Deciphering ancient rapid radiations.

[1]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[2]  Michael A. Thomas,et al.  Model use in phylogenetics: nine key questions. , 2007, Trends in ecology & evolution.

[3]  Kristoffer Forslund,et al.  QNet: an agglomerative method for the construction of phylogenetic networks from weighted quartets. , 2006, Molecular biology and evolution.

[4]  S. Carroll,et al.  Bushes in the Tree of Life , 2006, PLoS biology.

[5]  Daniel H. Huson,et al.  Reducing Distortion in Phylogenetic Networks , 2006, WABI.

[6]  E. Kellogg,et al.  Systematics and phylogeny of the Brassicaceae (Cruciferae): an overview , 2006, Plant Systematics and Evolution.

[7]  J. Banks,et al.  Dissecting the ancient rapid radiation of microgastrine wasp genera using additional nuclear genes , 2006, Molecular Phylogenetics and Evolution.

[8]  D. Penny,et al.  Early penguin fossils, plus mitochondrial genomes, calibrate avian evolution. , 2006, Molecular biology and evolution.

[9]  N. Rosenberg,et al.  Discordance of Species Trees with Their Most Likely Gene Trees , 2006, PLoS genetics.

[10]  Vincent Moulton,et al.  Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny. , 2006, Molecular biology and evolution.

[11]  W. Maddison,et al.  Inferring phylogeny despite incomplete lineage sorting. , 2006, Systematic biology.

[12]  S. Carroll,et al.  Animal Evolution and the Molecular Signature of Radiations Compressed in Time , 2005, Science.

[13]  M. Steel,et al.  A tale of two processes. , 2005, Systematic biology.

[14]  D. Harris,et al.  How much data are needed to resolve a difficult phylogeny?: case study in Lamiales. , 2005, Systematic biology.

[15]  R. Gray,et al.  Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks. , 2005, Systematic biology.

[16]  Mike Steel,et al.  Should phylogenetic models be trying to "fit an elephant"? , 2005, Trends in genetics : TIG.

[17]  W. Martin,et al.  Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution. , 2005, Trends in plant science.

[18]  D. Penny,et al.  The place of Amborella within the radiation of angiosperms. , 2005, Trends in plant science.

[19]  Frédéric Delsuc,et al.  Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods. , 2005, Systematic biology.

[20]  J. Boore,et al.  Beyond linear sequence comparisons: the use of genome-level characters for phylogenetic reconstruction , 2004, Philosophical Transactions of the Royal Society B: Biological Sciences.

[21]  D. Swofford,et al.  Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA. , 2004, Molecular phylogenetics and evolution.

[22]  Bryan Kolaczkowski,et al.  Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous , 2004, Nature.

[23]  Michael P. Cummings,et al.  PAML (Phylogenetic Analysis by Maximum Likelihood) , 2004 .

[24]  Michael P. Cummings,et al.  PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)] , 2004 .

[25]  Pamela S Soltis,et al.  Genome-scale data, angiosperm relationships, and "ending incongruence": a cautionary tale in phylogenetics. , 2004, Trends in plant science.

[26]  Daniel H. Huson,et al.  Phylogenetic super-networks from partial trees , 2004, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[27]  S. Ho,et al.  Tracing the decay of the historical signal in biological sequence data. , 2004, Systematic biology.

[28]  Faisal Ababneh,et al.  The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated. , 2004, Systematic biology.

[29]  Elchanan Mossel,et al.  How much can evolved characters tell us about the tree that generated them? , 2004, Mathematics of Evolution and Phylogeny.

[30]  Elchanan Mossel,et al.  A phase transition for a random cluster model on phylogenetic trees. , 2004, Mathematical biosciences.

[31]  S. Poe,et al.  BIRDS IN A BUSH: FIVE GENES INDICATE EXPLOSIVE EVOLUTION OF AVIAN ORDERS , 2004, Evolution; international journal of organic evolution.

[32]  Stephane Aris-Brosou,et al.  Bayesian models of episodic evolution support a late precambrian explosive diversification of the Metazoa. , 2003, Molecular biology and evolution.

[33]  Vincent Moulton,et al.  Consensus Networks: A Method for Visualising Incompatibilities in Collections of Trees , 2003, WABI.

[34]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[35]  D. Penny,et al.  Outgroup misplacement and phylogenetic inaccuracy under a molecular clock--a simulation study. , 2003, Systematic biology.

[36]  J. Moulton.  Can the current molecular arsenal adequately track rapid divergence events within Simuliidae (Diptera)? , 2003, Molecular phylogenetics and evolution.

[37]  R. Gray,et al.  Rapid evolutionary divergences in reef fishes of the family Acanthuridae (Perciformes: Teleostei). , 2003, Molecular phylogenetics and evolution.

