A phylogenetic model for investigating correlated evolution of substitution rates and continuous phenotypic characters
Open accessAbstract
The comparative approach is routinely used to test for possible correlations between phenotypic or life-history traits. To correct for phylogenetic inertia, the method of independent contrasts assumes that continuous characters evolve along the phylogeny according to a multivariate Brownian process. Brownian diffusion processes have also been used to describe time variations of the parameters of the substitution process, such as the rate of substitution or the ratio of synonymous to nonsynonymous substitutions. Here, we develop a probabilistic framework for testing the coupling between continuous characters and parameters of the molecular substitution process. Rates of substitution and continuous characters are jointly modeled as a multivariate Brownian diffusion process of unknown covariance matrix. The covariance matrix, the divergence times and the phylogenetic variations of substitution rates and continuous characters are all jointly estimated in a Bayesian Monte Carlo framework, imposing on the covariance matrix a prior conjugate to the Brownian process so as to achieve a greater computational efficiency. The coupling between rates and phenotypes is assessed by measuring the posterior probability of positive or negative covariances, whereas divergence dates and phenotypic variations are marginally reconstructed in the context of the joint analysis. As an illustration, we apply the model to a set of 410 mammalian cytochrome b sequences. We observe a negative correlation between the rate of substitution and mass and longevity, which was previously observed. We also find a positive correlation between ω = dN/dS and mass and longevity, which we interpret as an indirect effect of variations of effective population size, thus in partial agreement with the nearly neutral theory. The method can easily be extended to any parameter of the substitution process and to any continuous phenotypic or environmental character.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Coevol jointly models parameters of substitution process and continuous phenotypes as a multivariate Brownian process and outputs the posterior distribution of the correlation between phenotypes and substitution parameters, but does not allow for discrete phenotypes.
“Coevol (Lartillot and Poujol 2011) jointly models parameters of substitution process (e.g., substitution rates) and continuous phenotypes as a multivariate Brownian process and outputs the posterior distribution of the correlation between phenotypes and substitution parameters, but does not allow for discrete phenotypes.”
From Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees (2019) · cites this paper as Lartillot and Poujol 2011
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Gelman, A., Carlin, J. B., Stern, H. S., Dunson, D. B., Vehtari, A., & Rubin, D. B. (2013) · doi:10.1201/b16018 · Cited by 27,276 · see citing works
Evolutionary trees from DNA sequences: A maximum likelihood approach.
Felsenstein, J. (1981) · Journal of Molecular Evolution · doi:10.1007/bf01734359 · Cited by 14,571 · see citing works
Phylogenies and the Comparative Method
Felsenstein, J. (1985) · The American Naturalist · doi:10.1086/284325 · Cited by 9,793 · see citing works
Estimating the rate of evolution of the rate of molecular evolution
Thorne, J. L., Kishino, H., & Painter, I. S. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025892 · Cited by 1,317 · see citing works
Body size, metabolic rate, generation time, and the molecular clock.
Martin, A. P., & Palumbi, S. R. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.9.4087 · Cited by 1,239 · see citing works
Slightly Deleterious Mutant Substitutions in Evolution
OHTA, T. (1973) · Nature · doi:10.1038/246096a0 · Cited by 1,104 · see citing works
Divergence time and evolutionary rate estimation with multilocus data.
Thorne, J. L., & Kishino, H. (2002) · Systematic Biology · doi:10.1080/10635150290102456 · Cited by 962 · see citing works
Performance of a divergence time estimation method under a probabilistic model of rate evolution.
Kishino, H., Thorne, J. L., & Bruno, W. J. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003811 · Cited by 633 · cited 2× · see citing works
“With calibrations, we proceed as in Kishino et al. (2001), that is, we use a gamma density for the age of the root, and conditional on this age, we impose a uniform density on relative ages, truncated so as to be compatible with the intervals specified by the calibrations.”
