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PAML: a program package for phylogenetic analysis by maximum likelihood
- COMPUT APPL BIOSCI 13:555–556
, 1997
"... PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree, the tr ..."
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Cited by 1459 (17 self)
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PAML, currently in version 1.2, is a package of programs for phylogenetic analyses of DNA and protein sequences using the method of maximum likelihood (ML). The programs can be used for (i) maximum likelihood estimation of evolutionary parameters such as branch lengths in a phylogenetic tree, the transition/transversion rate ratio, the shape parameter of the gamma distribution for variable evolutionary rates at sites, and rate parameters for different genes; (ii) likelihood ratio test of hypotheses concerning sequence evolution, such as rate con-stancy and independence among sites and rate constancy among lineages (the molecular clock); (iii) calculation of sub-stitution rates at sites and reconstruction of ancestral nucleo-tide or amino acid sequences; and (iv) phylogenetic tree reconstruction by maximum likelihood and Bayesian methods.
BEAST: Bayesian evolutionary analysis by sampling trees.
- BMC Evol. Biol.
, 2007
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Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution.
- Mol. Biol. Evol.
, 1998
"... An excess of nonsynonymous substitutions over synonymous ones is an important indicator of positive selection at the molecular level. A lineage that underwent Darwinian selection may have a nonsynonymous/synonymous rate ratio (d N /d S ) that is different from those of other lineages or greater tha ..."
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Cited by 309 (17 self)
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An excess of nonsynonymous substitutions over synonymous ones is an important indicator of positive selection at the molecular level. A lineage that underwent Darwinian selection may have a nonsynonymous/synonymous rate ratio (d N /d S ) that is different from those of other lineages or greater than one. In this paper, several codon-based likelihood models that allow for variable d N /d S ratios among lineages were developed. They were then used to construct likelihood ratio tests to examine whether the d N /d S ratio is variable among evolutionary lineages, whether the ratio for a few lineages of interest is different from the background ratio for other lineages in the phylogeny, and whether the d N /d S ratio for the lineages of interest is greater than one. The tests were applied to the lysozyme genes of 24 primate species. The d N /d S ratios were found to differ significantly among lineages, indicating that the evolution of primate lysozymes is episodic, which is incompatible with the neutral theory. Maximum-likelihood estimates of parameters suggested that about nine nonsynonymous and zero synonymous nucleotide substitutions occurred in the lineage leading to hominoids, and the d N /d S ratio for that lineage is significantly greater than one. The corresponding estimates for the lineage ancestral to colobine monkeys were nine and one, and the d N /d S ratio for the lineage is not significantly greater than one, although it is significantly higher than the background ratio. The likelihood analysis thus confirmed most, but not all, conclusions Messier and Stewart reached using reconstructed ancestral sequences to estimate synonymous and nonsynonymous rates for different lineages.
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 non-synonymous (aminoacid -changing) substitution rate
Combining phylogenetic and hidden Markov models in biosequence analysis
- J. Comput. Biol
, 2004
"... 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 individ ..."
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Cited by 135 (13 self)
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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 gene finding, for example, 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-sensitive 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.
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 sub-Saharan Africa, Madagascar, and neighboring islands are monophyletic. Feylinia, a limbless group of previously uncertain relationships, is nested within a "scincine" clade from sub-Saharan 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.
Phylogenetic Tree Construction Using Markov Chain Monte Carlo
, 1999
"... We describe a Bayesian method based on Markov chain simulation to study the phylogenetic relationship in a group of DNA sequences. Under simple models of mutational events, our method produces a Markov chain whose stationary distribution is the conditional distribution of the phylogeny given the obs ..."
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Cited by 86 (0 self)
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We describe a Bayesian method based on Markov chain simulation to study the phylogenetic relationship in a group of DNA sequences. Under simple models of mutational events, our method produces a Markov chain whose stationary distribution is the conditional distribution of the phylogeny given the observed sequences. Our algorithm strikes a reasonable balance between the desire to move globally through the space of phylogenies and the need to make computationally feasible moves in areas of high probability. Since phylogenetic information is described by a tree, we have created new diagnostics to handle this type of data structure. An important by-product of the Markov chain Monte Carlo phylogeny building technique is that it provides estimates and corresponding measures of variability for any aspect of the phylogeny under study.
Asymmetric sequence divergence of duplicate genes. Genome Res.
, 2003
"... Much like humans, gene duplicates may be created equal, but they do not stay that way for long. For four completely sequenced genomes we show that 20%-30% of duplicate gene pairs show asymmetric evolution in the amino acid sequence of their protein products. That is, one of the duplicates evolves m ..."
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Cited by 71 (5 self)
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Much like humans, gene duplicates may be created equal, but they do not stay that way for long. For four completely sequenced genomes we show that 20%-30% of duplicate gene pairs show asymmetric evolution in the amino acid sequence of their protein products. That is, one of the duplicates evolves much faster than the other. The greater this asymmetry, the greater the ratio K a /K s of amino acid substitutions (K a ) to silent substitutions (K s ) in a gene pair. This indicates that most asymmetric divergence may be caused by relaxed selective constraints on one of the duplicates. However, we also find some candidate duplicates where positive (directional) selection of beneficial mutations (K a /K s > 1) may play a role in asymmetric divergence. Our analysis rests on a codon-based model of molecular evolution that allows a test for asymmetric divergence in K a . The method is also more sensitive in detecting positive selection (K a /K s > 1) than models relying only on pairwise gene comparisons. [Supplemental material is available online at www.genome.org. A list of all identified asymmetric duplicate pairs is available at http://www.unm.edu/∼ compbio/Supplemental_Data/Sequence_Asymm.] Gene duplications are an engine of biochemical innovation Mounting evidence indicates that gene duplicates can assume unequal roles in divergence. A study by one of us suggests that gene function, as indicated by protein interactions and gene expression patterns, diverges asymmetrically for many gene duplicates in the yeast S. cerevisiae Previous work on asymmetric sequence divergence relies on relative rate tests between two duplicates and an outgroup gene, using either nucleotide or amino acid substitutions ( Codon-based models of sequence evolution can address questions in both phylogenetics and molecular evolution (for discussion, see
