Ziheng Yang

Summary

Affiliation: University College London
Country: UK

Publications

  1. doi request reprint Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors
    Ralph Burgess
    Galton Laboratory, Department of Biology, University College London, London, United Kingdom
    Mol Biol Evol 25:1979-94. 2008
  2. doi request reprint Phylogenetic inference using whole genomes
    Bruce Rannala
    Genome Center and Department of Evolution and Ecology, University of California, Davis, California 95616, USA
    Annu Rev Genomics Hum Genet 9:217-31. 2008
  3. doi request reprint Molecular phylogenetics: principles and practice
    Ziheng Yang
    Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    Nat Rev Genet 13:303-14. 2012
  4. pmc Rate variation and estimation of divergence times using strict and relaxed clocks
    Richard P Brown
    School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool L3 3AF, UK
    BMC Evol Biol 11:271. 2011
  5. pmc Unusual conservation among genes encoding small secreted salivary gland proteins from a gall midge
    Ming Shun Chen
    USDA ARS, Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
    BMC Evol Biol 10:296. 2010
  6. pmc A likelihood ratio test of speciation with gene flow using genomic sequence data
    Ziheng Yang
    Galton Laboratory, Department of Biology, University College London, United Kingdom
    Genome Biol Evol 2:200-11. 2010
  7. pmc Empirical evaluation of a prior for Bayesian phylogenetic inference
    Ziheng Yang
    Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
    Philos Trans R Soc Lond B Biol Sci 363:4031-9. 2008
  8. ncbi request reprint Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes
    Ziheng Yang
    Galton Laboratory, Department of Biology, University College London, 4 Stephenson Way, London NW1 2HE, UK
    Mol Biol Evol 19:49-57. 2002
  9. doi request reprint Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage
    Ziheng Yang
    Department of Biology, Galton Laboratory, University College London, London, United Kingdom
    Mol Biol Evol 25:568-79. 2008
  10. ncbi request reprint Fair-balance paradox, star-tree paradox, and Bayesian phylogenetics
    Ziheng Yang
    Department of Biology, Galton Laboratory, University College London, London, UK
    Mol Biol Evol 24:1639-55. 2007

Collaborators

Detail Information

Publications93

  1. doi request reprint Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors
    Ralph Burgess
    Galton Laboratory, Department of Biology, University College London, London, United Kingdom
    Mol Biol Evol 25:1979-94. 2008
    ....
  2. doi request reprint Phylogenetic inference using whole genomes
    Bruce Rannala
    Genome Center and Department of Evolution and Ecology, University of California, Davis, California 95616, USA
    Annu Rev Genomics Hum Genet 9:217-31. 2008
    ..Genomic datasets provide computational and statistical challenges that are likely to be a focus of research for years to come...
  3. doi request reprint Molecular phylogenetics: principles and practice
    Ziheng Yang
    Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    Nat Rev Genet 13:303-14. 2012
    ..Here, we review the major methods of phylogenetic analysis, including parsimony, distance, likelihood and Bayesian methods. We discuss their strengths and weaknesses and provide guidance for their use...
  4. pmc Rate variation and estimation of divergence times using strict and relaxed clocks
    Richard P Brown
    School of Natural Sciences and Psychology, Liverpool John Moores University, Liverpool L3 3AF, UK
    BMC Evol Biol 11:271. 2011
    ....
  5. pmc Unusual conservation among genes encoding small secreted salivary gland proteins from a gall midge
    Ming Shun Chen
    USDA ARS, Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan, KS 66506, USA
    BMC Evol Biol 10:296. 2010
    ....
  6. pmc A likelihood ratio test of speciation with gene flow using genomic sequence data
    Ziheng Yang
    Galton Laboratory, Department of Biology, University College London, United Kingdom
    Genome Biol Evol 2:200-11. 2010
    ..The test is applied to genomic data from the human, chimpanzee, and gorilla...
  7. pmc Empirical evaluation of a prior for Bayesian phylogenetic inference
    Ziheng Yang
    Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
    Philos Trans R Soc Lond B Biol Sci 363:4031-9. 2008
    ..This prior may be useful in reducing apparent conflicts in the results of Bayesian analysis or in making the method less sensitive to model violations...
