Evolutionary Biology

Probabilities of tree topologies with temporal constraints and diversification shifts

10.24072/pcjournal.73 - Peer Community Journal, Volume 1 (2021), article no. e65.

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Dating the tree of life is a task far more complicated than only determining the evolutionary relationships between species. It is therefore of interest to develop approaches apt to deal with undated phylogenetic trees. The main result of this work is a method to compute probabilities of undated phylogenetic trees under Markovian diversification models by constraining some of the divergence times to belong to given time intervals and by allowing diversification shifts on certain clades. If the diversification models considered are lineage-homogeneous, the time complexity of this computation is quadratic with the number of species of the phylogenetic tree and linear with the number of temporal constraints. The interest of this computation method is illustrated with three applications, namely, to compute the distribution of the divergence times of a tree topology with temporal constraints, to directly sample the divergence times of a tree topology, and to test for a diversification shift at a given clade.

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DOI: 10.24072/pcjournal.73
Didier, Gilles 1

1 Univ Montpellier, CNRS, IMAG, Montpellier, France
License: CC-BY 4.0
Copyrights: The authors retain unrestricted copyrights and publishing rights
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Didier, Gilles. Probabilities of tree topologies with temporal constraints and diversification shifts. Peer Community Journal, Volume 1 (2021), article  no. e65. doi : 10.24072/pcjournal.73. https://peercommunityjournal.org/articles/10.24072/pcjournal.73/

Peer reviewed and recommended by PCI : 10.24072/pci.evolbiol.100088

Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.

[1] Alfaro, M. E.; Santini, F.; Brock, C.; Alamillo, H.; Dornburg, A.; Rabosky, D. L.; Carnevale, G.; Harmon, L. J. Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates, Proceedings of the National Academy of Sciences, Volume 106 (2009) no. 32, pp. 13410-13414 | DOI

[2] Devroye, L. Non-Uniform Random Variate Generation, Springer New York, New York, NY, (1986) | DOI

[3] Didier, G.; Fau, M.; Laurin, M. Likelihood of Tree Topologies with Fossils and Diversification Rate Estimation, Systematic Biology, Volume 66 (2017) no. 6, pp. 964-987 | DOI

[4] Didier, G.; Laurin, M. Exact Distribution of Divergence Times from Fossil Ages and Tree Topologies, Systematic Biology, Volume 69 (2020) no. 6, pp. 1068-1087 | DOI

[5] Donoghue, P. C. J.; Yang, Z. The evolution of methods for establishing evolutionary timescales, Philosophical Transactions of the Royal Society B: Biological Sciences, Volume 371 (2016) no. 1699 | DOI

[6] dos Reis, M. Notes on the birth–death prior with fossil calibrations for Bayesian estimation of species divergence times, Philosophical Transactions of the Royal Society B: Biological Sciences, Volume 371 (2016) no. 1699 | DOI

[7] Reis, M. D.; Gunnell, G. F.; Barba-Montoya, J.; Wilkins, A.; Yang, Z.; Yoder, A. D. Using Phylogenomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case, Systematic Biology, Volume 67 (2018) no. 4, pp. 594-615 | DOI

[8] Drummond, A. J.; Suchard, M. A.; Xie, D.; Rambaut, A. Bayesian Phylogenetics with BEAUti and the BEAST 1.7, Molecular Biology and Evolution, Volume 29 (2012) no. 8, pp. 1969-1973 | DOI

[9] Gavryushkina, A.; Heath, T. A.; Ksepka, D. T.; Stadler, T.; Welch, D.; Drummond, A. J. Bayesian Total-Evidence Dating Reveals the Recent Crown Radiation of Penguins, Systematic Biology, Volume 67 (2017), pp. 57-73 | DOI

[10] Gernhard, T. The conditioned reconstructed process, Journal of Theoretical Biology, Volume 253 (2008) no. 4, pp. 769-778 | DOI

[11] Gernhard, T.; Ford, D.; Vos, R.; Steel, M. Estimating the Relative Order of Speciation or Coalescence Events on a Given Phylogeny, Evolutionary Bioinformatics, Volume 2 (2006), pp. 285-293 | DOI

[12] Grafen A The phylogenetic regression, Philosophical Transactions of the Royal Society of London. B, Biological Sciences, Volume 326 (1989) no. 1233, pp. 119-157 | DOI

[13] Harding, E. F. The probabilities of rooted tree-shapes generated by random bifurcation, Advances in Applied Probability, Volume 3 (1971) no. 1, pp. 44-77 | DOI

[14] Heath, T. A. A Hierarchical Bayesian Model for Calibrating Estimates of Species Divergence Times, Systematic Biology, Volume 61 (2012) no. 5, pp. 793-809 | DOI

[15] Heled, J.; Drummond, A. J. Calibrated Birth–Death Phylogenetic Time-Tree Priors for Bayesian Inference, Systematic Biology, Volume 64 (2015) no. 3, pp. 369-383 | DOI

[16] Ho, S. Y. W.; Phillips, M. J. Accounting for Calibration Uncertainty in Phylogenetic Estimation of Evolutionary Divergence Times, Systematic Biology, Volume 58 (2009) no. 3, pp. 367-380 | DOI