[38]  S. O’Brien,et al.  Placental mammal diversification and the Cretaceous–Tertiary boundary , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[39]  David Bryant,et al.  NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks , 2002 .

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

[41]  W. Murphy,et al.  Resolution of the Early Placental Mammal Radiation Using Bayesian Phylogenetics , 2001, Science.

[42]  M Fishbein,et al.  Phylogeny of Saxifragales (angiosperms, eudicots): analysis of a rapid, ancient radiation. , 2001, Systematic biology.

[43]  R. Nichols,et al.  Gene trees and species trees are not the same. , 2001, Trends in ecology & evolution.

[44]  P. Mardulyn,et al.  Multiple molecular data sets suggest independent origins of highly eusocial behavior in bees (Hymenoptera:Apinae). , 2001, Systematic biology.

[45]  P. Lockhart,et al.  Trees for bees. , 2001, Trends in ecology & evolution.

[46]  N. Moran,et al.  Molecular data support a rapid radiation of aphids in the Cretaceous and multiple origins of host alternation , 2000 .

[47]  M. Donoghue,et al.  The root of angiosperm phylogeny inferred from duplicate phytochrome genes. , 1999, Science.

[48]  P. Mardulyn,et al.  Phylogenetic signal in the COI, 16S, and 28S genes for inferring relationships among genera of Microgastrinae (Hymenoptera; Braconidae): evidence of a high diversification rate in this group of parasitoids. , 1999, Molecular phylogenetics and evolution.

[49]  T. Moum,et al.  POLYTOMIES AND THE POWER OF PHYLOGENETIC INFERENCE , 1999, Evolution; international journal of organic evolution.

[50]  K. Strimmer,et al.  Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[51]  H. Shaffer,et al.  Tests of turtle phylogeny: molecular, morphological, and paleontological approaches. , 1997, Systematic biology.

[52]  Andrew Rambaut,et al.  Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees , 1997, Comput. Appl. Biosci..

[53]  D Penny,et al.  Mass Survival of Birds Across the Cretaceous- Tertiary Boundary: Molecular Evidence , 1997, Science.

[54]  Junhyong Kim,et al.  GENERAL INCONSISTENCY CONDITIONS FOR MAXIMUM PARSIMONY: EFFECTS OF BRANCH LENGTHS AND INCREASING NUMBERS OF TAXA , 1996 .

[55]  J. Huelsenbeck,et al.  Hobgoblin of phylogenetics? , 1994, Nature.

[56]  G. Hoelzer,et al.  Patterns of speciation and limits to phylogenetic resolution. , 1994, Trends in ecology & evolution.

[57]  A. Dress,et al.  Split decomposition: a new and useful approach to phylogenetic analysis of distance data. , 1992, Molecular phylogenetics and evolution.

[58]  Douglas E. Soltis,et al.  Molecular Systematics of Plants , 1992, Springer US.

[59]  M. Miyamoto,et al.  Phylogenetic Analysis of DNA Sequences , 1991 .

[60]  Michael D. Hendy,et al.  A Framework for the Quantitative Study of Evolutionary Trees , 1989 .

[61]  W. Maddison.  RECONSTRUCTING CHARACTER EVOLUTION ON POLYTOMOUS CLADOGRAMS , 1989, Cladistics : the international journal of the Willi Hennig Society.

[62]  J. Felsenstein.  Cases in which Parsimony or Compatibility Methods will be Positively Misleading , 1978 .

[63]  C. Kiefer,et al.  Supernetwork identifies multiple events of plastid trnF(GAA) pseudogene evolution in the Brassicaceae. , 2007, Molecular biology and evolution.

[64]  Hervé Philippe,et al.  Lack of resolution in the animal phylogeny: closely spaced cladogeneses or undetected systematic errors? , 2007, Molecular biology and evolution.

[65]  Olivier Gascuel,et al.  Mathematics of Evolution and Phylogeny , 2005 .

[66]  V. Moulton,et al.  Neighbor-net: an agglomerative method for the construction of phylogenetic networks. , 2004, Molecular biology and evolution.

[67]  D. SIAMJ..  SUFFICIENT CONDITIONS FOR TWO TREE RECONSTRUCTION TECHNIQUES TO SUCCEED ON SUFFICIENTLY LONG SEQUENCES , 2000 .

[68]  H. Bandelt,et al.  Median-joining networks for inferring intraspecific phylogenies. , 1999, Molecular biology and evolution.

[69]  D. Penny,et al.  Use of spectral analysis to test hypotheses on the origin of pinnipeds. , 1995, Molecular biology and evolution.

[70]  M. Donoghue,et al.  The Suitability of Molecular and Morphological Evidence in Reconstructing Plant Phylogeny , 1992 .