  8. ncbi request reprint Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes
    Ziheng Yang
    Galton Laboratory, Department of Biology, University College London, 4 Stephenson Way, London NW1 2HE, UK
    Mol Biol Evol 19:49-57. 2002
    ..The analysis demonstrates the utility of the fixed-sites models, as well as the power of previous random-sites models, which do not use the prior information to partition sites...
  9. doi request reprint Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage
    Ziheng Yang
    Department of Biology, Galton Laboratory, University College London, London, United Kingdom
    Mol Biol Evol 25:568-79. 2008
    ..Estimates of selection coefficients nevertheless suggest that selection on codon usage is weak and most mutations are nearly neutral. The sensitivity of the analysis on the assumed mutation model is discussed...
  10. ncbi request reprint Fair-balance paradox, star-tree paradox, and Bayesian phylogenetics
    Ziheng Yang
    Department of Biology, Galton Laboratory, University College London, London, UK
    Mol Biol Evol 24:1639-55. 2007
    ..Both appear to be effective in resolving the paradox, but the latter is simpler to implement. The posterior tree probabilities are found to be very sensitive to the prior...
  11. ncbi request reprint PAML 4: phylogenetic analysis by maximum likelihood
    Ziheng Yang
    Department of Biology, Galton Laboratory, University College London, London, UK
    Mol Biol Evol 24:1586-91. 2007
    ..The package is written in ANSI C, and runs under Windows, Mac OSX, and UNIX systems. It is available at -- (http://abacus.gene.ucl.ac.uk/software/paml.html)...
  12. ncbi request reprint Inference of selection from multiple species alignments
    Ziheng Yang
    Galton Laboratory, Department of Biology, University College London, Darwin Building, Gower Street, WC1E 6BT, London, UK
    Curr Opin Genet Dev 12:688-94. 2002
    ..Their application has led to detection of adaptive Darwinian selection in a number of genes and organisms...
  13. pmc Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci
    Ziheng Yang
    Galton Laboratory, Department of Biology, University College London, London WC1E 6BT, England
    Genetics 162:1811-23. 2002
    ..1-1.7 million years earlier. The analysis suggests that typical data sets contain useful information about the ancestral population sizes and that it is advantageous to analyze data of several species simultaneously...
  14. ncbi request reprint On the varied pattern of evolution of 2 fungal genomes: a critique of Hughes and Friedman
    Ziheng Yang
    Department of Biology, University College London, London, United Kingdom
    Mol Biol Evol 23:2279-82. 2006
    ..I also apply likelihood ratio tests of positive selection to the yeast data and illustrate empirically that Hughes and Friedman's criticisms on such tests are not valid...
  15. ncbi request reprint Branch-length prior influences Bayesian posterior probability of phylogeny
    Ziheng Yang
    Department of Biology, University College London, Darwin Building, Gower Street London WC1E 6BT, United Kingdom
    Syst Biol 54:455-70. 2005
    ....
  16. ncbi request reprint Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene Loci and calibration points, with application to a radiation of cute-looking mouse lemur species
    Ziheng Yang
    Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, United Kingdom
    Syst Biol 52:705-16. 2003
    ..The divergence of the mouse lemurs is dated to be around 7-10 million years ago, indicating a surprisingly early species radiation for such a morphologically uniform group of primates...
  17. pmc The power of phylogenetic comparison in revealing protein function
    Ziheng Yang
    Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, England
    Proc Natl Acad Sci U S A 102:3179-80. 2005
  18. ncbi request reprint Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    Ziheng Yang
    Galton Laboratory, Department of Biology, University College London
    Mol Biol Evol 19:908-17. 2002
    ..Additional tests on several data sets suggest that the new models may be useful in detecting positive selection after gene duplication in gene family evolution...
  19. doi request reprint Statistical properties of the branch-site test of positive selection
    Ziheng Yang
    Department of Genetics, Evolution and Environment, University College London, United Kingdom
    Mol Biol Evol 28:1217-28. 2011
    ..The test is sensitive to sequence and alignment errors and caution should be exercised concerning its use when data quality is in doubt...
