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PubMed1999

Effect of nonindependent substitution on phylogenetic accuracy.

All current phylogenetic methods assume that DNA substitutions are independent among sites. However, ample empirical evidence suggests that the process of substitution is not independent but is, in fact, temporally and spatially correlated. The robustness of several commonly used phylogenetic methods to the assumption of independent substitution is examined. A compound Poisson process is used to model DNA substitution. This model assumes that substitution events are Poisson-distributed in time and that the number of substitutions associated with each event is geometrically distributed. The asymptotic properties of phylogenetic methods do not appear to change under a compound Poisson process of DNA substitution. Moreover, the rank order of the performance of different methods does not change. However, all phylogenetic methods become less efficient when substitution follows a compound Poisson process.

Base Composition↗

PubMed2000

Using the Past to Predict the Present: Confidence Intervals for Regression Equations in Phylogenetic Comparative Methods.

Two phylogenetic comparative methods, independent contrasts and generalized least squares models, can be used to determine the statistical relationship between two or more traits. We show that the two approaches are functionally identical and that either can be used to make statistical inferences about values at internal nodes of a phylogenetic tree (hypothetical ancestors), to estimate relationships between characters, and to predict values for unmeasured species. Regression equations derived from independent contrasts can be placed back onto the original data space, including computation of both confidence intervals and prediction intervals for new observations. Predictions for unmeasured species (including extinct forms) can be made increasingly accurate and precise as the specificity of their placement on a phylogenetic tree increases, which can greatly increase statistical power to detect, for example, deviation of a single species from an allometric prediction. We reexamine published data for basal metabolic rates (BMR) of birds and show that conventional and phylogenetic allometric equations differ significantly. In new results, we show that, as compared with nonpasserines, passerines exhibit a lower rate of evolution in both body mass and mass-corrected BMR; passerines also have significantly smaller body masses than their sister clade. These differences may justify separate, clade-specific allometric equations for prediction of avian basal metabolic rates.

allometry↗

PubMed2001

Phylogenetic and familial estimates of mitochondrial substitution rates: study of control region mutations in deep-rooting pedigrees.

We studied mutations in the mtDNA control region (CR) using deep-rooting French-Canadian pedigrees. In 508 maternal transmissions, we observed four substitutions (0.0079 per generation per 673 bp, 95% CI 0.0023-0.186). Combined with other familial studies, our results add up to 18 substitutions in 1,729 transmissions (0.0104), confirming earlier findings of much greater mutation rates in families than those based on phylogenetic comparisons. Only 12 of these mutations occurred at independent sites, whereas three positions mutated twice each, suggesting that pedigree studies preferentially reveal a fraction of highly mutable sites. Fitting the data through use of a nonuniform rate model predicts the presence of 40 (95% CI 27-54) such fast sites in the whole CR, characterized by the mutation rate of 274 per site per million generations (95% CI 138-410). The corresponding values for hypervariable regions I (HVI; 1,729 transmissions) and II (HVII; 1,956 transmissions), are 19 and 22 fast sites, with rates of 224 and 274, respectively. Because of the high probability of recurrent mutations, such sites are expected to be of no or little informativity for the evaluation of mutational distances at the phylogenetic time scale. The analysis of substitution density in the alignment of 973 HVI and 650 HVII unrelated European sequences reveals that the bulk of the sites mutate at relatively moderate and slow rates. Assuming a star-like phylogeny and an average time depth of 250 generations, we estimate the rates for HVI and HVII at 23 and 24 for the moderate sites and 1.3 and 1.0 for the slow sites. The fast, moderate, and slow sites, at the ratio of 1:2:13, respectively, describe the mutation-rate heterogeneity in the CR. Our results reconcile the controversial rate estimates in the phylogenetic and familial studies; the fast sites prevail in the latter, whereas the slow and moderate sites dominate the phylogenetic-rate estimations.

Canada↗

PubMed2002

Phylogenetic distribution of virulence-associated genes among Escherichia coli isolates associated with neonatal bacterial meningitis in the Netherlands.

Seventy cerebrospinal fluid Escherichia coli isolates from infants with neonatal bacterial meningitis (NBM), as submitted to the Netherlands Reference Laboratory for Bacterial Meningitis from 1989 through 1997, were assessed for phylogenetic background and extended virulence genotypes, in comparison with the E. coli reference collection, by using molecular methods. Phylogenetic group B2 significantly predominated overall (81%). The 4 major phylogenetic clusters exhibited distinctive virulence genotypes, suggesting diverse evolutionary histories for the individual genes. Many genes not previously studied in NBM, notably diarrhea-associated cdtB (cytolethal distending toxin [46%]) and urinary tract infection-associated ompT (outer membrane protease T [96%]), were as or more prevalent than traditional NBM-associated traits, such as ibeA (invasion of brain endothelium [33%]), sfaS (S fimbriae [59%]), and K1 capsule (81%). These findings provide novel insights into the phylogenetic origins of NBM-associated E. coli and suggest numerous new potential targets for preventive interventions against this dire disease.

