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Original Articles

Building trees of algae: some advances in phylogenetic and evolutionary analysis

&
Pages 229-252 | Received 15 Jan 2008, Accepted 12 Jun 2008, Published online: 09 Sep 2008

References

  • Alfaro , ME and Holder , MT . 2006 . The posterior and the prior in Bayesian phylogenetics . Ann. Rev. Ecol. Evol. Systemat. , 37 : 19 – 42 .
  • Altekar , G , Dwarkadas , S , Huelsenbeck , JP and Ronquist , F . 2004 . Parallel metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference . Bioinformatics , 20 : 407 – 415 .
  • Alverson , AJ , Jansen , RK and Theriot , EC . 2007 . Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms . Mol. Phylogenet. Evol. , 45 : 193 – 121 .
  • Aris-Brosou , S . 2003 . How Bayes tests of molecular phylogenies compare with frequentist approaches . Bioinformatics , 19 : 618 – 624 .
  • Aris-Brosou , S and Yang , ZH . 2002 . Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny . Syst. Biol. , 51 : 703 – 714 .
  • Baele , G , Raes , J , Van de Peer , Y and Vansteelandt , S . 2006 . An improved statistical method for detecting heterotachy in nucleotide sequences . Mol. Biol. Evol. , 23 : 1397 – 1405 .
  • Barker , FK and Lutzoni , FM . 2002 . The utility of the incongruence length difference test . Syst. Biol. , 51 : 625 – 637 .
  • Beiko , RG , Keith , JM , Harlow , TJ and Ragan , MA . 2006 . Searching for convergence in phylogenetic Markov chain Monte Carlo . Syst. Biol. , 55 : 553 – 565 .
  • Bergsten , J . 2005 . A review of long-branch attraction . Cladistics , 21 : 163 – 193 .
  • Berry , V and Gascuel , O . 1996 . On the interpretation of bootstrap trees: appropriate threshold of clade selection and induced gain . Mol. Biol. Evol. , 13 : 999 – 1011 .
  • Bininda-Emonds , ORP . 2004 . Phylogenetic Supertrees: combining Information to Reveal the Tree of Life , Dordrecht, , Germany : Kluwer .
  • Björklund , M . 1999 . Are third positions really that bad? A test using vertebrate cytochrome b . Cladistics , 15 : 191 – 197 .
  • Blouin , MS , Yowell , CA , Courtney , CH and Dame , JB . 1998 . Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics . Mol. Biol. Evol. , 15 : 1719 – 1727 .
  • Brandley , MC , Schmitz , A and Reeder , T . 2005 . Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards . Syst. Biol. , 54 : 373 – 390 .
  • Brodie , J and Lewis , J . 2007 . Unravelling the Algae: the Past, Present and Future of Algal Systematics , Boca Raton, , USA : CRC Press .
  • Bromham , L and Penny , D . 2003 . The modern molecular clock . Nat. Rev. Genet. , 4 : 216 – 224 .
  • Brown , JM and Lemmon , AR . 2007 . The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics . Syst. Biol. , 56 : 643 – 655 .
  • Buckley , TR . 2002 . Model misspecification and probabilistic tests of topology: evidence from empirical data sets . Syst. Biol. , 51 : 509 – 523 .
  • Bull , JJ , Huelsenbeck , JP , Cunningham , CW , Swofford , DL and Waddell , PJ . 1993 . Partitioning and combining data in phylogenetic analysis . Syst. Biol. , 42 : 384 – 397 .
  • Burleigh , JG and Mathews , S . 2004 . Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life . Am. J. Bot. , 91 : 1599 – 1613 .
  • Carstens , BC and Knowles , LL . 2007 . Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers . Syst. Biol. , 56 : 400 – 411 .
  • Castresana , J . 2000 . Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis . Mol. Biol. Evol. , 17 : 540 – 552 .
  • Chen , D , Burleigh , GJ and Fernández-Baca , D . 2007 . Spectral partitioning of phylogenetic data sets based on compatibility . Syst. Biol. , 56 : 623 – 632 .
  • Conant , GC and Lewis , PO . 2001 . Effects of nucleotide composition bias on the success of the parsimony criterion in phylogenetic inference . Mol. Biol. Evol. , 18 : 1024 – 1033 .
  • Darlu , P and Lecointre , G . 2002 . When does the incongruence length difference test fail? . Mol. Biol. Evol. , 19 : 432 – 437 .