  20. ncbi request reprint Synonymous and nonsynonymous rate variation in nuclear genes of mammals
    Z Yang
    Department of Integrative Biology, University of California, Berkeley, 94720 3140, USA
    J Mol Evol 46:409-18. 1998
    ..The likelihood approach is preferable, even for pairwise sequence comparison, because more realistic models about the mutation and substitution processes can be incorporated in the analysis...
  21. ncbi request reprint Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    Z Yang
    Department of Biology, University College, London, United Kingdom
    Mol Biol Evol 15:568-73. 1998
    ..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...
  22. ncbi request reprint Models of amino acid substitution and applications to mitochondrial protein evolution
    Z Yang
    Department of Biology Galton Laboratory, University College London, England
    Mol Biol Evol 15:1600-11. 1998
    ..Rates of amino acid substitution were found to be highly variable among sites...
  23. ncbi request reprint Estimation of the transition/transversion rate bias and species sampling
    Z Yang
    Department of Biology Galton Laboratory, University College London, England
    J Mol Evol 48:274-83. 1999
    ..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...
  24. ncbi request reprint Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
    Z Yang
    Department of Biology, University College London, England
    Mol Biol Evol 17:32-43. 2000
    ..The new method is, in general, superior to earlier approximate methods and may be useful for analyzing large data sets, although maximum likelihood appears to always be the method of choice...
  25. pmc Complexity of the simplest phylogenetic estimation problem
    Z Yang
    Department of Biology Galton Laboratory, University College London, UK
    Proc Biol Sci 267:109-16. 2000
    ..The solution to this real phylogeny estimation problem will be useful for studying the problem of significance evaluation...
  26. pmc Codon-substitution models for heterogeneous selection pressure at amino acid sites
    Z Yang
    Department of Biology, University College London, London NW1 2HE, United Kingdom
    Genetics 155:431-49. 2000
    ..However, we encountered difficulties in estimating the precise distribution of omega among sites from real data sets...
  27. ncbi request reprint Maximum-likelihood analysis of molecular adaptation in abalone sperm lysin reveals variable selective pressures among lineages and sites
    Z Yang
    Galton Laboratory, Department of Biology, University College London, London, England
    Mol Biol Evol 17:1446-55. 2000
    ..Sites under potential diversifying selection were identified. Ancestral lysins were inferred to trace the route of evolution at individual sites and to provide lysin sequences for future laboratory studies...
  28. ncbi request reprint Evolutionary rate variation among vertebrate beta globin genes: implications for dating gene family duplication events
    Gabriela Aguileta
    University College London, Department of Biology, Darwin Building, Gower Street, London WC1E 6BT, England
    Gene 380:21-9. 2006
    ..Lastly, phylogenetic analyses do not support a previous report that avian globins are members of a relic lineage of omega globins...
  29. ncbi request reprint A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution
    Joseph P Bielawski
    Department of Biology, University College London, London, WC1E 6BT, UK
    J Mol Evol 59:121-32. 2004
    ..Limitations of the new method are discussed...
  30. ncbi request reprint Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa
    Stephane Aris-Brosou
    Department of Biology, University College London, England
    Mol Biol Evol 20:1947-54. 2003
    ..We stress the importance of assumptions about rates on date estimation and suggest that the large discrepancies between the molecular and fossil dates of metazoan divergences might partly be due to biases in molecular date estimation...
  31. ncbi request reprint Gene conversion and functional divergence in the beta-globin gene family
    Gabriela Aguileta
    Department of Biology, University College London, Darwin Building, Gower Street, WC1E 6BT, London, England
    J Mol Evol 59:177-89. 2004
    ..Overall, our results suggest that following gene duplications, paralogous copies of beta-globin genes evolved under a nonepisodic process of functional divergence...
  32. ncbi request reprint Molecular evolution of the hepatitis delta virus antigen gene: recombination or positive selection?
    Maria Anisimova
    Department of Biology, University College London, London WC1E 6BT, UK
    J Mol Evol 59:815-26. 2004
    ..Possible interplay between positive selection and recombination on the gene is discussed but no significant evidence for recombination was found...
