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233
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 ..."
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Cited by 225 (3 self)
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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
Adaptive Molecular Evolution
 In Balding,D., Bishop,M. and Cannings,C. (eds), Handbook of Statistical Genetics
, 2001
"... INTRODUCTION While Darwin's theory of evolution by natural selection is accepted by biologists for morphological traits, the importance of selection in molecular evolution has been much debated. The neutral theory (Kimura, 1983) maintains that most observed molecular vari ation (both diversit ..."
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Cited by 167 (20 self)
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INTRODUCTION While Darwin's theory of evolution by natural selection is accepted by biologists for morphological traits, the importance of selection in molecular evolution has been much debated. The neutral theory (Kimura, 1983) maintains that most observed molecular vari ation (both diversity within species and divergence between species) is due to random fixation of mutations with fitness effects so small that random drift rather than natural selection dominates their fate. Population geneticists have developed a number of tests of neutrality (see Wayne and Simonsen, 1998, for a review). Those tests often easily reject the strictly neutral model when applied to real data. However, they are often unable to distinguish different forms of natural selection, or to demonstrate molecular adaptation. Up to now, the most convincing evidence of adaptive molecular evolution appears to have come from comparison of synonymous (silent) and nonsynonymous (aminoacid changing) substitution rate
MOLPHY version 2.3: programs for molecular phylogenetics based on maximum likelihood
 Computer Science Monograph
, 1996
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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 ..."
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Cited by 112 (7 self)
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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.
Molecular systematics of the eastern fence lizard (Sceloporus undulatus): A comparison of parsimony, likelihood, and Bayesian approaches
 Syst. Biol
, 2002
"... Abstract.—Phylogenetic analysis of large datasets using complex nucleotide substitution models under a maximum likelihood framework can be computationally infeasible, especially when attempting to infer con�dence values by way of nonparametric bootstrapping. Recent developments in phylogenetics sugg ..."
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Cited by 91 (8 self)
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Abstract.—Phylogenetic analysis of large datasets using complex nucleotide substitution models under a maximum likelihood framework can be computationally infeasible, especially when attempting to infer con�dence values by way of nonparametric bootstrapping. Recent developments in phylogenetics suggest the computational burden can be reduced by using Bayesian methods of phylogenetic inference. However, few empirical phylogenetic studies exist that explore the ef�ciency of Bayesian analysis of large datasets. To this end, we conducted an extensive phylogenetic analysis of the wideranging and geographically variable Eastern Fence Lizard (Sceloporus undulatus). Maximum parsimony, maximum likelihood, and Bayesian phylogenetic analyses were performed on a combined mitochondrial DNA dataset (12S and 16S rRNA, ND1 proteincoding gene, and associated tRNA; 3,688 bp total) for 56 populations of S. undulatus (78 total terminals including other S. undulatus group species and outgroups). Maximum parsimony analysis resulted in numerous equally parsimonious trees (82,646 from equally weighted parsimony and 335 from weighted parsimony). The majority rule consensus tree derived from the Bayesian analysis was topologically identical to the single best phylogeny inferred from the maximum likelihood analysis, but required �80 % less computational time. The mtDNA data provide strong support for the monophyly of the S. undulatus group and
Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference. Bioinformatics
, 2004
"... Motivation: Bayesian estimation of phylogeny is based on the posterior probability distribution of trees. Currently, the only numerical method that can effectively approximate posterior probabilities of trees is Markov chain Monte Carlo (MCMC). Standard implementations of MCMC can be prone to entrap ..."
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Cited by 73 (0 self)
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Motivation: Bayesian estimation of phylogeny is based on the posterior probability distribution of trees. Currently, the only numerical method that can effectively approximate posterior probabilities of trees is Markov chain Monte Carlo (MCMC). Standard implementations of MCMC can be prone to entrapment in local optima. Metropolis coupled MCMC [(MC) 3], a variant of MCMC, allows multiple peaks in the landscape of trees to be more readily explored, but at the cost of increased execution time. Results: This paper presents a parallel algorithm for (MC) 3. The proposed parallel algorithm retains the ability to explore multiple peaks in the posterior distribution of trees while maintaining a fast execution time. The algorithm has been implemented using two popular parallel programming models: message passing and shared memory. Performance results indicate nearly linear speed improvement in both programming models for small and large data sets. Availability: MrBayes v3.0 is available at
Inferring Speciation Times under an Episodic Molecular Clock
, 2007
"... We extend our recently developed Markov chain Monte Carlo algorithm for Bayesian estimation of species divergence times to allow variable evolutionary rates among lineages. The method can use heterogeneous data from multiple gene loci and accommodate multiple fossil calibrations. Uncertainties in f ..."
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Cited by 66 (18 self)
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We extend our recently developed Markov chain Monte Carlo algorithm for Bayesian estimation of species divergence times to allow variable evolutionary rates among lineages. The method can use heterogeneous data from multiple gene loci and accommodate multiple fossil calibrations. Uncertainties in fossil calibrations are described using flexible statistical distributions. The prior for divergence times for nodes lacking fossil calibrations is specified by use of a birthdeath process with species sampling. The prior for lineagespecific substitution rates is specified using either a model with autocorrelated rates among adjacent lineages (based on a geometric Brownian motion model of rate drift) or a model with independent rates among lineages specified by a lognormal probability distribution. We develop an infinitesites theory, which predicts that when the amount of sequence data approaches infinity, the width of the posterior credibility interval and the posterior mean of divergence times form a perfect linear relationship, with the slope indicating uncertainties in time estimates that cannot be reduced by sequence data alone. Simulations are used to study the influence of amonglineage rate variation and the number of loci sampled on the uncertainty of divergence time estimates. The analysis suggests that posterior time estimates typically involve considerable uncertainties even with an infinite amount of sequence data, and that the reliability and precision of fossil calibrations are critically important to divergence time estimation. We apply our new algorithms to two empirical data sets and compare the results with those obtained in previous Bayesian and likelihood analyses. The results demonstrate the utility of our new algorithms.
Improved pairwise alignment of genomic DNA
, 2007
"... Graduate School iii Advances in DNA sequencing technology have fueled a rapid increase in the number of sequenced vertebrate genomes, and we anticipate an explosion in the number of genomes sequenced in the near future. Detecting similarities between genomes is a valuable technique in discovering fu ..."
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Cited by 65 (0 self)
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Graduate School iii Advances in DNA sequencing technology have fueled a rapid increase in the number of sequenced vertebrate genomes, and we anticipate an explosion in the number of genomes sequenced in the near future. Detecting similarities between genomes is a valuable technique in discovering functional elements, and sequence alignment is the primary tool for discovering similarities. The quality of alignments is affected by several userspecified control parameters. The parameters are so little understood that most users simply use default settings. We seek to change that, to have the program automatically infer appropriate parameter choices from statistics derived automatically from the sequences. We introduce a program, INFERZ, which addresses part of the inference problem, inferring substitution and gap scores according to a mathematically sound model. Further, we explore the usefulness of iterating inferred scores to convergence. We test this process on both simulated and actual genomic data, and show that iteration will converge in