[17] Kendall, D. G. On the Generalized "Birth-and-Death" Process, The Annals of Mathematical Statistics, Volume 19 (1948) no. 1, pp. 1-15 | DOI

[18] Kishino, H.; Thorne, J. L.; Bruno, W. J. Performance of a Divergence Time Estimation Method under a Probabilistic Model of Rate Evolution, Molecular Biology and Evolution, Volume 18 (2001) no. 3, pp. 352-361 | DOI

[19] Lambert, A.; Stadler, T. Birth–death models and coalescent point processes: The shape and probability of reconstructed phylogenies, Theoretical Population Biology, Volume 90 (2013), pp. 113-128 | DOI

[20] Marshall, C. R. A Simple Method for Bracketing Absolute Divergence Times on Molecular Phylogenies Using Multiple Fossil Calibration Points, The American Naturalist, Volume 171 (2008) no. 6, pp. 726-742 | DOI

[21] Nee S et al Extinction rates can be estimated from molecular phylogenies, Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, Volume 344 (1994) no. 1307, pp. 77-82 | DOI

[22] O’Reilly, J. E.; dos Reis, M.; Donoghue, P. C. Dating Tips for Divergence-Time Estimation, Trends in Genetics, Volume 31 (2015) no. 11, pp. 637-650 | DOI

[23] Paradis, E.; Claude, J.; Strimmer, K. APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, Volume 20 (2004) no. 2, pp. 289-290 | DOI

[24] Rannala, B.; Yang, Z. Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference, Journal of Molecular Evolution, Volume 43 (1996) no. 3, pp. 304-311 | DOI

[25] Rannala, B.; Yang, Z. Inferring Speciation Times under an Episodic Molecular Clock, Systematic Biology, Volume 56 (2007) no. 3, pp. 453-466 | DOI

[26] Ronquist, F.; Klopfstein, S.; Vilhelmsen, L.; Schulmeister, S.; Murray, D. L.; Rasnitsyn, A. P. A Total-Evidence Approach to Dating with Fossils, Applied to the Early Radiation of the Hymenoptera, Systematic Biology, Volume 61 (2012) no. 6, pp. 973-999 | DOI

[27] Ronquist, F.; Teslenko, M.; van der Mark, P.; Ayres, D. L.; Darling, A.; Höhna, S.; Larget, B.; Liu, L.; Suchard, M. A.; Huelsenbeck, J. P. MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space, Systematic Biology, Volume 61 (2012) no. 3, pp. 539-542 | DOI

[28] Sims, H. J.; McConway, K. J. Nonstochastic variation of species-level diversification rates within angiosperms, Evolution, Volume 57 (2003) no. 3, pp. 460-479 | DOI

[29] Slater, G. J.; Price, S. A.; Santini, F.; Alfaro, M. E. Diversity versus disparity and the radiation of modern cetaceans, Proceedings of the Royal Society B: Biological Sciences, Volume 277 (2010) no. 1697, pp. 3097-3104 | DOI

[30] Slowinski, J. B.; Guyer, C. Testing the Stochasticity of Patterns of Organismal Diversity: An Improved Null Model, The American Naturalist, Volume 134 (1989) no. 6, pp. 907-921 | DOI

[31] Stadler, T. On incomplete sampling under birth–death models and connections to the sampling-based coalescent, Journal of Theoretical Biology, Volume 261 (2009) no. 1, pp. 58-66 | DOI

[32] Stadler, T. Mammalian phylogeny reveals recent diversification rate shifts, Proceedings of the National Academy of Sciences, Volume 108 (2011) no. 15, pp. 6187-6192 | DOI

[33] Stadler, T.; Yang, Z. Dating Phylogenies with Sequentially Sampled Tips, Systematic Biology, Volume 62 (2013) no. 5, pp. 674-688 | DOI

[34] Thorne, J. L.; Kishino, H. Estimation of Divergence Times from Molecular Sequence Data, Statistical Methods in Molecular Evolution, Springer-Verlag, New York, (2005), pp. 233-256 | DOI

[35] Wertheim, J. O.; Sanderson, M. J. Estimating diversification rates: how useful are divergence times?, Evolution, Volume 65 (2010) no. 2, pp. 309-320 | DOI

[36] Yang, Z. Empirical evaluation of a prior for Bayesian phylogenetic inference, Philosophical Transactions of the Royal Society B: Biological Sciences, Volume 363 (2008) no. 1512, pp. 4031-4039 | DOI

[37] Yang, Z.; Rannala, B. Bayesian phylogenetic inference using DNA sequences: a Markov Chain Monte Carlo Method, Molecular Biology and Evolution, Volume 14 (1997) no. 7, pp. 717-724 | DOI

[38] Yang, Z.; Rannala, B. Bayesian Estimation of Species Divergence Times Under a Molecular Clock Using Multiple Fossil Calibrations with Soft Bounds, Molecular Biology and Evolution, Volume 23 (2006) no. 1, pp. 212-226 | DOI

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