Affiliation: University of Reading
- Molecular phylogenies link rates of evolution and speciationAndrea J Webster
School of Animal and Microbial Sciences, University of Reading, UK
Science 301:478. 2003
- Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte CarloMark 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...
- Assembly rules for protein networks derived from phylogenetic-statistical analysis of whole genomesMark 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...
- Large punctuational contribution of speciation to evolutionary divergence at the molecular levelMark 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...
- A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state dataMark 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...
- Bayesian estimation of ancestral character states on phylogeniesMark 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...
- Model misspecification not the node-density artifactChris Venditti
School of Biological Sciences, University of Reading
Evolution 62:2125-6. 2008
- On the stability of populations of mammals, birds, fish and insectsRichard 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...
- Detecting the node-density artifact in phylogeny reconstructionChris 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...
- Modelling heterotachy in phylogenetic inference by reversible-jump Markov chain Monte CarloMark 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...
- Phylogenetic mixture models can reduce node-density artifactsChris 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...
- Languages evolve in punctuational burstsQuentin 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...
- Ultraconserved words point to deep language ancestry across EurasiaMark 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...
- Speciation as an active force in promoting genetic evolutionChris 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...
- The slow road to the eukaryotic genomeLeo 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...
- Human language as a culturally transmitted replicatorMark 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...
- On the regulation of populations of mammals, birds, fish, and insectsRichard 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...
- How do we use language? Shared patterns in the frequency of word use across 17 world languagesAndreea 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...
- Phylogenies reveal new interpretation of speciation and the Red QueenChris Venditti
School of Biological Sciences, University of Reading, Reading, Berkshire, RG6 6BX, UK
Nature 463:349-52. 2010....
- Rise of the digital machineMark Pagel
School of Biological Sciences, University of Reading, Reading RG6 6AJ, UK
Nature 452:699. 2008
- Frequency of word-use predicts rates of lexical evolution throughout Indo-European historyMark 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...
- Constrained models of evolution lead to improved prediction of functional linkage from correlated gain and loss of genesDaniel 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...
- Relating traits to diversification: a simple testRobert 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...
- Origin of avian genome size and structure in non-avian dinosaursChris 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...
- The cultural wealth of nationsMark Pagel
Nature 428:275-8. 2004
- Bergmann's rule and body size in mammalsRobert P Freckleton
Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom
Am Nat 161:821-5. 2003
- Evolutionary shifts between host oak sections and host-plant organs in Andricus gallwaspsJames 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...