Parsimony, phylogeny, and genomics

Preface 1. Parsimony and phylogenetics in the genomic age THE PHILOSOPHY OF PARSIMONY ANALYSIS, INCLUDING COMPARISON WITH MODEL-BASED APPROACHES 2. What is the rationale for 'Ockham's Razor' (a.k.a. parsimony) in phylogenetic inference? 3. Parsimony and its presuppositions PARSIMONY, CHARACTER ANALYSIS, AND OPTIMIZATION OF SEQUENCE CHARACTERS 4. The logic of the data matrix in phylogenetic analysis 5. Alignment, dynamic homology, and optimization 6. Parsimony and the problem of inapplicables in sequence data COMPUTATIONAL LIMITS OF PARSIMONY ANALYSIS: FROM HISTORICAL ASPECTS TO COMPETITION WITH FAST MODEL-BASED APPROACHES 7. The limits of conventional cladistic analysis 8. Parsimony and Bayesian phylogenetics MATHEMATICAL ATTRIBUTES OF PARSIMONY 9. Maximum parsimony and the phylogenetic information in multi-state characters PARSIMONY AND GENOMICS 10. Using phylogeny to understand genomic evolution 11. Dollo parsimony and reconstruction of genome evolution References Index

[1]  David A Liberles,et al.  The Adaptive Evolution Database (TAED) , 2001, Genome Biology.

[2]  W. K. Hastings,et al.  Monte Carlo Sampling Methods Using Markov Chains and Their Applications , 1970 .

[3]  M. Simmons,et al.  From basepairs to birdsongs : phylogenetic data in the age of genomics , 2003 .

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

[5]  Fabienne Thomarat,et al.  Genome sequence and gene compaction of the eukaryote parasite Encephalitozoon cuniculi , 2001, Nature.

[6]  R. Lande.  NATURAL SELECTION AND RANDOM GENETIC DRIFT IN PHENOTYPIC EVOLUTION , 1976, Evolution; international journal of organic evolution.

[7]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[8]  S. Blair Hedges,et al.  The origin and evolution of model organisms , 2002, Nature Reviews Genetics.

[9]  J. Farris.  Estimating Phylogenetic Trees from Distance Matrices , 1972, The American Naturalist.

[10]  Nick Goldman,et al.  MAXIMUM LIKELIHOOD INFERENCE OF PHYLOGENETIC TREES, WITH SPECIAL REFERENCE TO A POISSON PROCESS MODEL OF DNA SUBSTITUTION AND TO PARSIMONY ANALYSES , 1990 .

[11]  K. Kjer,et al.  Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs. , 1995, Molecular phylogenetics and evolution.

[12]  A. Friday,et al.  Problems of phylogenetic reconstruction , 1984 .

[13]  M. Newton,et al.  Phylogenetic Inference for Binary Data on Dendograms Using Markov Chain Monte Carlo , 1997 .

[14]  Steven A. Benner,et al.  Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily , 1995, Nature.

[15]  James S. Farms.  ON THE BOUNDARIES OF PHYLOGENETIC SYSTEMATICS , 1986, Cladistics : the international journal of the Willi Hennig Society.

[16]  J. Huelsenbeck,et al.  MRBAYES : Bayesian inference of phylogeny , 2001 .

[17]  A. Kluge,et al.  Philosophical conjectures and their refutation. , 2001, Systematic biology.

[18]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[19]  D. Adams,et al.  Are the fossil data really at odds with the molecular data? Morphological evidence for cetartiodactyla phylogeny reexamined. , 2001, Systematic biology.

[20]  N. Moran,et al.  Microbial Minimalism Genome Reduction in Bacterial Pathogens , 2002, Cell.

[21]  Daniel G. Blackburn.  From Whale Toes to Snake Eyes: Comments on the Reversibility of Evolution , 1984 .

[22]  David S. Gladstein,et al.  Efficient Incremental Character Optimization , 1997, Cladistics : the international journal of the Willi Hennig Society.

[23]  K. Popper.  The Poverty of Historicism , 1959 .