Escherichia coli↗

PubMed1991

Ribosomal DNA: molecular evolution and phylogenetic inference.

Ribosomal DNA (rDNA) sequences have been aligned and compared in a number of living organisms, and this approach has provided a wealth of information about phylogenetic relationships. Studies of rDNA sequences have been used to infer phylogenetic history across a very broad spectrum, from studies among the basal lineages of life to relationships among closely related species and populations. The reasons for the systematic versatility of rDNA include the numerous rates of evolution among different regions of rDNA (both among and within genes), the presence of many copies of most rDNA sequences per genome, and the pattern of concerted evolution that occurs among repeated copies. These features facilitate the analysis of rDNA by direct RNA sequencing, DNA sequencing (either by cloning or amplification), and restriction enzyme methodologies. Constraints imposed by secondary structure of rRNA and concerted evolution need to be considered in phylogenetic analyses, but these constraints do not appear to impede seriously the usefulness of rDNA. An analysis of aligned sequences of the four nuclear and two mitochondrial rRNA genes identified regions of these genes that are likely to be useful to address phylogenetic problems over a wide range of levels of divergence. In general, the small subunit nuclear sequences appear to be best for elucidating Precambrian divergences, the large subunit nuclear sequences for Paleozoic and Mesozoic divergences, and the organellar sequences of both subunits for Cenozoic divergences. Primer sequences were designed for use in amplifying the entire nuclear rDNA array in 15 sections by use of the polymerase chain reaction; these "universal" primers complement previously described primers for the mitochondrial rRNA genes. Pairs of primers can be selected in conjunction with the analysis of divergence of the rRNA genes to address systematic problems throughout the hierarchy of life.

Animals↗

PubMed2004

Virulence factor profiles and phylogenetic background of Escherichia coli isolates from veterans with bacteremia and uninfected control subjects.

BACKGROUND: Escherichia coli is the most common cause of gram-negative bloodstream infections, causing an estimated 40,000 deaths from sepsis each year in the United States. The present study sought to determine specifically which virulence factors (VFs) and phylogenetic groups of E. coli are epidemiologically associated with bacteremia. METHODS: E. coli isolates from 63 veterans with bacteremia and rectal isolates from 71 matched uninfected control subjects were compared both for phylogenetic group and for the presence of VFs and O antigens. RESULTS: Bacteremia isolates exhibited a significantly greater prevalence of most VFs studied. In multivariate logistic regression analysis, ompT (outer membrane protein T) was the strongest VF predictor of bacteremia (P<.001). Despite the concentration of most individual VFs within group B2, bacteremia and rectal isolates differed little by phylogenetic distribution, a finding explained by the greater prevalence of VFs among bacteremia isolates than rectal isolates within groups B2 and D. CONCLUSIONS: Although phylogenetic group partially corresponds with virulence potential in E. coli bacteremia, VFs are more-powerful predictors of pathogenic potential. Bacteremia isolates exhibit an arsenal of VFs that distinguishes them from rectal isolates from uninfected hosts, which makes these differences attractive potential targets in vaccine or drug development.

Aged↗

PubMed2006

Range size: disentangling current traits and phylogenetic and biogeographic factors.

The range size of a species can be determined by its current traits and by phylogenetic and biogeographic factors. However, only rarely have these factors been studied in combination. We use data on the geographic range sizes of all 26 Sylvia warblers to explicitly test whether range size was determined by current species-specific traits (e.g., body size, dispersal ability), phylogenetic factors (e.g., age of the lineage), or environmental, biogeographic factors (e.g., latitudinal position of the range). The results demonstrated that current traits and phylogenetic and biogeographic factors were interrelated. While a number of factors were significant in simple regression analyses, only one factor determined range size in the multiple regression analyses--dispersal ability. Species with better dispersal ability had larger ranges than species with poorer dispersal ability. Apparent increases of range size with latitude or with the age of the species resulted from correlations with dispersal ability. While the most significant factor that influences the range size of a group of species might differ from one group to the next, these results demonstrate that studies that focus only on a single, for example, phylogenetic, factor might yield misleading results.

