Results 1  10
of
2,522
A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood
, 2003
"... The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle, which clearly satisfies these requirements. The ..."
Abstract

Cited by 2182 (27 self)
 Add to MetaCart
The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on the maximumlikelihood principle, which clearly satisfies these requirements. The core of this method is a simple hillclimbing algorithm that adjusts tree topology and branch lengths simultaneously. This algorithm starts from an initial tree built by a fast distancebased method and modifies this tree to improve its likelihood at each iteration. Due to this simultaneous adjustment of the topology and branch lengths, only a few iterations are sufficient to reach an optimum. We used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximumlikelihood programs and much higher than the performance of distancebased and parsimony approaches. The reduction of computing time is dramatic in comparison with other maximumlikelihood packages, while the likelihood maximization ability tends to be higher. For example, only 12 min were required on a standard personal computer to analyze a data set consisting of 500 rbcL sequences with 1,428 base pairs from plant plastids, thus reaching a speed of the same order as some popular distancebased and parsimony algorithms. This new method is implemented in the PHYML program, which is freely available on our web page:
Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees.
 Mol Biol Evol
, 1993
"... Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA ( mtDNA ) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide sub ..."
Abstract

Cited by 925 (4 self)
 Add to MetaCart
Examining the pattern of nucleotide substitution for the control region of mitochondrial DNA ( mtDNA ) in humans and chimpanzees, we developed a new mathematical method for estimating the number of transitional and transversional substitutions per site, as well as the total number of nucleotide substitutions. In this method, excess transitions, unequal nucleotide frequencies, and variation of substitution rate among different sites are all taken into account. Application of this method to human and chimpanzee data suggested that the transition / transversion ratio for the entire control region was 15 and nearly the same for the two species. The 95% confidence interval of the age of the common ancestral mtDNA was estimated to be 80,000480,000 years in humans and 0.572.72 Myr in common chimpanzees.
Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies.
 Mol. Biol. Evol.
, 1996
"... A versatile method, quartet puzzling, is introduced to reconstruct the topology (branching pattern) of a phylogenetic tree based on DNA or amino acid sequence data. This method applies maximumlikelihood tree reconstruction to all possible quartets that can be formed from n sequences. The quartet t ..."
Abstract

Cited by 433 (9 self)
 Add to MetaCart
A versatile method, quartet puzzling, is introduced to reconstruct the topology (branching pattern) of a phylogenetic tree based on DNA or amino acid sequence data. This method applies maximumlikelihood tree reconstruction to all possible quartets that can be formed from n sequences. The quartet trees serve as starting points to reconstruct a set of optimal ntaxon trees. The majority rule consensus of these trees defines the quartet puzzling tree and shows groupings that are well supported. Computer simulations show that the performance of quartet puzzling to reconstruct the true tree is always equal to or better than that of neighbor joining. For some cases with high transition/transversion bias quartet puzzling outperforms neighbor joining by a factor of 10. The application of quartet puzzling to mitochondrial RNA and tRNAVd' sequences from amniotes demonstrates the power of the approach. A PHYLIPcompatible ANSI C program, PUZZLE, for analyzing nucleotide or amino acid sequence data is available.
Model Selection and Model Averaging in Phylogenetics: Advantages of Akaike Information Criterion and Bayesian Approaches Over Likelihood Ratio Tests
, 2004
"... Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of phylogenetics. We start by reviewing different aspects of the sel ..."
Abstract

Cited by 407 (8 self)
 Add to MetaCart
Model selection is a topic of special relevance in molecular phylogenetics that affects many, if not all, stages of phylogenetic inference. Here we discuss some fundamental concepts and techniques of model selection in the context of phylogenetics. We start by reviewing different aspects of the selection of substitution models in phylogenetics from a theoretical, philosophical and practical point of view, and summarize this comparison in table format. We argue that the most commonly implemented model selection approach, the hierarchical likelihood ratio test, is not the optimal strategy for model selection in phylogenetics, and that approaches like the Akaike Information Criterion (AIC) and Bayesian methods offer important advantages. In particular, the latter two methods are able to simultaneously compare multiple nested or nonnested models, assess model selection uncertainty, and allow for the estimation of phylogenies and model parameters using all available models (modelaveraged inference or multimodel inference). We also describe how the relative importance of the different parameters included in substitution models can be depicted. To illustrate some of these points, we have applied AICbased model averaging to 37 mitochondrial DNA sequences from the subgenus Ohomopterus (genus Carabus) ground beetles described by Sota and Vogler (2001).
Likelihoodbased tests of topologies in phylogenetics. Syst. Biol
, 2000
"... Abstract.—Likelihoodbased statistical tests of competing evolutionary hypotheses (tree topologies) have been available for approximately a decade. By far the most commonly used is the Kishino–Hasegawa test. However, the assumptions that have to be made to ensure the validity of the Kishino–Hasegawa ..."
Abstract