[24]  A. Phillips,et al.  Multiple sequence alignment in phylogenetic analysis. , 2000, Molecular phylogenetics and evolution.

[25]  Pablo A. Goloboff,et al.  Tree Searches Under Sankoff Parsimony , 1998, Cladistics : the international journal of the Willi Hennig Society.

[26]  W. Doolittle,et al.  Prokaryotic evolution in light of gene transfer. , 2002, Molecular biology and evolution.

[27]  F. Crick.  Origin of the Genetic Code , 1967, Nature.

[28]  T Gojobori,et al.  Large-scale search for genes on which positive selection may operate. , 1996, Molecular biology and evolution.

[29]  J. Farris.  A Probability Model for Inferring Evolutionary Trees , 1973 .

[30]  Bengt Oxelman,et al.  Improvements to resampling measures of group support , 2003 .

[31]  Jodie J. Yin,et al.  A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes , 2004, Genome Biology.

[32]  E V Koonin,et al.  Gene order is not conserved in bacterial evolution. , 1996, Trends in genetics : TIG.

[33]  A. Kluge,et al.  Testability and the Refutation and Corroboration of Cladistic Hypotheses , 1997, Cladistics : the international journal of the Willi Hennig Society.

[34]  J. Farris,et al.  Synapomorphy, parsimony, and evidence , 1986 .

[35]  Larry Laudan,et al.  Science and Relativism: Some Key Controversies in the Philosophy of Science , 1990 .

[36]  M. Ghiselin.  On Semantic Pitfalls of Biological Adaptation , 1966, Philosophy of Science.

[37]  C. Darwin.  Charles Darwin The Origin of Species by means of Natural Selection or The Preservation of Favoured Races in the Struggle for Life , 2004 .

[38]  I. Holmes,et al.  A "Long Indel" model for evolutionary sequence alignment. , 2003, Molecular biology and evolution.

[39]  R. Raff.  Understanding Evolution: The Next Step. (Book Reviews: The Shape of Life. Genes, Development, and the Evolution of Animal Form.) , 1996 .

[40]  J. Farris,et al.  Homoplasy Increases Phylogenetic Structure , 1999 .

[41]  C. Ouzounis,et al.  The balance of driving forces during genome evolution in prokaryotes. , 2003, Genome research.

[42]  C. Gallut,et al.  Cladistic coding of genomic maps , 2002, Cladistics : the international journal of the Willi Hennig Society.

[43]  William L. Fink,et al.  The conceptual relationship between ontogeny and phylogeny , 1982, Paleobiology.

[44]  J. Huelsenbeck,et al.  Frequent inconsistency of parsimony under a simple model of cladogenesis. , 2003, Systematic biology.

[45]  James F. Smith.  Phylogenetics of seed plants : An analysis of nucleotide sequences from the plastid gene rbcL , 1993 .

[46]  Kevin C. Nixon,et al.  Populations, Genetic Variation, and the Delimitation of Phylogenetic Species , 1992 .

[47]  M. Friedman.  Foundations of space-time theories : relativistic physics and philosophy of science , 1986 .

[48]  K. Lange.  Reconstruction of Evolutionary Trees , 1997 .

[49]  K. de Queiroz,et al.  Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration. , 2001, Systematic biology.

[50]  Joseph T. Chang,et al.  Full reconstruction of Markov models on evolutionary trees: identifiability and consistency. , 1996, Mathematical biosciences.

[51]  David Posada,et al.  MODELTEST: testing the model of DNA substitution , 1998, Bioinform..

[52]  H. Bandelt,et al.  Mitochondrial portraits of human populations using median networks. , 1995, Genetics.

[53]  J R Roth,et al.  Selfish operons: horizontal transfer may drive the evolution of gene clusters. , 1996, Genetics.

[54]  Antonis Rokas,et al.  Comparing bootstrap and posterior probability values in the four-taxon case. , 2003, Systematic biology.

[55]  Jan De Laet,et al.  On the Three-Taxon Approach to Parsimony Analysis☆ , 1998 .

[56]  J. Neyman.  MOLECULAR STUDIES OF EVOLUTION: A SOURCE OF NOVEL STATISTICAL PROBLEMS* , 1971 .