Animal Migration↗

PubMed2002

A structural EM algorithm for phylogenetic inference.

A central task in the study of molecular evolution is the reconstruction of a phylogenetic tree from sequences of current-day taxa. The most established approach to tree reconstruction is maximum likelihood (ML) analysis. Unfortunately, searching for the maximum likelihood phylogenetic tree is computationally prohibitive for large data sets. In this paper, we describe a new algorithm that uses Structural Expectation Maximization (EM) for learning maximum likelihood phylogenetic trees. This algorithm is similar to the standard EM method for edge-length estimation, except that during iterations of the Structural EM algorithm the topology is improved as well as the edge length. Our algorithm performs iterations of two steps. In the E-step, we use the current tree topology and edge lengths to compute expected sufficient statistics, which summarize the data. In the M-Step, we search for a topology that maximizes the likelihood with respect to these expected sufficient statistics. We show that searching for better topologies inside the M-step can be done efficiently, as opposed to standard methods for topology search. We prove that each iteration of this procedure increases the likelihood of the topology, and thus the procedure must converge. This convergence point, however, can be a suboptimal one. To escape from such "local optima," we further enhance our basic EM procedure by incorporating moves in the flavor of simulated annealing. We evaluate these new algorithms on both synthetic and real sequence data and show that for protein sequences even our basic algorithm finds more plausible trees than existing methods for searching maximum likelihood phylogenies. Furthermore, our algorithms are dramatically faster than such methods, enabling, for the first time, phylogenetic analysis of large protein data sets in the maximum likelihood framework.

Algorithms↗

PubMed2004

Combining phylogenetic and hidden Markov models in biosequence analysis.

A few models have appeared in recent years that consider not only the way substitutions occur through evolutionary history at each site of a genome, but also the way the process changes from one site to the next. These models combine phylogenetic models of molecular evolution, which apply to individual sites, and hidden Markov models, which allow for changes from site to site. Besides improving the realism of ordinary phylogenetic models, they are potentially very powerful tools for inference and prediction--for example, for gene finding or prediction of secondary structure. In this paper, we review progress on combined phylogenetic and hidden Markov models and present some extensions to previous work. Our main result is a simple and efficient method for accommodating higher-order states in the HMM, which allows for context-dependent models of substitution--that is, models that consider the effects of neighboring bases on the pattern of substitution. We present experimental results indicating that higher-order states, autocorrelated rates, and multiple functional categories all lead to significant improvements in the fit of a combined phylogenetic and hidden Markov model, with the effect of higher-order states being particularly pronounced.

Computational Biology↗

PubMed2004

From a phylogenetic tree to a reticulated network.

In many phylogenetic problems, assuming that species have evolved from a common ancestor by a simple branching process is unrealistic. Reticulate phylogenetic models, however, have been largely neglected because the concept of reticulate evolution have not been supported by using appropriate analytical tools and software. The reticulate model can adequately describe such complicated mechanisms as hybridization between species or lateral gene transfer in bacteria. In this paper, we describe a new algorithm for inferring reticulate phylogenies from evolutionary distances among species. The algorithm is capable of detecting contradictory signals encompassed in a phylogenetic tree and identifying possible reticulate events that may have occurred during evolution. The algorithm produces a reticulate phylogeny by gradually improving upon the initial solution provided by a phylogenetic tree model. The new algorithm is compared to the popular SplitsGraph method in a reanalysis of the evolution of photosynthetic organisms. A computer program to construct and visualize reticulate phylogenies, called T-Rex (Tree and Reticulogram Reconstruction), is available to researchers at the following URL: www.fas.umontreal.ca/biol/casgrain/en/labo/t-rex.

Algorithms↗

PubMed2006

Genetic and phylogenetic characterization of structural genes from non-B HIV-1 subtypes in Italy.

A molecular and phylogenetic characterization on env and gag subgenomic regions has been performed in our laboratory on HIV-1 variants identified in seropositive individuals residing in Italy, infected in the 1999-2001 period, and five non-B-subtype HIV-1 isolates have been described. To confirm the phylogenetic characterization and to determine the genomic organization of three non-B HIV-1 isolates (A, G, and CRF02- AG), the complete gag, pol, and gp120 ORFs (approx. 6900 bp) have been sequenced for each of them. The phylogenetic tree analyses performed on the whole sequence or on individual genes suggested, for the A and G isolates, the identification of divergent strains that do not cluster into any of the known subsubtypes. This has been further validated by pairwise distance analysis. On the contrary, the phylogenetic classification of the CRF02-AG isolate has been confirmed and an overall typical pattern of intragenomic breakpoints has been observed by a Simplot analysis. These results confirm the constant HIV-1 molecular evolution and indicate the relevance of a continuous molecular monitoring of HIV-1 isolates for the development of appropriate vaccine candidates.

