Likelihood-based tree reconstruction on a concatenation of aligned sequence data sets can be statistically inconsistent.

[1]  F. Tajima Evolutionary relationship of DNA sequences in finite populations. , 1983, Genetics.

[2]  W. Maddison Gene Trees in Species Trees , 1997 .

[3]  Mike Steel,et al.  Links between maximum likelihood and maximum parsimony under a simple model of site substitution , 1997 .

[4]  Bin Ma,et al.  From Gene Trees to Species Trees , 2000, SIAM J. Comput..

[5]  Loren H. Rieseberg,et al.  Gene trees and species trees are not the same , 2001 .

[6]  Noah A Rosenberg,et al.  The probability of topological concordance of gene trees and species trees. , 2002, Theoretical population biology.

[7]  R. Durrett Probability Models for DNA Sequence Evolution , 2002 .

[8]  S. Carroll,et al.  Genome-scale approaches to resolving incongruence in molecular phylogenies , 2003, Nature.

[9]  Sudhindra R Gadagkar,et al.  Inferring species phylogenies from multiple genes: concatenated sequence tree versus consensus gene tree. , 2005, Journal of experimental zoology. Part B, Molecular and developmental evolution.

[10]  L. Kubatko,et al.  Inconsistency of phylogenetic estimates from concatenated data under coalescence. , 2007, Systematic biology.

[11]  Scott V Edwards,et al.  A maximum pseudo-likelihood approach for estimating species trees under the coalescent model , 2010, BMC Evolutionary Biology.

[12]  R. 19 A hierarchy of species concepts : the denouement in the saga of the species problem , 2009 .

[13]  Laura Salter Kubatko,et al.  STEM: species tree estimation using maximum likelihood for gene trees under coalescence , 2009, Bioinform..

[14]  D. Pearl,et al.  Estimating species phylogenies using coalescence times among sequences. , 2009, Systematic biology.

[15]  Scott V Edwards,et al.  Coalescent methods for estimating phylogenetic trees. , 2009, Molecular phylogenetics and evolution.

[16]  Noah A Rosenberg,et al.  Gene tree discordance, phylogenetic inference and the multispecies coalescent. , 2009, Trends in ecology & evolution.

[17]  David Bryant,et al.  Properties of consensus methods for inferring species trees from gene trees. , 2008, Systematic biology.

[18]  Qixin He,et al.  Sources of error inherent in species-tree estimation: impact of mutational and coalescent effects on accuracy and implications for choosing among different methods. , 2010, Systematic biology.

[19]  J. Degnan,et al.  Fast and consistent estimation of species trees using supermatrix rooted triples. , 2010, Molecular biology and evolution.

[20]  A. Drummond,et al.  Bayesian Inference of Species Trees from Multilocus Data , 2009, Molecular biology and evolution.

[21]  Elchanan Mossel,et al.  Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci , 2007, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[22]  Liang Liu,et al.  Maximum tree: a consistent estimator of the species tree , 2010, Journal of mathematical biology.

[23]  Laura Kubatko,et al.  Estimating species trees : practical and theoretical aspects , 2010 .

[24]  Colin N. Dewey,et al.  BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis , 2010, Bioinform..

[25]  T. J. Robinson,et al.  Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification , 2011, Science.

[26]  Bruce Rannala,et al.  The accuracy of species tree estimation under simulation: a comparison of methods. , 2011, Systematic biology.

[27]  Sen Song,et al.  Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model , 2012, Proceedings of the National Academy of Sciences.

[28]  Mike Steel Consistency of Bayesian inference of resolved phylogenetic trees. , 2013, Journal of theoretical biology.

[29]  Tandy J. Warnow,et al.  Naive binning improves phylogenomic analyses , 2013, Bioinform..

[30]  M. Springer,et al.  Concatenation versus coalescence versus “concatalescence” , 2013, Proceedings of the National Academy of Sciences.

[31]  Sen Song,et al.  Reply to Gatesy and Springer: The multispecies coalescent model can effectively handle recombination and gene tree heterogeneity , 2013, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Sébastien Roch,et al.  An Analytical Comparison of Multilocus Methods Under the Multispecies Coalescent: The Three-Taxon Case , 2012, Pacific Symposium on Biocomputing.

[33]  Robert D. Nowak,et al.  New sample complexity bounds for phylogenetic inference from multiple loci , 2014, 2014 IEEE International Symposium on Information Theory.

[34]  Md. Shamsuzzoha Bayzid,et al.  RH : Evaluating species tree methods for ILS Evaluating summary methods for multi-locus species tree estimation in the presence of incomplete lineage sorting , 2014 .

[35]  Laura Kubatko,et al.  Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites. , 2014, Journal of theoretical biology.