[57]  Dennis Shasha,et al.  Trait-to-Gene A Computational Method for Predicting the Function of Uncharacterized Genes , 2003, Current Biology.

[58]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.

[59]  D. Hull.  Historical Narratives and Integrating Explanations , 1981 .

[60]  A. Kluge,et al.  A CONSIDERATION OF EPISTEMOLOGY IN SYSTEMATIC BIOLOGY, WITH SPECIAL REFERENCE TO SPECIES , 1994 .

[61]  K. Bremer.  THE LIMITS OF AMINO ACID SEQUENCE DATA IN ANGIOSPERM PHYLOGENETIC RECONSTRUCTION , 1988, Evolution; international journal of organic evolution.

[62]  Atte Moilanen,et al.  Simulated Evolutionary Optimization and Local Search: Introduction and Application to Tree Search , 2001 .

[63]  J. Huelsenbeck,et al.  Potential applications and pitfalls of Bayesian inference of phylogeny. , 2002, Systematic biology.

[64]  J. Farris.  Methods for Computing Wagner Trees , 1970 .

[65]  P. Goloboff.  METHODS FOR FASTER PARSIMONY ANALYSIS , 1996 .

[66]  Bob Mau,et al.  Markov chain Monte Carlo for the Bayesian analysis of evolutionary trees from aligned molecular sequences , 1999 .

[67]  G. Giribet,et al.  TNT: Tree Analysis Using New Technology , 2005 .

[68]  N. Platnick.  Philosophy and the Transformation of Cladistics , 1979 .

[69]  J. Farris.  Simplicity and informativeness in systematics and phylogeny , 1982 .

[70]  Gonzalo Giribet.  Relationships among metazoan phyla as inferred from 18S rRNA sequence data: a methodological approach. , 2002, EXS.

[71]  Carol E. Cleland.  On the individuation of events , 1991, Synthese.

[72]  G. A. Barnard,et al.  THE LOGIC OF STATISTICAL INFERENCE1 , 1972, The British Journal for the Philosophy of Science.

[73]  B. Snel,et al.  SHOT: a web server for the construction of genome phylogenies. , 2002, Trends in genetics : TIG.

[74]  RONALD H. BRADY,et al.  ON THE INDEPENDENCE OF SYSTEMATICS , 1985, Cladistics : the international journal of the Willi Hennig Society.

[75]  B. Snel,et al.  Conservation of gene order: a fingerprint of proteins that physically interact. , 1998, Trends in biochemical sciences.

[76]  Alexei Fedorov,et al.  Large-scale comparison of intron positions among animal, plant, and fungal genes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[77]  L. Foulds,et al.  Proving phylogenetic trees minimal with l-clustering and set partitioning , 1980 .

[78]  K. Bremer,et al.  BRANCH SUPPORT AND TREE STABILITY , 1994 .

[79]  Atte Moilanen,et al.  Searching for Most Parsimonious Trees with Simulated Evolutionary Optimization , 1999 .

[80]  Dan Gusfield,et al.  Algorithms on Strings, Trees, and Sequences - Computer Science and Computational Biology , 1997 .

[81]  Patrick Forterre,et al.  An Alternative Flavin-Dependent Mechanism for Thymidylate Synthesis , 2002, Science.

[82]  J. S. Farris,et al.  Inferring Phylogenetic Trees from Chromosome Inversion Data , 1978 .

[83]  M. Steel,et al.  Corrected Parsimony, Minimum Evolution, and Hadamard Conjugations , 1996 .

[84]  S A Benner,et al.  Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences. , 2002, Journal of molecular biology.

[85]  Joseph T. Chang,et al.  THE MEASUREMENT OF HOMOPLASY: A STOCHASTIC VIEW , 1996 .

[86]  R. Graham,et al.  The steiner problem in phylogeny is NP-complete , 1982 .

[87]  R. Raff,et al.  Evidence for a clade of nematodes, arthropods and other moulting animals , 1997, Nature.

[88]  W. Fitch.  Distinguishing homologous from analogous proteins. , 1970, Systematic zoology.