Cited by 225 (3 self)
 Add to MetaCart
Abstract.—Likelihoodbased statistical tests of competing evolutionary hypotheses (tree topologies) have been available for approximately a decade. By far the most commonly used is the Kishino–Hasegawa test. However, the assumptions that have to be made to ensure the validity of the Kishino–Hasegawa test place important restrictions on its applicability. In particular, it is only valid when the topologies being compared are speci�ed a priori. Unfortunately, this means that the Kishino–Hasegawa test may be severely biased in many cases in which it is now commonly used: for example, in any case in which one of the competing topologies has been selected for testing because it is the maximum likelihood topology for the data set at hand. We review the theory of the Kishino–Hasegawa test and contend that for the majority of popular applications this test should not be used. Previously published results from invalid applications of the Kishino–Hasegawa test should be treated extremely cautiously, and future applications should use appropriate alternative tests instead. We review such alternative tests, both nonparametric and parametric, and give two examples which illustrate the importance of our contentions. [Kishino– Hasegawa test; maximum likelihood; phylogeny; Shimodaira–Hasegawa test; statistical tests; tree topology.] Hasegawa and Kishino (1989) and Kishino and Hasegawa(1989)developed methods for estimating the standard error and con�dence intervals for the difference in loglikelihoods between two topologically distinct phylogenetic trees representing hypotheses that might explain particular aligned sequence data sets. The method initially was introduced to compute con�dence intervals on posterior probabilities for topologies in a
Full reconstruction of Markov models on evolutionary trees: identifiability and consistency
 Math. Biosci
, 1996
"... A Markov model of evolution of characters on a phylogenetic tree consists of a tree topology together with a speci cation of probability transition matrices on the edges of the tree. Previous work has shown that under mild conditions, the tree topology may be reconstructed, in the sense that the top ..."
Abstract

Cited by 114 (1 self)
 Add to MetaCart
(Show Context)
A Markov model of evolution of characters on a phylogenetic tree consists of a tree topology together with a speci cation of probability transition matrices on the edges of the tree. Previous work has shown that under mild conditions, the tree topology may be reconstructed, in the sense that the topology is identi able from knowledge of the joint distribution of character states at pairs of terminal nodes of the tree. Also, the method of maximum likelihood is statistically consistent for inferring the tree topology. In this paper we answer the analogous questions for reconstruction of the full model, including the edge transition matrices: under mild conditions, such full reconstruction is achievable, not by using pairs of terminal nodes, but rather by using triples of terminal nodes. The identi ability result generalizes previous results that were restricted either to characters having two states or to transition matrices having special structure. The proof develops matrix relationships that may be exploited to identify the model. We also use the identi ability result to prove that the method of maximum likelihood is consistent for reconstructing the full model. 1 markov models on evolutionary trees 2 1
Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards
 Syst
, 2005
"... Abstract.Partitioned Bayesian analyses of ∼2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of a ..."
Abstract

Cited by 112 (7 self)
 Add to MetaCart
(Show Context)
Abstract.Partitioned Bayesian analyses of ∼2.2 kb of nucleotide sequence data (mtDNA) were used to elucidate phylogenetic relationships among 30 scincid lizard genera. Few partitioned Bayesian analyses exist in the literature, resulting in a lack of methods to determine the appropriate number of and identity of partitions. Thus, a criterion, based on the Bayes factor, for selecting among competing partitioning strategies is proposed and tested. Improvements in both mean −lnL and estimated posterior probabilities were observed when specific models and parameter estimates were assumed for partitions of the total data set. This result is expected given that the 95% credible intervals of model parameter estimates for numerous partitions do not overlap and it reveals that different data partitions may evolve quite differently. We further demonstrate that how one partitions the data (by gene, codon position, etc.) is shown to be a greater concern than simply the overall number of partitions. Using the criterion of the 2ln Bayes factor >10, the phylogenetic analysis employing the largest number of partitions was decisively better than all other strategies. Strategies that partitioned the ND1 gene by codon position performed better than other partition strategies, regardless of the overall number of partitions. Scincidae, Acontinae, Lygosominae, east Asian and North American "Eumeces" + Neoseps; North African Eumeces, Scincus, and Scincopus, and a large group primarily from subSaharan Africa, Madagascar, and neighboring islands are monophyletic. Feylinia, a limbless group of previously uncertain relationships, is nested within a "scincine" clade from subSaharan Africa. We reject the hypothesis that the nearly limbless dibamids are derived from within the Scincidae, but cannot reject the hypothesis that they represent the sister taxon to skinks. Amphiglossus, Chalcides, the acontines Acontias and Typhlosaurus, and Scincinae are paraphyletic. The globally widespread "Eumeces" is polyphyletic and we make necessary taxonomic changes.
Fast and accurate phylogeny reconstruction algorithms based on the minimumevolution principle
, 2002
"... ..."
Identification of a novel Gammaretrovirus in prostate tumors of patients homozygous for R462Q RNASEL variant. PLoS Pathog 2: e25
, 2006
"... Ribonuclease L (RNase L) is an important effector of the innate antiviral response. Mutations or variants that impair function of RNase L, particularly R462Q, have been proposed as susceptibility factors for prostate cancer. Given the role of this gene in viral defense, we sought to explore the poss ..."
Abstract

Cited by 89 (10 self)
 Add to MetaCart
(Show Context)
Ribonuclease L (RNase L) is an important effector of the innate antiviral response. Mutations or variants that impair function of RNase L, particularly R462Q, have been proposed as susceptibility factors for prostate cancer. Given the role of this gene in viral defense, we sought to explore the possibility that a viral infection might contribute to prostate cancer in individuals harboring the R462Q variant. A viral detection DNA microarray composed of oligonucleotides corresponding to the most conserved sequences of all known viruses identified the presence of gammaretroviral sequences in cDNA samples from seven of 11 R462Qhomozygous (QQ) cases, and in one of eight heterozygous (RQ) and homozygous wildtype (RR) cases. An expanded survey of 86 tumors by specific RTPCR detected the virus in eight of 20 QQ cases (40%), compared with only one sample (1.5%) among 66 RQ and RR cases. The fulllength viral genome was cloned and sequenced independently from three positive QQ cases. The virus, named XMRV, is closely related to xenotropic murine leukemia viruses (MuLVs), but its sequence is clearly distinct from all known members of this group.