  33. doi request reprint Approximate likelihood calculation on a phylogeny for Bayesian estimation of divergence times
    Mario dos Reis
    Department of Biology, University College London, Darwin Building, Gower Street, London, United Kingdom
    Mol Biol Evol 28:2161-72. 2011
    ..The results suggest that the approximate method may be useful for Bayesian dating analysis using large data sets...
  34. pmc Improved reversible jump algorithms for Bayesian species delimitation
    Bruce Rannala
    Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    Genetics 194:245-53. 2013
    ..The new algorithms are found to improve mixing of the Markov chain for both simulated and empirical data sets...
  35. pmc Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny
    Mario dos Reis
    Department of Genetics, Evolution and Environment, University College London, Darwin Building, Gower Street, London, UK
    Proc Biol Sci 279:3491-500. 2012
    ..Therefore we reject a pre K-Pg model of placental ordinal diversification. We suggest other infamous instances of mismatch between molecular and palaeontological divergence time estimates will be resolved with this same approach...
  36. pmc Bayesian species delimitation using multilocus sequence data
    Ziheng Yang
    Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    Proc Natl Acad Sci U S A 107:9264-9. 2010
    ..The statistical performance of the method is examined using simulations, and the method is illustrated by analyzing sequence data from rotifers, fence lizards, and human populations...
  37. doi request reprint The impact of the representation of fossil calibrations on Bayesian estimation of species divergence times
    Jun Inoue
    Department of Biology, Galton Laboratory, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
    Syst Biol 59:74-89. 2010
    ....
  38. ncbi request reprint Bayesian estimation of species divergence times under a molecular clock using multiple fossil calibrations with soft bounds
    Ziheng Yang
    Department of Biology, University College London, London, United Kingdom
    Mol Biol Evol 23:212-26. 2006
    ..4) Soft bounds allow more reliable assessment of estimation errors, while hard bounds generate misleadingly high precisions when fossils and molecules are in conflict...
  39. ncbi request reprint Looking for Darwin in genomic sequences--validity and success of statistical methods
    Weiwei Zhai
    Center for Computational Biology and Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China
    Mol Biol Evol 29:2889-93. 2012
    ..Our analyses suggest that codon-based tests are useful tools for comparative analysis of genomic data sets...
  40. doi request reprint Tail paradox, partial identifiability, and influential priors in Bayesian branch length inference
    Bruce Rannala
    Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
    Mol Biol Evol 29:325-35. 2012
    ..Our analysis highlights the need for careful thought in the specification of high-dimensional priors in Bayesian analyses...
  41. ncbi request reprint Maximum likelihood methods for detecting adaptive evolution after gene duplication
    Joseph P Bielawski
    Department of Biology, University College London, Darwin Building, Gower Street, London WCIE 6BT, United Kingdom
    J Struct Funct Genomics 3:201-12. 2003
    ..We also comment on the limitations of these methods and discuss directions for further improvements...
  42. ncbi request reprint Inferring speciation times under an episodic molecular clock
    Bruce Rannala
    Genome Center and Section of Evolution and Ecology, University of California, Davis, California, USA
    Syst Biol 56:453-66. 2007
    ..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...
  43. ncbi request reprint Robustness of compound Dirichlet priors for Bayesian inference of branch lengths
    Chi Zhang
    Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
    Syst Biol 61:779-84. 2012
    ..Our results suggest that the compound Dirichlet priors may be useful for correcting branch-length overestimation in phylogenetic analyses of empirical data sets...
  44. pmc The role of positive selection in determining the molecular cause of species differences in disease
    Jessica J Vamathevan
    1Department of Biology, University College London, Darwin Bldg, Gower Street, London WC1E 6BT, UK
    BMC Evol Biol 8:273. 2008
    ..Thus we investigate whether biomedical disease differences between species can be attributed to positively selected genes...
  45. ncbi request reprint Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny
    Stephane Aris-Brosou
    Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, England
    Syst Biol 51:703-14. 2002
    ..Estimates of the rates were in accordance with the Cambrian explosion hypothesis and suggested some more recent lineage-specific bursts of evolution...