[89]  P. Goloboff.  Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima , 1999, Cladistics : the international journal of the Willi Hennig Society.

[90]  X. Gu,et al.  Induced gene expression in human brain after the split from chimpanzee. , 2003, Trends in genetics : TIG.

[91]  Zbigniew Michalewicz,et al.  An Evolutionary Approach , 2004 .

[92]  A. Newman,et al.  Evidence that introns arose at proto‐splice sites. , 1989, The EMBO journal.

[93]  D. Maddison.  The discovery and importance of multiple islands of most , 1991 .

[94]  Masami Hasegawa,et al.  CONFIDENCE LIMITS ON THE MAXIMUM‐LIKELIHOOD ESTIMATE OF THE HOMINOID TREE FROM MITOCHONDRIAL‐DNA SEQUENCES , 1989, Evolution; international journal of organic evolution.

[95]  Peter K. Endress,et al.  Diversity and evolutionary biology of tropical flowers , 1994 .

[96]  R. Doolittle,et al.  Progressive sequence alignment as a prerequisitetto correct phylogenetic trees , 2007, Journal of Molecular Evolution.

[97]  J. Mallatt,et al.  Testing the new animal phylogeny: first use of combined large-subunit and small-subunit rRNA gene sequences to classify the protostomes. , 2002, Molecular biology and evolution.

[98]  Diana L. Lipscomb,et al.  PARSIMONY, HOMOLOGY AND THE ANALYSIS OF MULTISTATE CHARACTERS , 1992, Cladistics : the international journal of the Willi Hennig Society.

[99]  J. Farris.  Phylogenetic Analysis Under Dollo's Law , 1977 .

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

[101]  Liisa Holm,et al.  COFFEE: an objective function for multiple sequence alignments , 1998, Bioinform..

[102]  J. Farris.  Likelihood and Inconsistency , 1999, Cladistics : the international journal of the Willi Hennig Society.

[103]  W. Quine,et al.  On simple theories of a complex world , 2004, Synthese.

[104]  Inna Dubchak,et al.  Automated whole-genome multiple alignment of rat, mouse, and human. , 2004, Genome research.

[105]  M. Forster,et al.  Key Concepts in Model Selection: Performance and Generalizability. , 2000, Journal of mathematical psychology.

[106]  Karl Raimund Sir Popper,et al.  Realism and the aim of science , 1983 .

[107]  I N Sarkar,et al.  Systematic analysis of DNA microarray data: ordering and interpreting patterns of gene expression. , 2001, Genome research.

[108]  Nancy A. Neff,et al.  A Rational Basis for a Priori Character Weighting , 1986 .

[109]  Nicholas C. Wormald,et al.  On the Distribution of Lengths of Evolutionary Trees , 1990, SIAM J. Discret. Math..

[110]  Jotun Hein,et al.  An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree , 2000, Pacific Symposium on Biocomputing.

[111]  Brian Greene,et al.  The Fabric of the Cosmos , 2004 .

[112]  D. Eisenberg,et al.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[113]  Richard A. Goldstein,et al.  Probabilistic reconstruction of ancestral protein sequences , 1996, Journal of Molecular Evolution.

[114]  L. R. Foulds,et al.  Maximum savings in the Steiner problem in phylogeny , 1984 .

[115]  G. Churchill,et al.  Variation in gene expression within and among natural populations , 2002, Nature Genetics.

[116]  P. Bork,et al.  Measuring genome evolution. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[117]  J. Jurka,et al.  The Long Terminal Repeat of an Endogenous Retrovirus Induces Alternative Splicing and Encodes an Additional Carboxy-Terminal Sequence in the Human Leptin Receptor , 1999, Journal of Molecular Evolution.

[118]  Diego Pol,et al.  Biases in Maximum Likelihood and Parsimony: A Simulation Approach to a 10-Taxon Case , 2001 .

[119]  Jan De Laet.  A reconsideration of three-item analysis, the use of implied weights in cladistics, and a practical application in Gentianaceae , 1997 .

[120]  Gonzalo Giribet,et al.  DNA multiple sequence alignments. , 2002, EXS.