Genes, env↗

PubMed2000

Methicillin-resistant Staphylococcus aureus: phylogenetic relatedness between European epidemic clones and Swiss sporadic strains.

We have compared the phylogenetic diversity of methicillin-resistant Staphylococcus aureus (MRSA) strains from Switzerland and their phylogenetic relationships with European epidemic clones, using multiprimer random amplification polymorphic DNA (RAPD). Strains included 24 European epidemic clones (59 strains), 66 sporadic strains isolated in Switzerland in 1996-1997, and 15 reference strains of five other Staphylococcus species. Similarity and clustering analysis with the Jaccard's coefficient showed that the maximum genetic distance between MRSA strains was 0.43, whereas the minimum genetic distance between the six Staphylococcus species was 0.97, indicating that the method permits phylogenetic hierarchization. The 24 MRSA clones reported to be epidemic in European countries during the 1990s were distributed into seven different genetic clusters with a maximum distance of 0.29 among them. This clustering pattern was confirmed by the analysis of a subset of MRSA strains by multilocus enzyme electrophoresis at 12 loci. Most of the sporadic Swiss strains were distributed into these seven different genetic clusters, together with the epidemic MRSA clones. This suggests that there is no phylogenetic cluster specific to epidemic clones of MRSA.

Clone Cells↗

PubMed2005

Phylogenetic analysis of Petunia sensu Jussieu (Solanaceae) using chloroplast DNA RFLP.

BACKGROUND AND AIMS: The phylogenetic relationships of Petunia sensu Jussieu (Petunia sensu Wijsman plus Calibrachoa) are unclear. This study aimed to resolve this uncertainty using molecular evidence. METHODS: Phylogenetic trees of 52 taxa of Petunia sensu Jussieu were constructed using restriction fragment length polymorphism (RFLP) of chloroplast DNA digested with 19 restriction enzymes and hybridized with 12 cloned Nicotiana chloroplast DNA fragments as probes. KEY RESULTS: In all, 89 phylogenetically informative RFLPs were detected and one 50 % majority consensus tree was obtained, using the maximum parsimony method, and one distance matrix tree, using the neighbour joining method. Petunia sensu Wijsman and Calibrachoa were monophyletic sister clades in both trees. Calibrachoa parviflora and C. pygmaea, previously thought to differ from the other species in terms of their cross-compatibility, seed morphology, and nuclear DNA content, formed a basal clade that was sister to the remainder of Calibrachoa. Several clades found in the phylogenetic trees corresponded to their distribution ranges, suggesting that recent speciation in the genus Petunia sensu Jussieu occurred independently in several different regions. CONCLUSIONS: The separation of Petunia sensu Wijsman and Calibrachoa was supported by chloroplast DNA analysis. Two groups in the Calibrachoa were also recognized with a high degree of confidence.

DNA, Chloroplast↗

PubMed2006

Exine micromorphology of Orchidinae (Orchidoideae, Orchidaceae): phylogenetic constraints or ecological influences?

BACKGROUND AND AIMS: Pollen characters have been widely used in defining evolutionary trends in orchids. In recent years, information on pollination biology and phylogenetic patterns within Orchidinae has become available. Hence, the aim of the presented work is to re-evaluate exine micromorphology of Orchidinae in light of recent phylogenetic studies and to test whether pollen micromorphology strictly depends on phylogenetic relationships among species or whether it is influenced by the marked differences in pollination ecology also reported among closely related species. METHODS: Pollen sculpturing of 45 species of Orchidinae and related taxa was investigated using scanning electron microscopy. To cover potential intraspecific variation, several accessions of the same species were examined. KEY RESULTS: Orchidinae show remarkable variation in exine sculpturing, with a different level of variation within species groups. In some genera, such as Serapias (rugulate) and Ophrys (psilate to verrucate), intrageneric uniformity corresponds well to a common pollination strategy and close relationships among species. However, little exine variability (psilate-scabrate and scabrate-rugulate) was also found in the genus Anacamptis in spite of striking differences in floral architecture and pollination strategies. A larger variety of exine conditions was found in genera Dactylorhiza (psilate, psilate-scabrate and reticulate) and Orchis s.s. (psilate, reticulate, perforate-rugulate and baculate) where no unequivocal correspondence can be found to either phylogenetic patterns or pollination strategies. CONCLUSIONS: Changes in pollen characteristics do not consistently reflect shifts in pollination strategy. A unique trend of exine evolution within Orchidinae is difficult to trace. However, the clades comprising Anacamptis, Neotinea, Ophrys and Serapias show psilate to rugulate or scabrate pollen, while that of the clade comprising Chamorchis, Dactylorhiza, Gymnadenia, Orchis s.s., Platanthera, Pseudorchis and Traunsteinera ranges from psilate to reticulate. Comparison of the data with exine micromorphology from members of the tribe Orchidieae and related tribes suggests a possible general trend from reticulate to psilate.