  46. pmc Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
    Maria Anisimova
    Department of Biology, University College London, London WC1E 6BT, United Kingdom
    Genetics 164:1229-36. 2003
    ..Identification of sites under positive selection by the empirical Bayes method appears to be less affected than the LRT by recombination...
  47. pmc Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    R Nielsen
    Department of Integrative Biology, University of California, Berkeley 94720 3140, USA
    Genetics 148:929-36. 1998
    ..Positively selected sites are found in both the V3 region and the flanking regions...
  48. doi request reprint Multilocus estimation of divergence times and ancestral effective population sizes of Oryza species and implications for the rapid diversification of the genus
    Xin Hui Zou
    State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
    New Phytol 198:1155-64. 2013
    ..Such information helps better understand the evolutionary history of Oryza and provides further insights into the pattern and mechanism of diversification in plants in general...
  49. ncbi request reprint Widespread adaptive evolution in the human immunodeficiency virus type 1 genome
    Wa Yang
    Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK
    J Mol Evol 57:212-21. 2003
    ..Furthermore, amino acid residues at exposed positive selection sites were more physiochemically diverse than at buried positive selection sites. Our results demonstrate genomewide diversifying selection acting on the HIV-1...
  50. doi request reprint The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection
    William Fletcher
    Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
    Mol Biol Evol 27:2257-67. 2010
    ..Our examination of two previous studies suggests that alignment errors may impact the analysis of mammalian and vertebrate genes by the branch-site test, and it is important to use reliable alignment methods...
  51. ncbi request reprint Multiple hypothesis testing to detect lineages under positive selection that affects only a few sites
    Maria Anisimova
    Department of Biology, University College London, London, UK
    Mol Biol Evol 24:1219-28. 2007
    ..Both our simulation and real data analysis suggest that the multiple test procedures are useful when multiple branches have to be tested on the same data set...
  52. pmc Searching for efficient Markov chain Monte Carlo proposal kernels
    Ziheng Yang
    Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, United Kingdom
    Proc Natl Acad Sci U S A 110:19307-12. 2013
    ..Our results refute a previous claim that all proposals had nearly identical performance and will prompt further research into efficient MCMC proposals. ..
  53. doi request reprint Dating phylogenies with sequentially sampled tips
    Tanja Stadler
    Institut für Integrative Biologie, Eidgenössiche Technische Hochschule Zurich, 8092 Zurich, Switzerland Department of Biology, University College London, London WC1E 6BT, UK
    Syst Biol 62:674-88. 2013
    ..We found posterior time estimates for old nodes to be sensitive to the priors on times and rates and suggest that previous Bayesian dating studies may have produced overconfident estimates...
  54. ncbi request reprint Bayes empirical bayes inference of amino acid sites under positive selection
    Ziheng Yang
    Department of Biology, University College London, London, UK
    Mol Biol Evol 22:1107-18. 2005
    ..The results suggest that in small data sets the new BEB method does not generate false positives as did the old NEB approach, while in large data sets it retains the good power of the NEB approach for inferring positively selected sites...
  55. doi request reprint Bayesian relaxed clock estimation of divergence times in foraminifera
    Mathieu Groussin
    Galton Laboratory, Department of Biology, University College London, London WC1E 6BT, England, United Kingdom
    Mol Phylogenet Evol 61:157-66. 2011
    ..However, more coding genes appear necessary to obtain more precise estimates of divergence times and to resolve the conflicts between fossil and molecular date estimates...
  56. pmc Phylogenomic analysis of natural selection pressure in Streptococcus genomes
    Maria Anisimova
    Department of Biology, University College London, London, UK
    BMC Evol Biol 7:154. 2007
    ..The genus Streptococcus is comprised of a wide variety of both pathogenic and commensal lineages, and we relate our findings to the pre-existing knowledge of Streptococcus virulence factors...
  57. ncbi request reprint Proposed standard nomenclature for the alpha- and beta-globin gene families
    Gabriela Aguileta
    Department of Biology, University College London, London, England
    Genes Genet Syst 81:367-71. 2006
    ....
