Mark Pagel

Summary

Affiliation: University of Reading
Country: UK

Publications

  1. ncbi request reprint Molecular phylogenies link rates of evolution and speciation
    Andrea J Webster
    School of Animal and Microbial Sciences, University of Reading, UK
    Science 301:478. 2003
  2. doi request reprint Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo
    Mark Pagel
    School of Biological Sciences, University of Reading, Reading RG6 6AJ, United Kingdom
    Am Nat 167:808-25. 2006
  3. pmc Assembly rules for protein networks derived from phylogenetic-statistical analysis of whole genomes
    Mark Pagel
    School of Biological Sciences, University of Reading, Reading, UK
    BMC Evol Biol 7:S16. 2007
  4. ncbi request reprint Large punctuational contribution of speciation to evolutionary divergence at the molecular level
    Mark Pagel
    School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, UK
    Science 314:119-21. 2006
  5. ncbi request reprint A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data
    Mark Pagel
    School of Animal and Microbial Sciences, University of Reading, England
    Syst Biol 53:571-81. 2004
  6. ncbi request reprint Bayesian estimation of ancestral character states on phylogenies
    Mark Pagel
    School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading, England
    Syst Biol 53:673-84. 2004
  7. doi request reprint Model misspecification not the node-density artifact
    Chris Venditti
    School of Biological Sciences, University of Reading
    Evolution 62:2125-6. 2008
  8. ncbi request reprint On the stability of populations of mammals, birds, fish and insects
    Richard M Sibly
    School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
    Ecol Lett 10:970-6. 2007
  9. ncbi request reprint Detecting the node-density artifact in phylogeny reconstruction
    Chris Venditti
    School of Biological Sciences, University of Reading, Whiteknights RG6 6AJ, Reading, England
    Syst Biol 55:637-43. 2006
  10. pmc Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo
    Mark Pagel
    School of Biological Sciences, University of Reading, Lyle Building, Whiteknights, Reading RG6 6AJ, UK
    Philos Trans R Soc Lond B Biol Sci 363:3955-64. 2008

