROUND: Primary percutaneous coronary intervention ([PCI], percutaneous transluminal coronary angioplasty+stenting) for ST-segment elevation myocardial infarction (STEMI) is regarded as superior to fibrinolysis even if it means that patients need to be transferred from one center to another to undergo the procedure. However, this inevitable delay between symptom onset and PCI, caused by the time required to travel, might increase the occurrence of cardiac events. A hybrid method called facilitated PCI uses fibrinolysis and/or glycoprotein (GP) IIb/IIIa inhibitors before transfer to a tertiary medical center where urgent PCI might be performed. This approach, however, has not been systematically evaluated. OBJECTIVE: The purpose of this study was to compare the effectiveness (combined end point of in-hospital mortality, reinfarction, stroke, or emergency revascularization) and cost-effectiveness of utilizing a bolus thrombolytic agent with GP IIb/IIIa inhibitor followed by transfer to a tertiary institution for facilitated PCI or standard of care transfer without primary PCI drugs among patients presenting to a community hospital with STEMI. METHODS: This was a prospective, single-center, cohort study comprising data from STEMI patients transferred from community hospitals to Hartford Hospital, Hartford, Connecticut, from the years 2000 to 2003. At the time of analysis, patients receiving primary PCI were matched (1:1) with those receiving facilitated PCI, utilizing propensity scores to assure similar demographics. The combined incidence of major adverse cardiac end points (MACE) and total hospital costs was compared between groups. Non-parametric bootstrapping was conducted to calculate CIs for the incremental cost-effectiveness ratio and generate a quadrant analysis. RESULTS: Based on 254 propensity score-matched patients (127 facilitated PCI and 127 primary PCI), in-hospital MACE and total hospital costs were reduced by 61.3% and US 4563 dollars (2005), respectively, in patients receiving facilitated compared with primary PCI (P=0.021 and P=NS, respectively). Patients receiving facilitated PCI were more likely to have target lesion Thrombolysis in Myocardial Infarction (TIMI) III (normal) blood flow on cardiac catheterization than those receiving primary PCI (49.6% vs 30.7%; P=0.002). However, the rate of TIMI bleeding was similar in both groups (21.3% in the facilitated PCI group vs 18.9% in the primary PCI group). Nonsignificant reductions were observed in both intensive care unit (ICU) and total length of stay (LOS) (0.8 day and 1.0 day, respectively) compared with the primary PCI group. Bootstrap analysis revealed that of 25,000 samplings, facilitated PCI would likely be both more effective and less costly 94.6% of the time. CONCLUSIONS: The use of facilitated PCI in STEMI patients who initially presented to community hospitals and were transferred for PCI appeared to significantly reduce the incidence of MACE, and increase the likelihood of having baseline TIMI III blood flow at time of catheterization. Nonsignificant reductions were observed in total ICU and hospital LOS. However, there did not appear to be a significant effect on the incidence of bleeding in patients receiving facilitated PCI. Bootstrap analysis confirmed that facilitated PCI would be both a more effective and less costly strategy.

Adolescent↗

PubMed2005

Does a patient's self-reported health-related quality of life predict survival beyond key biomedical data in advanced colorectal cancer?

The purpose of this study was to determine whether baseline patients' self reported health-related quality of life (HRQOL) parameters could predict survival beyond key biomedical prognostic factors in patients with metastatic colorectal cancer. The analysis was conducted on 299 patients. HRQOL baseline scores were assessed using the European Organisation for Research and Treatment of Cancer, Quality of Life Questionnaire-Core30 (EORTC QLQ-C30). The Cox proportional hazards regression model was used for both univariate and multivariate analyses of survival. In addition, a bootstrap resampling technique was used to assess the stability of the outcomes. The final multivariate Cox regression model retained four variables as independent prognostic factors for survival: white blood cell (WBC) count with a hazard ratio (HR) of 1.961 (95% CI, 1.439-2.672; P<0.001), alkaline phosphatase with HR=1.509 (95% CI, 1.126-2.022; P=0.005), number of sites involved with HR=1.108 (95% CI, 1.024-1.198; P=0.01) and the patient's score on the social functioning scale with HR=0.991 (95% CI, 0.987-0.996; P<0.001) which translates into a 9% decrease in the patient's hazard of death for any 10 point increase. The independent prognostic importance of social functioning and the stability of the final Cox regression model were also confirmed by the additional bootstrap model averaging analysis, based on 1000 bootstrap-generated samples. The results suggest that social functioning, acts as a prognostic measure of survival beyond a number of previously known biomedical parameters.

Adult↗

PubMed2004

Different methodologies to quantify uncertainties of air emissions.