  58. pmc INDELible: a flexible simulator of biological sequence evolution
    William Fletcher
    Department of Genetics, Evolution and Environment and Centre for Mathematics and Physics in the Life Sciences and Experimental Biology, University College London, London, UK
    Mol Biol Evol 26:1879-88. 2009
    ....
  59. doi request reprint Diversifying and purifying selection in the peptide binding region of DRB in mammals
    Rebecca F Furlong
    Department of Biology, University College London, Darwin Building, Gower Street, London, WC1E 6BT, UK
    J Mol Evol 66:384-94. 2008
    ....
  60. ncbi request reprint Positive and negative selection in the DAZ gene family
    J P Bielawski
    Department of Biology, Galton Laboratory, University College London, England
    Mol Biol Evol 18:523-9. 2001
    ..Lineage-specific analysis indicated that human members of this gene family were evolving by positive Darwinian selection, although the evidence was not strong...
  61. pmc Substitution rates in Drosophila nuclear genes: implications for translational selection
    K A Dunn
    Department of Biology, Galton Laboratory, University College, London NW1 2HE, United Kingdom
    Genetics 157:295-305. 2001
    ..Implications of the results for translational selection are discussed...
  62. ncbi request reprint Molecular adaptation of alanine:glyoxylate aminotransferase targeting in primates
    J D Holbrook
    MRC Laboratory for Molecular Cell Biology, University College London, England, United Kingdom
    Mol Biol Evol 17:387-400. 2000
    ....
  63. pmc Rates of nucleotide substitution and mammalian nuclear gene evolution. Approximate and maximum-likelihood methods lead to different conclusions
    J P Bielawski
    Department of Biology, University College London, London NW1 2HE, United Kingdom
    Genetics 156:1299-308. 2000
    ..Failure to properly account for transition/transversion rate bias and unequal codon usage appears to have caused substantial biases in approximate estimates of substitution rates...
  64. ncbi request reprint Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution
    M Anisimova
    Department of Biology, Galton Laboratory, University College London, London, England
    Mol Biol Evol 18:1585-92. 2001
    ..The exact distribution assumed for the omega ratio over sites was found not to affect the effectiveness of the LRT...
  65. doi request reprint Evaluation of a bayesian coalescent method of species delimitation
    Chi Zhang
    Center for Computational and Evolutionary Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
    Syst Biol 60:747-61. 2011
    ....
  66. ncbi request reprint Accuracy and power of bayes prediction of amino acid sites under positive selection
    Maria Anisimova
    Department of Biology, Galton Laboratory, University College London, United Kingdom
    Mol Biol Evol 19:950-8. 2002
    ....
  67. doi request reprint Neither phylogenomic nor palaeontological data support a Palaeogene origin of placental mammals
    Mario dos Reis
    Department of Genetics, Evolution and Environment, University College London, Gower St, London WC1E 6BT, UK
    Biol Lett 10:20131003. 2014
    ..Our combined analysis of fossils and molecules demonstrates that Placentalia originated in the Cretaceous. ..
  68. ncbi request reprint Host-symbiont conflicts: positive selection on an outer membrane protein of parasitic but not mutualistic Rickettsiaceae
    Francis M Jiggins
    Department of Genetics, University of Cambridge, United Kingdom
    Mol Biol Evol 19:1341-9. 2002
    ..The regions of the wsp and map1 genes we identified as likely to be involved in host-parasite arms races should be examined in future studies of parasite virulence and host immune responses, and during the design of vaccines...
  69. pmc Why do more divergent sequences produce smaller nonsynonymous/synonymous rate ratios in pairwise sequence comparisons?
    Mario dos Reis
    Department of Genetics, Evolution, and Environment, University College London, London, WC1E 6BT, United Kingdom
    Genetics 195:195-204. 2013
    ..We point out that tests of positive selection based on the ω ratio are invariant to the parameterization of the model and thus unaffected by bias in the ω estimates or the correlation between estimates of ω and d. ..
