Abstract
One of the criteria for inferring a species tree from a collection of gene trees, when gene tree incongruence is assumed to be due to incomplete lineage sorting (ILS), is minimize deep coalescence, or MDC. Exact algorithms for inferring the species tree from rooted, binary trees under MDC were recently introduced. Nevertheless, in phylogenetic analyses of biological data sets, estimated gene trees may differ from true gene trees, be incompletely resolved, and not necessarily rooted. In this paper, we propose new MDC formulations for the cases where the gene trees are unrooted/binary, rooted/non-binary, and unrooted/non-binary. Further, we prove structural theorems that allow us to extend the algorithms for the rooted/binary gene tree case to these cases in a straightforward manner. Finally, we study the performance of these methods in coalescent-based computer simulations.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
Dawkins, R.: The Ancestor’s Tale. Houghton Mifflin, New York (2004)
Degnan, J.H., DeGiorgio, M., Bryant, D., Rosenberg, N.A.: Properties of consensus methods for inferring species trees from gene trees. Syst. Biol. 58, 35–54 (2009)
Degnan, J.H., Rosenberg, N.A.: Discordance of species trees with their most likely gene trees. PLoS Genet. 2, 762–768 (2006)
Degnan, J.H., Rosenberg, N.A.: Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends Ecol. Evol. 24, 332–340 (2009)
Edwards, S.V., Liu, L., Pearl, D.K.: High-resolution species trees without concatenation. PNAS 104, 5936–5941 (2007)
Jukes, T.H., Cantor, C.R.: Evolution of protein molecules. In: Munro, H.N. (ed.) Mammalian Protein Metabolism, pp. 21–132. Academic Press, New York (1969)
Kubatko, L.S., Carstens, B.C., Knowles, L.L.: STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics 25(7), 971–973 (2009)
Kuo, C.-H., Wares, J.P., Kissinger, J.C.: The Apicomplexan whole-genome phylogeny: An analysis of incongruence among gene trees. Mol. Biol. Evol. 25(12), 2689–2698 (2008)
Liu, L., Pearl, D.K.: Species trees from gene trees: Reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions. Systematic Biology 56(3), 504–514 (2007)
Maddison, W.P.: Gene trees in species trees. Syst. Biol. 46, 523–536 (1997)
Maddison, W.P., Knowles, L.L.: Inferring phylogeny despite incomplete lineage sorting. Systematic Biology 55(1), 21–30 (2006)
Maddison, W.P., Maddison, D.R.: Mesquite: A modular system for evolutionary analysis (2004), version 1.01 http://mesquiteproject.org
Nei, M.: Stochastic errors in DNA evolution and molecular phylogeny. In: Gershowitz, H., Rucknagel, D.L., Tashian, R.E. (eds.) Evolutionary Perspectives and the New Genetics, pp. 133–147. Alan R. Liss, New York (1986)
Pollard, D.A., Iyer, V.N., Moses, A.M., Eisen, M.B.: Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet. 2, 1634–1647 (2006)
Rambaut, A., Grassly, N.C.: Seq-gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comp. Appl. Biosci. 13, 235–238 (1997)
Robinson, D.R., Foulds, L.R.: Comparison of phylogenetic trees. Math. Biosci. 53, 131–147 (1981)
Rokas, A., Williams, B.L., King, N., Carroll, S.B.: Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature 425, 798–804 (2003)
Semple, C., Steel, M.: Phylogenetics. Oxford University Press, Oxford (2003)
Syring, J., Willyard, A., Cronn, R., Liston, A.: Evolutionary relationships among Pinus (Pinaceae) subsections inferred from multiple low-copy nuclear loci. American Journal of Botany 92, 2086–2100 (2005)
Tajima, F.: Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437–460 (1983)
Takahata, N.: Gene genealogy in three related populations: consistency probability between gene and population trees. Genetics 122, 957–966 (1989)
Than, C., Nakhleh, L.: Species tree inference by minimizing deep coalescences. PLoS Computational Biology 5(9), e1000501 (2009)
Than, C., Nakhleh, L.: Inference of parsimonious species phylogenies from multi-locus data by minimizing deep coalescences. In: Knowles, L.L., Kubatko, L.S. (eds.) Estimating Species Trees: Practical and Theoretical Aspects, pp. 79–98. Wiley-VCH, Chichester (2010)
Than, C., Ruths, D., Nakhleh, L.: PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics 9, 322 (2008)
Than, C., Sugino, R., Innan, H., Nakhleh, L.: Efficient inference of bacterial strain trees from genome-scale multi-locus data. Bioinformatics 24, i123–i131 (2008); Proceedings of the 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008)
Wu, C.-I.: Inferences of species phylogeny in relation to segregation of ancient polymorphisms. Genetics 127, 429–435 (1991)
Wu, C.-I.: Reply to Richard R. Hudson. Genetics 131, 513 (1992)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Yu, Y., Warnow, T., Nakhleh, L. (2011). Algorithms for MDC-Based Multi-locus Phylogeny Inference. In: Bafna, V., Sahinalp, S.C. (eds) Research in Computational Molecular Biology. RECOMB 2011. Lecture Notes in Computer Science(), vol 6577. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-20036-6_47
Download citation
DOI: https://doi.org/10.1007/978-3-642-20036-6_47
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-20035-9
Online ISBN: 978-3-642-20036-6
eBook Packages: Computer ScienceComputer Science (R0)