[121]  M. Gouy,et al.  HOVERGEN: a database of homologous vertebrate genes. , 1994, Nucleic acids research.

[122]  M. Pagel,et al.  The comparative method in evolutionary biology , 1991 .

[123]  Dong-Chan Lee,et al.  A Reconsideration of the Coding of Inapplicable Characters: Assumptions and Problems , 1999, Cladistics : the international journal of the Willi Hennig Society.

[124]  J. Felsenstein.  Numerical Methods for Inferring Evolutionary Trees , 1982, The Quarterly Review of Biology.

[125]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[126]  E. Koonin,et al.  The Impact of Comparative Genomics on Our Understanding of Evolution , 2000, Cell.

[127]  Daniel H. Huson,et al.  Phylogenetic trees based on gene content , 2004, Bioinform..

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

[129]  M. Nei,et al.  Molecular Evolution and Phylogenetics , 2000 .

[130]  David L. Hull,et al.  Philosophy Of Biological Science , 1974 .

[131]  D. Penny,et al.  Branch and bound algorithms to determine minimal evolutionary trees , 1982 .

[132]  James S. Farris,et al.  Outgroups and Parsimony , 1982 .

[133]  Michael Brudno,et al.  Fast and sensitive multiple alignment of large genomic sequences , 2003, BMC Bioinformatics.

[134]  K. Peterson,et al.  Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences , 2001, Evolution & development.

[135]  W. J. Quesne,et al.  A Method of Selection of Characters in Numerical Taxonomy , 1969 .

[136]  Jerrold I. Davis,et al.  A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values , 2004 .

[137]  T. Gaasterland,et al.  Microbial genescapes: phyletic and functional patterns of ORF distribution among prokaryotes. , 1998, Microbial & comparative genomics.

[138]  A. Kluge.  On total evidence: for the record , 2004, Cladistics : the international journal of the Willi Hennig Society.

[139]  Michael Y. Galperin,et al.  Sequence — Evolution — Function , 2003, Springer US.

[140]  M. O. Dayhoff,et al.  Atlas of protein sequence and structure , 1965 .

[141]  Jan De Laet,et al.  Branch Lengths Do Not Indicate Support—Even in Maximum Likelihood , 2001, Cladistics : the international journal of the Willi Hennig Society.

[142]  John McNeill,et al.  International Code of Botanical Nomenclature , 1983 .

[143]  W. Wheeler,et al.  Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathelminthes, and Chaetognatha: a combined approach of 18S rDNA sequences and morphology. , 2000, Systematic biology.

[144]  J D Palmer,et al.  Seven newly discovered intron positions in the triose-phosphate isomerase gene: evidence for the introns-late theory. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[145]  J. Felsenstein.  Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. , 1996, Methods in enzymology.

[146]  D. Higgins,et al.  See Blockindiscussions, Blockinstats, Blockinand Blockinauthor Blockinprofiles Blockinfor Blockinthis Blockinpublication Clustal: Blockina Blockinpackage Blockinfor Blockinperforming Multiple Blockinsequence Blockinalignment Blockinon Blockina Minicomputer Article Blockin Blockinin Blockin , 2022 .

[147]  Arlin Stoltzfus,et al.  Molecular evolution: Recent cases of spliceosomal intron gain? , 1998, Current Biology.

[148]  Tal Pupko,et al.  A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families , 2002, Bioinform..

[149]  K. Nixon.  The Parsimony Ratchet, a New Method for Rapid Parsimony Analysis , 1999 .

[150]  R. O'HARA,et al.  Homage to Clio, or, Toward an Historical Philosophy for Evolutionary Biology , 1988 .

[151]  T. A. Goudge.  The Ascent of Life , 1961 .

[152]  K. Nixon,et al.  Functional Constraints and rbcL Evidence for Land Plant Phylogeny , 1994 .

[153]  Robert N. Brandon,et al.  Individuality, pluralism, and the phylogenetic species concept , 1987 .

[154]  J. Felsenstein.  Phylogenies from molecular sequences: inference and reliability. , 1988, Annual review of genetics.