Detail Information

Publications27

  1. ncbi request reprint Molecular phylogenies link rates of evolution and speciation
    Andrea J Webster
    School of Animal and Microbial Sciences, University of Reading, UK
    Science 301:478. 2003
  2. doi request reprint Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo
    Mark Pagel
    School of Biological Sciences, University of Reading, Reading RG6 6AJ, United Kingdom
    Am Nat 167:808-25. 2006
    ..We implement the method in a program called RJ Discrete and illustrate it by analyzing the question of whether mating system and advertisement of estrus by females have coevolved in the Old World monkeys and great apes...
  3. pmc Assembly rules for protein networks derived from phylogenetic-statistical analysis of whole genomes
    Mark Pagel
    School of Biological Sciences, University of Reading, Reading, UK
    BMC Evol Biol 7:S16. 2007
    ..Phylogenetic methods identify pairs of proteins that co-evolve on a phylogenetic tree, and have been shown to have a high probability of correctly identifying known functional links...
  4. ncbi request reprint Large punctuational contribution of speciation to evolutionary divergence at the molecular level
    Mark Pagel
    School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, UK
    Science 314:119-21. 2006
    ..Punctuational episodes of evolution may play a larger role in promoting evolutionary divergence than has previously been appreciated...
  5. ncbi request reprint A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data
    Mark Pagel
    School of Animal and Microbial Sciences, University of Reading, England
    Syst Biol 53:571-81. 2004
    ..We make the model available within a Bayesian Markov-chain Monte Carlo framework for phylogenetic inference, as an easy-to-use computer program...
  6. ncbi request reprint Bayesian estimation of ancestral character states on phylogenies
    Mark Pagel
    School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading, England
    Syst Biol 53:673-84. 2004
    ..We illustrate the methods with data on ribonuclease evolution in the Artiodactyla. Software implementing the methods (BayesMultiState) is available from the authors...
  7. doi request reprint Model misspecification not the node-density artifact
    Chris Venditti
    School of Biological Sciences, University of Reading
    Evolution 62:2125-6. 2008
  8. ncbi request reprint On the stability of populations of mammals, birds, fish and insects
    Richard M Sibly
    School of Biological Sciences, University of Reading, Whiteknights, Reading RG6 6AS, UK
    Ecol Lett 10:970-6. 2007
    ..Our estimates of return rates were generally well below the threshold for chaos, which makes it unlikely that chaotic dynamics occur in natural populations--one of ecology's key unanswered questions...
  9. ncbi request reprint Detecting the node-density artifact in phylogeny reconstruction
    Chris Venditti
    School of Biological Sciences, University of Reading, Whiteknights RG6 6AJ, Reading, England
    Syst Biol 55:637-43. 2006
    ..The ability to screen phylogenies for the node-density artifact is important for phylogenetic inference and for researchers using phylogenetic trees to infer evolutionary processes, including their use in molecular clock dating...
  10. pmc Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte Carlo
    Mark Pagel
    School of Biological Sciences, University of Reading, Lyle Building, Whiteknights, Reading RG6 6AJ, UK
    Philos Trans R Soc Lond B Biol Sci 363:3955-64. 2008
    ..The model is available from the authors' website, and can be used for the analysis of both nucleotide and morphological data...
  11. ncbi request reprint Phylogenetic mixture models can reduce node-density artifacts
    Chris Venditti
    School of Biological Sciences, University of Reading, Reading, United Kingdom
    Syst Biol 57:286-93. 2008
    ..Routine use of mixture models alongside other approaches to phylogenetic inference may often reveal hidden or unexpected patterns of sequence evolution and can improve phylogenetic inference...
  12. doi request reprint Languages evolve in punctuational bursts
    Quentin D Atkinson
    School of Biological Sciences, University of Reading, Reading RG6 6AS, UK
    Science 319:588. 2008
    ..Our findings identify a general tendency for increased rates of linguistic evolution in fledgling languages, perhaps arising from a linguistic founder effect or a desire to establish a distinct social identity...
  13. pmc Ultraconserved words point to deep language ancestry across Eurasia
    Mark Pagel
    School of Biological Sciences, University of Reading, Reading, Berkshire RG6 6AS, United Kingdom
    Proc Natl Acad Sci U S A 110:8471-6. 2013
    ..Our results suggest a remarkable fidelity in the transmission of some words and give theoretical justification to the search for features of language that might be preserved across wide spans of time and geography...
  14. ncbi request reprint Speciation as an active force in promoting genetic evolution
    Chris Venditti
    School of Biological Sciences, University of Reading, Reading RG6 6BX, UK
    Trends Ecol Evol 25:14-20. 2010
    ..Speciation might often owe more to ephemeral and essentially arbitrary events that cause reproductive isolation than to the gradual and regular tug of natural selection that draws a species into a new niche...
  15. ncbi request reprint The slow road to the eukaryotic genome
    Leo Lester
    School of Animal and Microbial Sciences, The University of Reading, UK
    Bioessays 28:57-64. 2006
    ..Progress in understanding eukaryotes may come from identifying ancestral features such as the eukaryotic splicesome that could explain why this lineage invaded, or created, the eukaryotic niche...
  16. doi request reprint Human language as a culturally transmitted replicator
    Mark Pagel
    School of Biological Sciences, University of Reading, Reading, Berkshire RG6 6AH, UK
    Nat Rev Genet 10:405-15. 2009
    ..For many comparative questions of anthropology and human behavioural ecology, historical processes estimated from linguistic phylogenies may be more relevant than those estimated from genes...
  17. ncbi request reprint On the regulation of populations of mammals, birds, fish, and insects
    Richard M Sibly
    School of Animal and Microbial Sciences, University of Reading, Whiteknights, Reading RG6 6AJ, UK
    Science 309:607-10. 2005
    ..These findings have fundamental implications for our understanding of animals' lives, suggesting in particular that many animals in these taxa will be found living at densities above the carrying capacity of their environments...
  18. pmc How do we use language? Shared patterns in the frequency of word use across 17 world languages
    Andreea S Calude
    School of Biological Sciences, University of Reading, Reading, UK
    Philos Trans R Soc Lond B Biol Sci 366:1101-7. 2011
    ..Our results point to a remarkable regularity in the way that human speakers use language, and hint that the words for a shared set of meanings have been slowly evolving and others more rapidly evolving throughout human history...
  19. ncbi request reprint Phylogenies reveal new interpretation of speciation and the Red Queen
    Chris Venditti
    School of Biological Sciences, University of Reading, Reading, Berkshire, RG6 6BX, UK
    Nature 463:349-52. 2010
    ....
  20. doi request reprint Rise of the digital machine
    Mark Pagel
    School of Biological Sciences, University of Reading, Reading RG6 6AJ, UK
    Nature 452:699. 2008
  21. ncbi request reprint Frequency of word-use predicts rates of lexical evolution throughout Indo-European history
    Mark Pagel
    School of Biological Sciences, University of Reading, Whiteknights, Reading, Berkshire, RG6 6AS, UK
    Nature 449:717-20. 2007
    ..Our findings are consistent with social models of word change that emphasize the role of selection, and suggest that owing to the ways that humans use language, some words will evolve slowly and others rapidly across all languages...
  22. ncbi request reprint Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genes
    Daniel Barker
    Sir Harold Mitchell Building, School of Biology, University of St Andrews St Andrews, Fife, KY16 9TH, UK
    Bioinformatics 23:14-20. 2007
    ..We further examine the effect of constraining the ML model by fixing the rate of gene gain at a low value, rather than estimating it from the data...
  23. ncbi request reprint Relating traits to diversification: a simple test
    Robert P Freckleton
    Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, United Kingdom
    Am Nat 172:102-15. 2008
    ..Clearly, there are inherent limitations in using only data on extant species to infer correlates of extinction; however, this approach is potentially a powerful tool in analyzing correlates of speciation...
  24. ncbi request reprint Origin of avian genome size and structure in non-avian dinosaurs
    Chris L Organ
    Museum of Comparative Zoology, Harvard University, 26 Oxford Street, Cambridge, Massachusetts 02138, USA
    Nature 446:180-4. 2007
    ..These genomic characteristics should be added to the list of attributes previously considered avian but now thought to have arisen in non-avian dinosaurs, such as feathers, pulmonary innovations, and parental care and nesting...
  25. ncbi request reprint The cultural wealth of nations
    Mark Pagel
    Nature 428:275-8. 2004
  26. ncbi request reprint Bergmann's rule and body size in mammals
    Robert P Freckleton
    Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
    Am Nat 161:821-5. 2003
  27. ncbi request reprint Evolutionary shifts between host oak sections and host-plant organs in Andricus gallwasps
    James M Cook
    Department of Biological Sciences, Imperial College, Ascot, Berkshire, United Kingdom
    Evolution 56:1821-30. 2002
    ..However, there are only so many ways to gall an oak, and rare shifts to new oak sections may contribute greatly to long-term diversification by opening up whole new adaptive zones...