  70. pmc Statistical properties of a DNA sample under the finite-sites model
    Z Yang
    Department of Integrative Biology, University of California, Berkeley 94720 3140, USA
    Genetics 144:1941-50. 1996
    ....
  71. ncbi request reprint Direct activation of cloned K(atp) channels by intracellular acidosis
    H Xu
    Department of Biology, Georgia State University, Atlanta, Georgia 30302 4010, USA
    J Biol Chem 276:12898-902. 2001
    ..The pH-dependent activation may enable the K(ATP) to control vascular tones, insulin secretion, and neuronal excitability in several pathophysiologic conditions...
  72. ncbi request reprint A new set of chemotaxis homologues is essential for Myxococcus xanthus social motility
    Z Yang
    School of Dentistry, Molecular Biology Institute, University of California, Los Angeles 90095 1668, USA
    Mol Microbiol 30:1123-30. 1998
    ..xanthus dif locus is required for social (S) motility. This is the first report of a M. xanthus chemotaxis-like signal transduction pathway that could regulate or co-ordinate the movement of M. xanthus cells to bring about S motility...
  73. pmc Kinesin-II is required for axonal transport of choline acetyltransferase in Drosophila
    K Ray
    Howard Hughes Medical Institute, Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093 0683, USA
    J Cell Biol 147:507-18. 1999
    ..Furthermore, the data lead to the conclusion that the cargo transport requirements of different classes of neurons may lead to upregulation of specific pathways of axonal transport...
  74. ncbi request reprint Crystal structure of native chicken fibrinogen at 2.7 A resolution
    Z Yang
    Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093 0634, USA
    Biochemistry 40:12515-23. 2001
    ..It is concluded that structural flexibility is an inherent feature of fibrinogen that plays a key role in both its conversion to fibrin and its subsequent destruction by plasmin...
  75. ncbi request reprint Regulation of two key nuclear enzymatic activities by the 7SK small nuclear RNA
    W J He
    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
    Cold Spring Harb Symp Quant Biol 71:301-11. 2006
    ..The demonstration of 7SK's suppression of yet another enzyme besides P-TEFb suggests a general role for this RNA in regulating key nuclear functions...
  76. ncbi request reprint Characterization of KIFC2, a neuronal kinesin superfamily member in mouse
    D W Hanlon
    Department of Pharmacology, University of California, San Diego, La Jolla 92093 0683, USA
    Neuron 18:439-51. 1997
    ..Taken together, the data suggest that, unlike other C-terminal motor proteins that appear to be involved in cell division, KIFC2 may play a role in retrograde axonal transport...
  77. ncbi request reprint The SKS1 protein kinase is a multicopy suppressor of the snf3 mutation of Saccharomyces cerevisiae
    Z Yang
    Department of Viticulture and Enology, University of California, Davis 95616 8749, USA
    Yeast 12:1407-19. 1996
    ..The snf3 genomic suppressors, rgt1, RGT2 and ssn6, are also capable of suppressing snf3 associated growth defects in a strain lacking sks1...
  78. ncbi request reprint Comparative genomics coming of age
    Rebecca F Furlong
    Heredity (Edinb) 91:533-4. 2003
  79. ncbi request reprint Duplication and adaptive evolution of the chalcone synthase genes of Dendranthema (Asteraceae)
    Ji Yang
    College of Life Sciences, Peking University, Beijing, China
    Mol Biol Evol 19:1752-9. 2002
    ..Positive selective pressure appears to have driven the divergence of SF2 from SF1 and SF3...
  80. ncbi request reprint Rapid evolution of a pollen-specific oleosin-like gene family from Arabidopsis thaliana and closely related species
    Manja Schein
    Department of Genetics and Evolution, Max Planck Institute of Chemical Ecology, Jena, Germany
    Mol Biol Evol 21:659-69. 2004
    ....
  81. pmc Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
    Wendy S W Wong
    Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
    Genetics 168:1041-51. 2004
    ..The parsimony method has a very low rate of false positives but very little power for detecting positive selection or identifying positively selected sites...
  82. pmc Likelihood models of somatic mutation and codon substitution in cancer genes
    Ziheng Yang
    Department of Medical Genetics, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
    Genetics 165:695-705. 2003
    ....
