Maximum-likelihood models for combined analyses of multiple sequence data

Yang, Ziheng

doi:10.1007/bf02352289

Cited by 382 publications

(241 citation statements)

References 28 publications

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“…Our approach should not be confused with the dN/dS test, which seeks to identify sequence sites under positive selection (Yang, 1996). Unlike the dN/dS test, our application of the Fisher's exact test does not enable conclusions to be drawn about the strength of selection (Mugal, Wolf, & Kaj, 2014).…”

Section: Discussionmentioning

confidence: 99%

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

et al. 2017

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Ribulose 1,5‐bisphosphate (RuBP) carboxylase/oxygenase (RuBisCO, or Rubisco) catalyzes a key reaction by which inorganic carbon is converted into organic carbon in the metabolism of many aerobic and anaerobic organisms. Across the broader Rubisco protein family, homologs exhibit diverse biochemical characteristics and metabolic functions, but the evolutionary origins of this diversity are unclear. Evidence of the timing of Rubisco family emergence and diversification of its different forms has been obscured by a meager paleontological record of early Earth biota, their subcellular physiology and metabolic components. Here, we use computational models to reconstruct a Rubisco family phylogenetic tree, ancestral amino acid sequences at branching points on the tree, and protein structures for several key ancestors. Analysis of historic substitutions with respect to their structural locations shows that there were distinct periods of amino acid substitution enrichment above background levels near and within its oxygen‐sensitive active site and subunit interfaces over the divergence between Form III (associated with anoxia) and Form I (associated with oxia) groups in its evolutionary history. One possible interpretation is that these periods of substitutional enrichment are coincident with oxidative stress exerted by the rise of oxygenic photosynthesis in the Precambrian era. Our interpretation implies that the periods of Rubisco substitutional enrichment inferred near the transition from anaerobic Form III to aerobic Form I ancestral sequences predate the acquisition of Rubisco by fully derived cyanobacterial (i.e., dual photosystem‐bearing, oxygen‐evolving) clades. The partitioning of extant lineages at high clade levels within our Rubisco phylogeny indicates that horizontal transfer of Rubisco is a relatively infrequent event. Therefore, it is possible that the mutational enrichment periods between the Form III and Form I common ancestral sequences correspond to the adaptation of key oxygen‐sensitive components of Rubisco prior to, or coincident with, the Great Oxidation Event.

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Section: Discussionmentioning

confidence: 99%

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

et al. 2017

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“…It may be noted that the site-homogeneous algorithm is used for models that assume different substitution parameters for prior partitions of sites in the sequence. Examples include models of Yang (1996b), which assume different rates and transition/transversion rate ratios for the three codon positions. As we know a priori which codon position each site is from, those models are computationally different from the site-class models.…”

Section: Estimation Of Branch Lengths Under Site-class Modelsmentioning

confidence: 99%

“…Thus the branch length in the codon model is approximated by the sum of branch lengths at the three codon positions. Here I use a nucleotide model of Yang (1996b) that accounts for different substitution rates, base frequencies, and transition/transversion rate ratios at the three codon positions (BASEML, Mgene ‫ס‬ 4 in PAML). This model is very close to the codon model of Goldman and Yang (1994).…”

Section: Approximate Branch Lengths Under Models Of Codon Substitutionmentioning

confidence: 99%

“…The exact ML calculation and two approximate methods are used. The approximate methods calculate branch lengths either from pairwise estimates of d S and d N using the NG method (Nei and Gojobori 1986), or from a nucleotidebased analysis using the model of Yang (1996b). Apart from the way the branch lengths are obtained, there is no difference between the exact and approximate methods.…”

Section: Sequence Data and Analysismentioning

confidence: 99%

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Maximum Likelihood Estimation on Large Phylogenies and Analysis of Adaptive Evolution in Human Influenza Virus A

2000

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Abstract. Algorithmic details to obtain maximum likelihood estimates of parameters on a large phylogeny are discussed. On a large tree, an efficient approach is to optimize branch lengths one at a time while updating parameters in the substitution model simultaneously. Codon substitution models that allow for variable nonsynonymous/synonymous rate ratios ( ‫ס‬ d N /d S ) among sites are used to analyze a data set of human influenza virus type A hemagglutinin (HA) genes. The data set has 349 sequences. Methods for obtaining approximate estimates of branch lengths for codon models are explored, and the estimates are used to test for positive selection and to identify sites under selection. Compared with results obtained from the exact method estimating all parameters by maximum likelihood, the approximate methods produced reliable results. The analysis identified a number of sites in the viral gene under diversifying Darwinian selection and demonstrated the importance of including many sequences in the data in detecting positive selection at individual sites.

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“…The nucleotide substitution rates at the three codon positions in the cytochrome b genes are in the proportion 1:0.26:10.23, estimated by a likelihood model that accounts for different rates at the three positions (Yang 1996). The base frequencies and apparent ti/tv rate biases are also quite different at the three codon positions (Yoder et al 1996b).…”

Section: Variation Of Evolutionary Rates Among Codon Positions or Nucmentioning

confidence: 99%

Estimation of the Transition/Transversion Rate Bias and Species Sampling

1999

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Abstract. The transition/transversion (ti/tv) rate ratios are estimated by pairwise sequence comparison and joint likelihood analysis using mitochondrial cytochrome b genes of 28 primate species, representing both the Strepsirrhini (lemurs and lories) and the Anthropoidea (monkeys, apes, and humans). Pairwise comparison reveals a strong negative correlation between estimates of the ti/tv ratio and the sequence distance, even when both are corrected for multiple substitutions. The maximumlikelihood estimate of the ti/tv ratio changes with the species included in the analysis. The ti/tv bias within the lemuriform taxa is found to be as strong as in the anthropoids, in contradiction to an earlier study which sampled only one lemuriform. Simulations show the surprising result that both the pairwise correction method and the joint likelihood analysis tend to overcorrect for multiple substitutions and overestimate the ti/tv ratio, especially at low sequence divergence. The bias, however, is not large enough to account for the observed patterns. Nucleotide frequency biases, variation of substitution rates among sites, and different evolutionary dynamics at the three codon positions can be ruled out as possible causes. The likelihood-ratio test suggests that the ti/tv rate ratios may be variable among evolutionary lineages. Without any biological evidence for such a variation, however, we are left with no plausible explanations for the observed patterns other than a possible saturation effect due to the unrealistic nature of the model assumed.

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Maximum-likelihood models for combined analyses of multiple sequence data

Cited by 382 publications

References 28 publications

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

Constraining the timing of the Great Oxidation Event within the Rubisco phylogenetic tree

Maximum Likelihood Estimation on Large Phylogenies and Analysis of Adaptive Evolution in Human Influenza Virus A

Estimation of the Transition/Transversion Rate Bias and Species Sampling

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