[155]  C. Hutchison,et al.  Gene content phylogeny of herpesviruses. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[156]  M. Bhaskara Rao,et al.  Model Selection and Inference , 2000, Technometrics.

[157]  A. Kluge,et al.  Transformation Series as an Ideographic Character Concept , 2004, Cladistics : the international journal of the Willi Hennig Society.

[158]  David L. Hull,et al.  The Metaphysics of Evolution , 1967, The British Journal for the History of Science.

[159]  A. Force,et al.  Preservation of duplicate genes by complementary, degenerative mutations. , 1999, Genetics.

[160]  M. Donoghue,et al.  Recreating a functional ancestral archosaur visual pigment. , 2002, Molecular biology and evolution.

[161]  Arnold G. Kluge,et al.  A Numerical Approach to Phylogenetic Systematics , 1970 .

[162]  Some Comments On Truth and the Growth of Knowledge , 1966 .

[163]  J. Farris,et al.  Simultaneous parsimony jackknife analysis of 2538rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants , 1998, Plant Systematics and Evolution.

[164]  K. Queiroz**,et al.  Including the Characters of Interest During Tree Reconstruction and the Problems of Circularity and Bias in Studies of Character Evolution , 1996 .

[165]  J. Hartigan,et al.  Statistical Analysis of Hominoid Molecular Evolution , 1987 .

[166]  Jonathan P. Bollback,et al.  Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology , 2001, Science.

[167]  J. McAllister.  Beauty and Revolution in Science , 1996 .

[168]  Hani Doss,et al.  Phylogenetic Tree Construction Using Markov Chain Monte Carlo , 2000 .

[169]  J. Avise.  GENE TREES AND ORGANISMAL HISTORIES: A PHYLOGENETIC APPROACH TO POPULATION BIOLOGY , 1989, Evolution; international journal of organic evolution.

[170]  Mike Steel,et al.  Phylogenetic Closure Operations and Homoplasy-Free Evolution , 2004 .

[171]  S. Pääbo,et al.  Intra- and Interspecific Variation in Primate Gene Expression Patterns , 2002, Science.

[172]  On “Molecular Phylogeny of Vespidae (Hymenoptera) and the Evolution of Sociality in Wasps” , 2003 .

[173]  J. Farris.  The Logical Basis of Phylogenetic Analysis , 2004 .

[174]  Michael Lynch,et al.  The evolution of spliceosomal introns. , 2002, Current opinion in genetics & development.

[175]  B. Mishler.  Cladistic analysis of molecular and morphological data. , 1994, American journal of physical anthropology.

[176]  M. Chase,et al.  Character-state weighting for cladistic analysis of protein-coding DNA sequences , 1993 .

[177]  P. Buneman.  The Recovery of Trees from Measures of Dissimilarity , 1971 .

[178]  K. de Queiroz,et al.  Failed refutations: further comments on parsimony and likelihood methods and their relationship to Popper's degree of corroboration. , 2003, Systematic biology.

[179]  Bengt Sennblad,et al.  Bayesian gene/species tree reconciliation and orthology analysis using MCMC , 2003, ISMB.

[180]  J. Bull,et al.  Combining data in phylogenetic analysis. , 1996, Trends in ecology & evolution.

[181]  S. Benner,et al.  Functional inferences from reconstructed evolutionary biology involving rectified databases--an evolutionarily grounded approach to functional genomics. , 2000, Research in microbiology.

[182]  J. Hein,et al.  A tree reconstruction method that is economical in the number of pairwise comparisons used. , 1989, Molecular biology and evolution.

[183]  J. Crow,et al.  THE NUMBER OF ALLELES THAT CAN BE MAINTAINED IN A FINITE POPULATION. , 1964, Genetics.

[184]  P. Goloboff.  ESTIMATING CHARACTER WEIGHTS DURING TREE SEARCH , 1993, Cladistics : the international journal of the Willi Hennig Society.

[185]  Burkhard Morgenstern,et al.  DIALIGN: multiple DNA and protein sequence alignment at BiBiServ , 2004, Nucleic Acids Res..