Biological Evolution↗

PubMed1999

HICLAS: a taxonomic database system for displaying and comparing biological classification and phylogenetic trees.

MOTIVATION: Numerous database management systems have been developed for processing various taxonomic data bases on biological classification or phylogenetic information. In this paper, we present an integrated system to deal with interacting classifications and phylogenies concerning particular taxonomic groups. RESULTS: An information-theoretic view (taxon view) has been applied to capture taxonomic concepts as taxonomic data entities. A data model which is suitable for supporting semantically interacting dynamic views of hierarchic classifications and a query method for interacting classifications have been developed. The concept of taxonomic view and the data model can also be expanded to carry phylogenetic information in phylogenetic trees. We have designed a prototype taxonomic database system called HICLAS (HIerarchical CLAssification System) based on the concept of taxon view, and the data models and query methods have been designed and implemented. This system can be effectively used in the taxonomic revisionary process, especially when databases are being constructed by specialists in particular groups, and the system can be used to compare classifications and phylogenetic trees. AVAILABILITY: Freely available at the WWW URL: http://aims.cps.msu.edu/hiclas/ CONTACT: pramanik@cps.msu.edu; lotus@wipm.whcnc.ac.cn

Classification↗

PubMed2000

Phylogenetically enhanced statistical tools for RNA structure prediction.

MOTIVATION: Methods that predict the structure of molecules by looking for statistical correlation have been quite effective. Unfortunately, these methods often disregard phylogenetic information in the sequences they analyze. Here, we present a number of statistics for RNA molecular-structure prediction. Besides common pair-wise comparisons, we consider a few reasonable statistics for base-triple predictions, and present an elaborate analysis of these methods. All these statistics incorporate phylogenetic relationships of the sequences in the analysis to varying degrees, and the different nature of these tests gives a wide choice of statistical tools for RNA structure prediction. RESULTS: Starting from statistics that incorporate phylogenetic information only as independent sequence evolution models for each position of a multiple alignment, and extending this idea to a joint evolution model of two positions, we enhance the usual purely statistical methods (e.g. methods based on the Mutual Information statistic) with the use of phylogenetic information available in the sequences. In particular, we present a joint model based on the HKY evolution model, and consequently a X(2) test of independence for two positions. A significant part of this work is devoted to some mathematical analysis of these methods. We tested these statistics on regions of 16S and 23S rRNA, and tRNA.

Base Sequence↗

PubMed2001

TreeGeneBrowser: phylogenetic data mining of gene sequences from public databases.

MOTIVATION: Sequence databases represent an enormous resource of phylogenetic information, but there is a lack of tools for accessing that information in order to assess the amount of evolutionary information in these databases that may be suitable for phylogenetic reconstruction and for identifying areas of the taxonomy that are under-represented for specific gene sequences. RESULTS: We have developed TreeGeneBrowser which allows inspection and evaluation of gene sequence data for phylogenetic reconstruction. This program improves the efficiency of identification of genes that may be useful for particular phylogenetic studies and identifies taxa and taxonomic branches that are under-represented in sequence databases.

Algorithms↗

PubMed2004

APE: Analyses of Phylogenetics and Evolution in R language.

UNLABELLED: Analysis of Phylogenetics and Evolution (APE) is a package written in the R language for use in molecular evolution and phylogenetics. APE provides both utility functions for reading and writing data and manipulating phylogenetic trees, as well as several advanced methods for phylogenetic and evolutionary analysis (e.g. comparative and population genetic methods). APE takes advantage of the many R functions for statistics and graphics, and also provides a flexible framework for developing and implementing further statistical methods for the analysis of evolutionary processes. AVAILABILITY: The program is free and available from the official R package archive at http://cran.r-project.org/src/contrib/PACKAGES.html#ape. APE is licensed under the GNU General Public License.

Biological Evolution↗