  • Daugbjerg , N and Andersen , RA . 1997 . A molecular phylogeny of the heterokont algae based on analyses of chloroplast-encoded rbcL sequence data . J. Phycol. , 33 : 1031 – 1041 .
  • De Clerck , O , Leliaert , F , Verbruggen , H , Lane , CE , De Paula , JC , Payo , DA and Coppejans , E . 2006 . A revised classification of the Dictyoteae (Dictyotales, Phaeophyceae) based on rbcL and 26S ribosomal DNA sequence analyses . J. Phycol. , 42 : 1271 – 1288 .
  • Drummond , AJ and Rambaut , A . 2007 . BEAST: bayesian evolutionary analysis by sampling trees . BMC Evol. Biol. , 7 : 214
  • Drummond , AJ , Ho , SYW , Phillips , MJ and Rambaut , A . 2006 . Relaxed phylogenetics and dating with confidence . PLoS Biol. , 4 : e88
  • Edgar , SM and Theriot , EC . 2004 . Phylogeny of Aulacoseira (Bacillariophyta) based on molecules and morphology . J. Phycol. , 40 : 772 – 788 .
  • Eernisse , DJ and Kluge , AG . 1993 . Taxonomic congruence versus total evidence, and amniote phylogeny inferred from fossils, molecules, and morphology . Mol. Biol. Evol. , 10 ( 6 ) : 1170 – 1195 .
  • Efron , B , Halloran , E and Holmes , S . 1996 . Bootstrap confidence levels for phylogenetic trees . Proc. Natl. Acad. Sci. USA , 93 : 13429 – 13434 .
  • Erpenbeck , D , Nichols , S , Voigt , O , Dohrmann , M , Degnan , B , Hooper , J and Wörheide , G . 2007 . Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches: case studies with diploblast LSU . J. Mol. Evol. , 64 : 543 – 557 .
  • Farris , JS . 1972 . Estimating phylogenetic trees from distance matrices . Am. Nat. , 106 : 645 – 668 .
  • Farris , JS , Kallersjo , M , Kluge , AG and Bult , C . 1994 . Testing significance of incongruence . Cladistics , 10 : 315 – 319 .
  • Felsenstein , J . 2004 . Inferring Phylogenies , Sunderland, , USA : Sinauer Associates .
  • Fitch , WM . 1971 . Toward defining the course of evolution: minimum change for a specific tree topology . Syst. Zool. , 20 : 406 – 416 .
  • Foster , PG . 2004 . Modeling compositional heterogeneity . Syst. Biol. , 53 : 485 – 495 .
  • Galtier , N . 2008 . “ Paper presented at: statistical and computational challenges in molecular phylogenetics and evolution ” . In Phylogenomic Analyses with Horizontal Gene Transfer , London, UK : Royal Society .
  • Gaut , BS and Lewis , PO . 1995 . Success of maximum likelihood phylogeny inference in the four-taxon case . Mol. Biol. Evol. , 12 : 152 – 162 .
  • Geuten , K , Massingham , T , Darius , P , Smets , E and Goldman , N . 2007 . Experimental design criteria in phylogenetics: where to add taxa . Syst. Biol. , 56 : 609 – 622 .
  • Goertzen , LR and Theriot , EC . 2003 . Effect of taxon sampling, character weighting, and combined data on the interpretation of relationships among the heterokont algae . J. Phycol. , 39 : 423 – 439 .
  • Goldman , N . 1998 . Phylogenetic information and experimental design in molecular systematics . Proc. Roy. Soc. B – Biol. Sci. , 265 : 1779 – 1786 .
  • Goldman , N and Yang , ZH . 1994 . Codon-based model of nucleotide substitution for protein-coding DNA sequences . Mol. Biol. Evol. , 11 : 725 – 736 .
  • Goldman , N , Anderson , JP and Rodrigo , AG . 2000 . Likelihood-based tests of topologies in phylogenetics . Syst. Biol. , 49 : 652 – 670 .
  • Graybeal , A . 1994 . Evaluating the phylogenetic utility of genes: a search for genes informative about deep divergences among vertebrates . Syst. Biol. , 43 : 174 – 193 .
  • Graybeal , A . 1998 . Is it better to add taxa or characters to a difficult phylogenetic problem? . Syst. Biol. , 47 : 9 – 17 .
  • Gu , X , Fu , YX and Li , WH . 1995 . Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites . Mol. Biol. Evol. , 12 : 546 – 557 .