MethodA general comparison of relaxed molecular clock models
Lepage, T., Bryant, D., Philippe, H., & Lartillot, N. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm193 · Cited by 546 · cited 5× · see citing works
“This has been first proposed in the context of molecular dating methods, using Brownian diffusion processes (Thorne et al. 1998; Kishino et al. 2001; Thorne and Kishino 2002; Yang and Rannala 2006; Lepage et al. 2007; Rannala and Yang 2007).”
BackgroundMethodInfluentialSelf-citationInferring speciation times under an episodic molecular clock
Rannala, B., & Yang, Z. (2007) · Systematic Biology · doi:10.1080/10635150701420643 · Cited by 475 · see citing works
Rates of Nucleotide Substitution in Primates and Rodents and the Generation–Time Effect Hypothesis
Li, W.-H., Ellsworth, D. L., Krushkal, J., Chang, B. H.-J., & Hewett-Emmett, D. (1996) · Molecular Phylogenetics and Evolution · doi:10.1006/mpev.1996.0012 · Cited by 335 · see citing works
Determinants of rate variation in mammalian DNA sequence evolution.
Bromham, L., Rambaut, A., & Harvey, P. H. (1996) · Journal of Molecular Evolution · doi:10.1007/bf02202109 · Cited by 291 · see citing works
Model of effectively neutral mutations in which selective constraint is incorporated
Kimura, M. (1979) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.76.7.3440 · Cited by 254 · see citing works
Flagged first, then by citations
Research works printed but not linked: 8
- Calder WA. 1984. Size, function and life history. Cambridge: Harvard University Press.
- Dirac PAM. 1982. The principles of quantum mechanics. Oxford: Oxford University Press.
- Gillespie JH. 1991. The causes of molecular evolution. Oxford: Oxford University Press.
- Harvey PH, Pagel MD. 1991. The comparative method in evolutionary biology. Oxford: Oxford University Press.
- Jeffreys H. 1961. Theory of probability. Oxford: Oxford University Press.
- Kimura M. 1983. The neutral theory of molecular evolution. Cam- bridge: Cambridge University Press.
- Mardia KV, Kent JT, Bibby JM. 1979. Multivariate analysis. San Diego (CA): Academic Press.
- Martins EP, Hansen TF. 1996. The statistical analysis of interspecific data: a review and evaluation of phylogenetic comparative methods. In: Martins E, editor. Phylogenies and the comparative method in animal behavior. Oxford: Oxford University Press. p. 22-75.
Cited by
Sorted by citations
Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees
Hu, Z., Sackton, T. B., Edwards, S. V., & Liu, J. S. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz049 · Cited by 69 · see citing works
- Authors
- Lartillot, N., & Poujol, R.
- Affiliations
- Université de Montréal (CA)
- Corresponding author
- Lartillot, N.
- Venue
- Molecular Biology and Evolution
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-10-06
- Volume
- 28
- Issue
- 1
- Pages
- 729-744
- ISSN
- 0737-4038 (ISSN-L)
- 1537-1719
- OpenAlex
- W2127148540
- Cited by
- 243
- References
- 13
- Citations by year
- 2026: 18 · 2025: 17 · 2024: 19 · 2023: 9 · 2022: 7 · 2021: 17 · 2020: 15 · 2019: 18 · 2018: 12 · 2017: 12 · 2016: 14 · 2015: 20 · 2014: 24 · 2013: 17 · 2012: 15
- FWCI
- 6.81
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Molecular Biology and Evolution (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- correlated evolution, substitution rate, phylogenetic inertia, independent contrasts, covariance matrix estimation, divergence time estimation, body mass, longevity, dN/dS ratio, effective population size, nearly neutral theory, molecular evolution
- MeSH terms
- Animals, Codon, Computer Simulation, Biological Evolution, Female, Markov Chains, Mathematics, Models, Genetic, Monte Carlo Method, Phenotype, Phylogeny, Evolution, Molecular
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