Characterization of the uncertainty associated with air emission estimates is of critical importance especially in the compilation of air emission inventories. In this paper, two different theories are discussed and applied to evaluate air emissions uncertainty. In addition to numerical analysis, which is also recommended in the framework of the United Nation Convention on Climate Change guidelines with reference to Monte Carlo and Bootstrap simulation models, fuzzy analysis is also proposed. The methodologies are discussed and applied to an Italian example case study. Air concentration values are measured from two electric power plants: a coal plant, consisting of two boilers and a fuel oil plant, of four boilers; the pollutants considered are sulphur dioxide (SO(2)), nitrogen oxides (NO(X)), carbon monoxide (CO) and particulate matter (PM). Monte Carlo, Bootstrap and fuzzy methods have been applied to estimate uncertainty of these data. Regarding Monte Carlo, the most accurate results apply to Gaussian distributions; a good approximation is also observed for other distributions with almost regular features either positive asymmetrical or negative asymmetrical. Bootstrap, on the other hand, gives a good uncertainty estimation for irregular and asymmetrical distributions. The logic of fuzzy analysis, where data are represented as vague and indefinite in opposition to the traditional conception of neatness, certain classification and exactness of the data, follows a different description. In addition to randomness (stochastic variability) only, fuzzy theory deals with imprecision (vagueness) of data. Fuzzy variance of the data set was calculated; the results cannot be directly compared with empirical data but the overall performance of the theory is analysed. Fuzzy theory may appear more suitable for qualitative reasoning than for a quantitative estimation of uncertainty, but it suits well when little information and few measurements are available and when distributions of data are not properly known.

Air Pollutants↗

PubMed2005

Cryptobiosis: a new theoretical perspective.

The tardigrade is a microscopic creature that under environmental stress conditions undergoes cryptobiosis [Feofilova, E.P., 2003. Deceleration of vital activity as a universal biochemical mechanism ensuring adaptation of microorganisms to stress factors: A review. Appl. Biochem. Microbiol. 39, 1-18; Nelson, D.R., 2002. Current status of the tardigrada: Evolution and ecology. Integrative Comp. Biol. 42, 652-659]-a temporary metabolic depression-which is considered to be a third state between life and death [Clegg, J.S., 2001. Cryptobiosis-a peculiar state of biological organization. Comp. Biochem. Physiol. Part B 128, 613-624]. In contrast with death, cryptobiosis is a reversible state, and as soon as environmental conditions change, the tardigrade "returns to life." Cryptobiosis in general, and among the tardigrade in particular, is a phenomenon poorly understood [Guppy, M., 2004. The biochemistry of metabolic depression: a history of perceptions. Comp. Biochem. Physiol. Part B 139, 435-442; Schill, R.O., et al., 2004. Stress gene (hsp70) sequences and quantitative expression in Milensium tardigradum (Tardigrade) during active and cryptobiotic stages. J. Exp. Biol. 207, 1607-1613; Watanabe, M., et al., 2002. Mechanisn allowing an insect to survive complete dehydration and extreme temperatures. J. Exp. Biol. 205, 2799-2802; Wright, J.C., 2001. Cryptobiosis 300 years on from van Leuwenhoek: what have we learned about tardigrades? Zool. Anz. 240, 563-582]. Moreover, the ability of the tardigrade to bootstrap itself and to return to life seems paradoxical like the legendary Baron von Munchausen who pulled himself out of the swamp by grabbing his own hair. Two theoretical obstacles prevent us from advancing our knowledge of cryptobiosis. First, we lack appropriate theoretical understanding of reversible processes of biological computation in living systems. Second, we lack appropriate theoretical understanding of bootstrapping in living systems. In this short opinion article, I would like to present the idea that although cryptobiosis is obscure from a certain point of view, it makes sense within a scientific perspective suggesting that "organization becomes cause in the matter" [Strohman, R.C., 2000. Organization becomes cause in the matter. Nat. Biotechnol. 18, 575-576]. I present Bateson's idea that organisms have a "recursive hierarchical" form of organization [Neuman, Y., 2004. Meaning making in the immune system. Perspect. Biol. Med. 48, 320-327; Neuman, Y., in press. A theory of meaning. Inform. Sci.] and suggest that this form of organization allows bootstrapping through reversible process of computation as discussed by theoretical physicists [Bennett, C.H., 1982. The thermodynamics of computation-a review. Int. J. Theoret. Phys. 1, 905-940; Landauer and Bennett, 1985].

Adaptation, Physiological↗

PubMed2004

Cladogenesis in a starfish species complex from southern Australia: evidence for vicariant speciation?

DNA sequencing (cytochrome oxidase I; 82 sequences; 25 locations) of a species complex of Australian six-rayed sea-stars (genus Patiriella) reveals four well-supported mtDNA clades, corresponding to P. oriens, P. occidens, P. medius, and P. gunnii. These clades have non-random geographic distributions along an east to west axis that are broadly consistent with the biogeographic provinces of southern Australia proposed by. The taxa are deeply divergent (minimum 7.5%) and are estimated to have originated during the late Pliocene. By contrast, intra-clade divergences are small, typically less than 1.0%. Phylogenetic analysis of mtDNA provides strong support for the combined monophyly of multicoloured forms (P. oriens, P. occidens, and P. medius; 100% bootstrap support) and suggests that P. medius (central) and P. occidens (western) may be sister taxa (up to 76% bootstrap support). Maximum likelihood analysis of nuclear DNA sequences (actin; 1437 bp) yields an optimal tree largely consistent with mtDNA groupings, but with little bootstrap support. The biogeographic distribution of P. oriens (eastern) and P. occidens (western) is roughly consistent with a vicariant model involving allopatric divergence during glaciation. In addition, we propose that the Great Australian Bight may also have retained isolated populations during glacial periods, perhaps explaining the "central" distributions of P. gunnii and P. medius.

