Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent.

Journal of Mathematical Biology
Elizabeth S AllmanJohn A Rhodes

Abstract

Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals-each with many genes-splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sample...Continue Reading

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Citations

Jan 9, 2013·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Elizabeth S AllmanJohn A Rhodes
Dec 22, 2011·BMC Bioinformatics·Jimmy Yang, Tandy Warnow
May 2, 2012·Algorithms for Molecular Biology : AMB·Tanja Stadler, James H Degnan
Aug 28, 2014·Bioinformatics·S MirarabT Warnow
Aug 27, 2011·Journal of Theoretical Biology·Elizabeth S AllmanJohn A Rhodes
Mar 15, 2011·Molecular Phylogenetics and Evolution·Helen Hang Fan, Laura S Kubatko
May 15, 2015·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Filippo Disanto, Noah A Rosenberg
Oct 31, 2014·Proceedings of the National Academy of Sciences of the United States of America·Norman J WickettJames Leebens-Mack
Nov 15, 2011·Mathematical Biosciences·James H DegnanTanja Stadler
May 18, 2016·Molecular Biology and Evolution·Erfan Sayyari, Siavash Mirarab
Sep 11, 2016·Molecular Phylogenetics and Evolution·Yuan Tian, Laura S Kubatko
Oct 10, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Filippo Disanto, Noah A Rosenberg
Apr 12, 2013·Systematic Biology·James H Degnan
Jan 27, 2017·Systematic Biology·Elizabeth S AllmanJohn A Rhodes
Mar 31, 2011·Systematic Biology·Liang Liu, Lili Yu
May 31, 2018·Systematic Biology·James H Degnan
Nov 14, 2018·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Eliran Avni, Sagi Snir
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Nov 12, 2017·Bulletin of Mathematical Biology·Elizabeth S AllmanJohn A Rhodes
Aug 11, 2018·Bulletin of Mathematical Biology·Hector Baños
Dec 13, 2019·Algorithms for Molecular Biology : AMB·Elizabeth S AllmanJohn A Rhodes
Jul 18, 2020·Bulletin of Mathematical Biology·Samaneh Yourdkhani, John A Rhodes
Aug 16, 2017·Nature Ecology & Evolution·Dahiana ArcilaRicardo Betancur-R

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