  • Guindon , S and Gascuel , O . 2003 . A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood . Syst. Biol. , 52 : 696 – 704 .
  • Hansen , TF and Martins , EP . 1996 . Translating between microevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data . Evolution , 50 : 1404 – 1417 .
  • Harmon , LJ , Weir , JT , Brock , CD , Glor , RE and Challenger , W . 2008 . GEIGER: investigating evolutionary radiations . Bioinformatics , 24 : 129 – 131 .
  • Hedtke , S , Townsend , T and Hillis , D . 2006 . Resolution of phylogenetic conflict in large data sets by increased taxon sampling . Syst. Biol. , 55 ( 3 ) : 522 – 529 .
  • Hillis , DM and Bull , JJ . 1993 . An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis . Syst. Biol. , 42 : 182 – 192 .
  • Hillis , DM , Pollock , DD , McGuire , JA and Zwickl , DJ . 2003 . Is sparse taxon sampling a problem for phylogenetic inference? . Syst. Biol. , 52 : 124 – 126 .
  • Hipp , AL , Hall , JC and Sytsma , KJ . 2004 . Congruence versus phylogenetic accuracy: revisiting the incongruence length difference test . Syst. Biol. , 53 : 81 – 89 .
  • Ho , SYW and Jermiin , LS . 2004 . Tracing the decay of the historical signal in biological sequence data . Syst. Biol. , 53 : 623 – 637 .
  • Ho , JWK , Adams , CE , Lew , JB , Matthews , TJ , Ng , CC , Shahabi-Sirjani , A , Tan , LH , Zhao , Y , Easteal , S , Wilson , SR and Jermiin , LS . 2006 . SeqVis: visualization of compositional heterogeneity in large alignments of nucleotides . Bioinformatics , 22 : 2162 – 2163 .
  • Holder , M and Lewis , PO . 2003 . Phylogeny estimation: traditional and Bayesian approaches . Nat. Rev. Genet. , 4 : 275 – 284 .
  • Holland , BR , Penny , D and Hendy , MD . 2003 . Outgroup misplacement and phylogenetic inaccuracy under a molecular clock – A simulation study . Syst. Biol. , 52 : 229 – 238 .
  • Holland , BR , Huber , KT , Moulton , V and Lockhart , PJ . 2004 . Using consensus networks to visualize contradictory evidence for species phylogeny . Mol. Biol. Evol. , 21 : 1459 – 1461 .
  • Holland , BR , Jermiin , LS and Moulton , V . 2006 . Improved consensus network techniques for genome-scale phylogeny . Mol. Biol. Evol. , 23 : 848 – 855 .
  • Hommersand , MH , Freshwater , DW , Lopez-Bautista , JM and Fredericq , S . 2006 . Proposal of the Euptiloteae Hommersand et Fredericq, trib. nov and transfer of some Southern Hemisphere Ptiloteae to the Callithamnieae (Ceramiaceae, Rhodophyta) . J. Phycol. , 42 : 203 – 225 .
  • Huelsenbeck , JP . 1995 . Performance of phylogenetic methods in simulation . Syst. Biol. , 44 : 17 – 48 .
  • Huelsenbeck , JP . 1997 . Is the Felsenstein zone a fly trap? . Syst. Biol. , 46 : 69 – 74 .
  • Huelsenbeck , JP and Bull , JJ . 1996 . A likelihood ratio test to detect conflicting phylogenetic signal . Syst. Biol. , 45 : 92 – 98 .
  • Huelsenbeck , JP and Rannala , B . 2004 . Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models . Syst. Biol. , 53 : 904 – 913 .
  • Huelsenbeck , JP , Bull , JJ and Cunningham , CW . 1996 . Combining data in phylogenetic analysis . Trends Ecol. Evol. , 11 : 152 – 158 .
  • Huelsenbeck , JP , Ronquist , F , Nielsen , R and Bollback , JP . 2001 . Bayesian inference of phylogeny and its impact on evolutionary biology . Science , 294 : 2310 – 2314 .
  • Huelsenbeck , JP , Larget , B , Miller , RE and Ronquist , F . 2002a . Potential applications and pitfalls of Bayesian inference of phylogeny . Syst. Biol. , 51 : 673 – 688 .
  • Huelsenbeck , JP , Bollback , JP and Levine , AM . 2002b . Inferring the root of a phylogenetic tree . Syst. Biol. , 51 : 32 – 43 .
