Determining species tree topologies from clade probabilities under the coalescent

Allman, 2011, Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent, J. Math. Biol., 62, 833, 10.1007/s00285-010-0355-7 Ané, 2007, Bayesian estimation of concordance factors, Mol. Biol. Evol., 24, 412, 10.1093/molbev/msl170 Bryant, 2003, A classification of consensus methods for phylogenies, 163 Cranston, 2009, Species trees from highly incongruent gene trees in rice, Syst. Biol., 58, 489, 10.1093/sysbio/syp054 Degnan, 2009, Properties of consensus methods for inferring species trees from gene trees, Syst. Biol., 58, 35, 10.1093/sysbio/syp008 Degnan, 2009, Gene tree discordance, phylogenetic inference and the multispecies coalescent, Trends Ecol. Evol., 24, 332, 10.1016/j.tree.2009.01.009 Degnan, 2005, Gene tree distributions under the coalescent process, Evolution, 59, 24, 10.1111/j.0014-3820.2005.tb00891.x Ebersberger, 2007, Mapping human genetic ancestry, Mol. Biol. Evol., 24, 2266, 10.1093/molbev/msm156 Edwards, 2009, Is a new and general theory of systematics emerging?, Evolution, 63, 1, 10.1111/j.1558-5646.2008.00549.x Eldon, 2006, Coalescent processes when the distribution of offspring number among individuals is highly skewed, Genetics, 172, 2621, 10.1534/genetics.105.052175 Ewing, 2008, Rooted triple consensus and anomalous gene trees, BMC Evol. Biol., 8, 118, 10.1186/1471-2148-8-118 Greuel, G.-M., Pfister, G., Schönemann, H., 2009. Singular 3.1.0—A Computer Algebra System for Polynomial Computations. Technical Report, Centre for Computer Algebra, University of Kaiserslautern 〈http://www.singular.uni-kl.de〉. 2010 Larget, 2010, BUCKy: gene tree/species tree reconciliation with Bayesian concordance analysis, Bioinformatics, 26, 2910, 10.1093/bioinformatics/btq539 Liu, 2010, A maximum pseudo-likelihood approach for estimating species trees under the coalescent model, BMC Evol. Biol., 10, 302, 10.1186/1471-2148-10-302 Nei, 1987 Pamilo, 1988, Relationships between gene trees and species trees, Mol. Biol. Evol., 5, 568 Pitman, 1999, Coalescents with multiple collisions, Ann. Prob., 27, 1870, 10.1214/aop/1022677552 Rannala, 2003, Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci, Genetics, 164, 1645, 10.1093/genetics/164.4.1645 Rokas, 2003, Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, 425, 798, 10.1038/nature02053 Rosenberg, 2002, The probability of topological concordance of gene trees and species trees, Theor. Popul. Biol., 61, 225, 10.1006/tpbi.2001.1568 Semple, 2003