  83. ncbi request reprint Detecting site-specific physicochemical selective pressures: applications to the Class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system
    Raazesh Sainudiin
    Department of Statistical Science, Cornell University, Ithaca, NY14853, USA
    J Mol Evol 60:315-26. 2005
    ..An empirical Bayes approach is used to identify sites that may be important for ligand recognition in these proteins...
  84. pmc Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci
    Bruce Rannala
    Department of Medical Genetics, University of Alberta, Edmonton, Alberta T6G 2H7, Canada
    Genetics 164:1645-56. 2003
    ..Our estimates, however, are affected by model assumptions as well as data quality. We suggest that reliable estimates have yet to await more data and more realistic models...
  85. ncbi request reprint Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    Jianzhi Zhang
    Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, USA
    Mol Biol Evol 22:2472-9. 2005
    ..Bayes empirical Bayes identification of amino acid sites under positive selection along the foreground branches was found to be reliable, but lacked power...
  86. ncbi request reprint An empirical examination of the utility of codon-substitution models in phylogeny reconstruction
    Fengrong Ren
    Advanced Biomedical Information, Center for Information Medicine, Tokyo Medical and Dental University, Japan
    Syst Biol 54:808-18. 2005
    ..We discuss the relationship between a model's fit to data and its utility in phylogeny reconstruction and caution against use of overly complex substitution models...
  87. ncbi request reprint Divergence dates for Malagasy lemurs estimated from multiple gene loci: geological and evolutionary context
    Anne D Yoder
    Department of Ecology and Evolutionary Biology, Yale University, 21 Sachem Street, New Haven, CT 06520, USA
    Mol Ecol 13:757-73. 2004
    ..These differences appear to correlate with the nocturnal vs. diurnal lifestyles, respectively, of these two primate groups...
  88. ncbi request reprint A unique amino acid substitution, T126I, in human genotype C of hepatitis B virus S gene and its possible influence on antigenic structural change
    Fengrong Ren
    Center for Information Medicine, Tokyo Medical and Dental University, 1 5 45 Yushima, Bunkyo, Tokyo 113 8510, Japan
    Gene 383:43-51. 2006
    ..We suggest that an integrated approach of evolutionary comparison and structural prediction is useful in generating hypotheses for further laboratory validation...
  89. ncbi request reprint Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA
    Rasmus Nielsen
    Department of Biometrics, Cornell University, USA
    Mol Biol Evol 20:1231-9. 2003
    ....
  90. pmc A new time-scale for ray-finned fish evolution
    Imogen A Hurley
    Department of Organismal Biology and Anatomy, University of Chicago, Chicago, IL 60637, USA
    Proc Biol Sci 274:489-98. 2007
    ..While the date estimate of this event overlaps the probable range of the teleost stem group, a correlation between the genome duplication and the large-scale pattern of actinopterygian phylogeny remains elusive...
  91. ncbi request reprint Population genetics of speciation in nonmodel organisms: I. Ancestral polymorphism in mangroves
    Renchao Zhou
    State Key Laboratory of Biocontrol and Key Laboratory of Gene Engineering of the Ministry of Education, Sun Yat Sen University, Guangzhou, China
    Mol Biol Evol 24:2746-54. 2007
    ..This population structure would give rise to high level of polymorphism across species range. This approach of studying the speciation history by genomic means should be applicable to nonmodel organisms...
  92. pmc Duplicated paralogous genes subject to positive selection in the genome of Trypanosoma brucei
    Richard D Emes
    Institute for Science and Technology in Medicine, Keele University, Stoke on Trent, United Kingdom
    PLoS ONE 3:e2295. 2008
    ....
  93. ncbi request reprint Likelihood analysis of the chalcone synthase genes suggests the role of positive selection in morning glories (Ipomoea)
    Ji Yang
    College of Life Sciences, Peking, University, Beijing, 100871, China
    J Mol Evol 58:54-63. 2004
    ..Positive Darwinian selection appears to have promoted the divergence of subfamily ABC and subfamily DE and is at least partially responsible for a rate increase following gene duplication...