Actins↗

PubMed2004

RPB2 gene phylogeny in flowering plants, with particular emphasis on asterids.

Two, apparently functional, paralogues of the RPB2 gene, which encodes the second largest subunit of RNA polymerase II, are shown to be present in two major groups of asterid plants. Although all other land plants surveyed so far have been found to have only one of these two copies, the RPB2 gene phylogeny inferred from the 3' half of the gene for 35 angiosperm taxa and six other land plants indicates that the duplication of the RPB2 gene occurred earlier than the time for origin of the asterid group, probably near the origin of "core eudicots." The d copy is present in all plants which are unambiguously assigned to the core eudicots, whereas the I copy is retained only in the lamiid clade, Ericales, and Escallonia, all belonging to the asterid group of plants. Both parsimony and likelihood analyses of sequences from the 3' half of the gene give strong bootstrap support for these conclusions. There is no support for monophyly of the taxa having both copies. Thus, numerous losses of one of the copies must be inferred. Structurally, both paralogues appear functional, and transcription is demonstrated for both copies. In the lamiid group, the d copy has lost introns 18-23. The well supported phylogenetic relationships implied by the RPB2 gene phylogeny are largely congruent with well supported phylogenetic hypotheses based on other sequence data. However, Ilex, usually assigned to the campanuliid clade, is instead supported as being a member of the lamiid clade, both from sequence data and the presence of an I copy as well as the loss of introns 18-23 in the d copy. Escallonia, supported as a member of the campanuliid clade both by RPB2-d-sequences and previously published DNA sequence data, has all the introns 18-23 in its d copy, as do all other members studied from the campanuliid group. We used the Markov Chain Monte Carlo (MCMC) approach of the MrBayes program to implement Maximum Likelihood bootstrapping. Under the same model of evolution, bootstrapping frequencies are significantly lower than the Bayesian posterior probabilities inferred from the MCMC chain.

Gene Dosage↗

PubMed2004

Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory.

Despite the recent progress in molecular phylogenetics, many of the deepest relationships among the main lineages of the largest fungal phylum, Ascomycota, remain unresolved. To increase both resolution and support on a large-scale phylogeny of lichenized and non-lichenized ascomycetes, we combined the protein coding-gene RPB2 with the traditionally used nuclear ribosomal genes SSU and LSU. Our analyses resulted in the naming of the new subclasses Acarosporomycetidae and Ostropomycetidae, and the new class Lichinomycetes, as well as the establishment of the phylogenetic placement and novel circumscription of the lichen-forming fungi family Acarosporaceae. The delimitation of this family has been problematic over the past century, because its main diagnostic feature, true polyspory (numerous spores issued from multiple post-meiosis mitoses) with over 100 spores per ascus, is probably not restricted to the Acarosporaceae. This observation was confirmed by our reconstruction of the origin and evolution of this form of true polyspory using maximum likelihood as the optimality criterion. The various phylogenetic analyses carried out on our data sets allowed us to conclude that: (1) the inclusion of phylogenetic signal from ambiguously aligned regions into the maximum parsimony analyses proved advantageous in reconstructing phylogeny; however, when more data become available, Bayesian analysis using different models of evolution is likely to be more efficient; (2) neighbor-joining bootstrap proportions seem to be more appropriate in detecting topological conflict between data partitions of large-scale phylogenies than posterior probabilities; and (3) Bayesian bootstrap proportion provides a compromise between posterior probability outcomes (i.e., higher accuracy, but with a higher number of significantly supported wrong internodes) vs. maximum likelihood bootstrap proportion outcomes (i.e., lower accuracy, with a lower number of significantly supported wrong internodes).

Ascomycota↗

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↗

PubMed2003

Understanding how input matters: verb learning and the footprint of universal grammar.

Studies under the heading "syntactic bootstrapping" have demonstrated that syntax guides young children's interpretations during verb learning. We evaluate two hypotheses concerning the origins of syntactic bootstrapping effects. The "universalist" view, holding that syntactic bootstrapping falls out from universal properties of the syntax-semantics mapping, is shown to be superior to the "emergentist" view, which holds that argument structure patterns emerge from a process of categorization and generalization over the input. These theories diverge in their predictions about a language in which syntactic structure is not the most reliable cue to a certain meaning. In Kannada, causative morphology is a better predictor of causative meaning than transitivity is. Hence, the emergentist view predicts that Kannada-speaking children will associate causative morphology (in favor of transitive syntax) with causative meaning. The universalist theory, however, predicts the opposite pattern. Using an act-out task, we found that 3-year-old native speakers of Kannada associate argument number and not morphological form with causativity, supporting the universalist approach.

Adult↗