[186]  Norman A. Slade,et al.  Cladistic Analysis of Restriction Endonuclease Cleavage Maps Within a Maximum-Likelihood Framework , 1985 .

[187]  H. Ochman,et al.  Lateral gene transfer and the nature of bacterial innovation , 2000, Nature.

[188]  S. B. Needleman,et al.  A general method applicable to the search for similarities in the amino acid sequence of two proteins. , 1970, Journal of molecular biology.

[189]  J. Doob.  Stochastic processes , 1953 .

[190]  F. Pleijel.  ON CHARACTER CODING FOR PHYLOGENY RECONSTRUCTION , 1995 .

[191]  M. Chase,et al.  Character-State Weighting for Restriction Site Data in Phylogenetic Reconstruction, with an Example from Chloroplast DNA , 1992 .

[192]  D. Hull.  The Ontological Status of Species as Evolutionary Units , 1977 .

[193]  Joseph Felsenstein,et al.  The number of evolutionary trees , 1978 .

[194]  J Hein,et al.  A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given. , 1989, Molecular biology and evolution.

[195]  R. Shamir,et al.  A fast algorithm for joint reconstruction of ancestral amino acid sequences. , 2000, Molecular biology and evolution.

[196]  N. Platnick,et al.  ON MISSING ENTRIES IN CLADISTIC ANALYSIS , 1991 .

[197]  P. Lewis.  A likelihood approach to estimating phylogeny from discrete morphological character data. , 2001, Systematic biology.

[198]  W. Maddison.  Squared-Change Parsimony Reconstructions of Ancestral States for Continuous-Valued Characters on a Phylogenetic Tree , 1991 .

[199]  L. L. Cam,et al.  An approximation theorem for the Poisson binomial distribution. , 1960 .

[200]  M. Lidén.  REPLICATORS, HIERARCHY, AND THE SPECIES PROBLEM , 1990, Cladistics : the international journal of the Willi Hennig Society.

[201]  M A Newton,et al.  Bayesian Phylogenetic Inference via Markov Chain Monte Carlo Methods , 1999, Biometrics.

[202]  J. Farris.  Some Further Comments on Le Quesne's Methods , 1977 .

[203]  D. Lipman,et al.  The multiple sequence alignment problem in biology , 1988 .

[204]  J. Farris.  THE RETENTION INDEX AND THE RESCALED CONSISTENCY INDEX , 1989, Cladistics : the international journal of the Willi Hennig Society.

[205]  Emmon Bach.  Time, Tense, and Aspect: An Essay in English Metaphysics , 1981 .

[206]  J. Farris.  A Successive Approximations Approach to Character Weighting , 1969 .

[207]  B. Mishler,et al.  ON THE RATIONALE AND UTILITY OF WEIGHTING NUCLEOTIDE SEQUENCE DATA , 1992, Cladistics : the international journal of the Willi Hennig Society.

[208]  P. Wagner,et al.  Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. , 2000, Systematic biology.

[209]  J. Farris,et al.  Quantitative Phyletics and the Evolution of Anurans , 1969 .

[210]  David Bryant,et al.  A lower bound for the breakpoint phylogeny problem , 2000, J. Discrete Algorithms.

[211]  D. Eisenberg,et al.  A combined algorithm for genome-wide prediction of protein function , 1999, Nature.

[212]  Joseph Felsenstein,et al.  A likelihood approach to character weighting and what it tells us about parsimony and compatibility , 1981 .

[213]  H. Akaike,et al.  Information Theory and an Extension of the Maximum Likelihood Principle , 1973 .

[214]  Pablo A. Goloboff,et al.  CHARACTER OPTIMIZATION AND CALCULATION OF TREE LENGTHS , 1993 .

[215]  C. Martin,et al.  MYB transcription factors in plants. , 1997, Trends in genetics : TIG.

[216]  W. Doolittle,et al.  How big is the iceberg of which organellar genes in nuclear genomes are but the tip? , 2003, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[217]  W. Messier,et al.  Episodic adaptive evolution of primate lysozymes , 1997, Nature.

[218]  Daniel R. Brooks,et al.  Hennig's Parasitological Method: A Proposed Solution , 1981 .