  • Huson , DH and Bryant , D . 2006 . Application of phylogenetic networks in evolutionary studies . Mol. Biol. Evol. , 23 : 254 – 267 .
  • Jeffroy , O , Brinkmann , H , Delsuc , F and Philippe , H . 2006 . Phylogenomics: the beginning of incongruence? . Trends Genet. , 22 : 225 – 231 .
  • Jermiin , LS , Ho , SYW , Ababneh , F , Robinson , J and Larkum , AW . 2004 . The biasing effect of compositional heterogeneity on phylogenetic estimates may be underestimated . Syst. Biol. , 53 : 638 – 643 .
  • Jobb , G , von Haeseler , A and Strimmer , K . 2004 . TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics . BMC Evol. Biol. , 4 : 18
  • Källersjö , M , Albert , VA and Farris , JS . 1999 . Homoplasy increases phylogenetic structure . Cladistics , 15 : 91 – 93 .
  • Kass , RE and Raftery , AE . 1995 . Bayes factors . J. Am. Stat. Assoc. , 90 : 773 – 795 .
  • Kennedy , M , Holland , BR , Gray , RD and Spencer , HG . 2005 . Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks . Syst. Biol. , 54 : 620 – 633 .
  • Kishino , H and Hasegawa , M . 1989 . Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea . J. Mol. Evol. , 29 : 170 – 179 .
  • Kishino , H , Thorne , JL and Bruno , WJ . 2001 . Performance of a divergence time estimation method under a probabilistic model of rate evolution . Mol. Biol. Evol. , 18 : 352 – 361 .
  • Kluge , AG . 1989 . A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes) . Syst. Zool. , 38 : 7 – 25 .
  • Kolaczkowski , B and Thornton , JW . 2004 . Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous . Nature , 431 : 980 – 984 .
  • Kosakovsky Pond , SL , Frost , SDW and Muse , SV . 2005 . HyPhy: hypothesis testing using phylogenies . Bioinformatics , 21 : 676 – 679 .
  • Larget , B and Simon , DL . 1999 . Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees . Mol. Biol. Evol. , 16 : 750 – 759 .
  • Lartillot , N and Philippe , H . 2004 . A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process . Mol. Biol. Evol. , 21 : 1095 – 1109 .
  • Lartillot , N and Philippe , H . 2006 . Computing Bayes factors using thermodynamic integration . Syst. Biol. , 55 : 195 – 207 .
  • Lartillot , N , Blanquart , S and Lepage , T . 2007 . PhyloBayes. v2.3. http://www.lirmm.fr/mab/article.php3?id_article=329
  • Le Gall , L and Saunders , GW . 2007 . A nuclear phylogeny of the Florideophyceae (Rhodophyta) inferred from combined EF2, small subunit and large subunit ribosomal DNA: establishing the new red algal subclass Corallinophycidae . Mol. Phylogenet. Evol. , 43 : 1118 – 1130 .
  • Lee , C , Blay , S , Mooers , AO , Singh , A and Oakley , TH . 2006 . CoMET: a Mesquite package for comparing models of continuous character evolution on phylogenies . Evolutionary Bioinformatics Online , 2 : 193 – 196 .
  • Leliaert , F , De Clerck , O , Verbruggen , H , Boedeker , C and Coppejans , E . 2007 . Molecular phylogeny of the Siphonocladales (Chlorophyta: Cladophorophyceae) . Mol. Phylogenet. Evol. , 44 : 1237 – 1256 .
  • Lemieux , C , Otis , C and Turmel , M . 2007 . A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies . BMC Biol. , 5 : 2
  • Lemmon , AR and Moriarty , EC . 2004 . The importance of proper model assumption in Bayesian phylogenetics . Syst. Biol. , 53 : 265 – 277 .
  • Lepage , T , Bryant , D , Philippe , H and Lartillot , N . 2007 . A general comparison of relaxed molecular clock models . Mol. Biol. Evol. , 24 : 2669 – 2680 .
  • Lewis , PO . 2001a . Phylogenetic systematics turns over a new leaf . Trends Ecol. Evol. , 16 : 30 – 37 .
  • Lewis , PO . 2001b . A likelihood approach to estimating phylogeny from discrete morphological character data . Syst. Biol. , 50 : 913 – 925 .
  • Lockhart , PJ , Steel , MA , Barbrook , AC , Huson , DH , Charleston , MA and Howe , C . 1998 . A covariotide model explains apparent phylogenetic structure of oxygenic photosynthetic lineages . Mol. Biol. Evol. , 15 : 1183 – 1188 .
  • Lockhart , P , Novis , P , Milligan , BG , Riden , J , Rambaut , A and Larkum , T . 2006 . Heterotachy and tree building: a case study with plastids and eubacteria . Mol. Biol. Evol. , 23 : 40 – 45 .
  • Lopez , P , Casane , D and Philippe , H . 2002 . Heterotachy, an important process of protein evolution . Mol. Biol. Evol. , 19 : 1 – 7 .
  • Loytynoja , A and Milinkovitch , MC . 2001 . SOAP, cleaning multiple alignments from unstable blocks . Bioinformatics , 17 : 573 – 574 .
  • Lyons-Weiler , J , Hoelzer , GA and Tausch , RJ . 1998 . Optimal outgroup analysis . Biol. J. Linn. Soc. , 64 : 493 – 511 .
  • Maddison , WP . 1991 . Squared-change parsimony reconstructions of ancestral states for continuous-valued characters on a phylogenetic tree . Syst. Zool. , 40 : 304 – 314 .
  • Maddison , DR and Maddison , WP . 2000 . MacClade 4 , Sunderland, , Massachusets : Sinauer .
  • Maddison , WP and Maddison , DR . 2007 . Mesquite: a modular system for evolutionary analysis. v2.0. http://mesquiteproject.org
  • Magallón , SA . 2004 . Dating lineages: molecular and paleontological approaches to the temporal framework of clades . Int. J. Plant Sci. , 165 : S7 – S21 .
  • Maggs , CA , Verbruggen , H and De Clerck , O . 2007 . “ Molecular systematics of red algae: building future structures on firm foundations ” . In Unravelling the Algae: the Past, Present, and Future of Algal Systematics , Edited by: Brodie , J and Lewis , J . 103 – 121 . Boca Raton, , USA : CRC Press .
  • Mann , DG and Evans , KM . 2007 . “ Molecular genetics and the neglected art of diatomics ” . In Unravelling the Algae: the Past, Present, and Future of Algal Systematics , Edited by: Brodie , J and Lewis , J . 231 – 266 . Boca Raton, , USA : CRC Press .
  • Martins , EP . 1999 . Estimation of ancestral states of continuous characters: a computer simulation study . Syst. Biol. , 48 : 642 – 650 .
  • Martins , EP . 2004 . COMPARE, version 4.6b. Computer programs for the statistical analysis of comparative data. http://compare.bio.indiana.edu/
  • Martins , EP and Hansen , TF . 1997 . Phylogenies and the comparative method: a general approach to incorporating phylogenetic information into the analysis of interspecific data . Am. Nat. , 149 : 646 – 667 .
  • Mattox , KR and Stewart , KD . 1984 . “ Classification of the green algae: a concept based on comparative cytology ” . In Systematics of the Green Algae , Edited by: Irvine , DEG and John , DM . 29 – 72 . London, UK : Academic Press .
  • McIvor , L , Maggs , CA and Stanhope , MJ . 2002 . rbcL sequences indicate a single evolutionary origin of multinucleate cells in the red algal tribe Callithamnieae . Mol. Phylogenet. Evol. , 23 : 433 – 446 .
  • Minin , V , Abdo , Z , Joyce , P and Sullivan , J . 2003 . Performance-based selection of likelihood models for phylogeny estimation . Syst. Biol. , 52 : 674 – 683 .
  • Mooers , AO and Schluter , D . 1999 . Reconstructing ancestor states with maximum likelihood: support for one- and two-rate models . Syst. Biol. , 48 : 623 – 633 .
  • Moore , BR and Donoghue , MJ . 2007 . Correlates of diversification in the plant clade Dipsacales: geographic movement and evolutionary innovations . Am. Nat. , 170 : S28 – S55 .
  • Müller , KM , Oliveira , MC , Sheat , RG and Bhattacharya , D . 2001 . Ribosomal DNA phylogeny of the Bangiophycidae (Rhodophyta) and the origin of secondary plastids . Am. J. Bot. , 88 : 1390 – 1400 .
  • Müller , KF , Borsch , T and Hilu , KW . 2006 . Phylogenetic utility of rapidly evolving DNA at high taxonomical levels: contrasting matK, trnT-F, and rbcL in basal angiosperms . Mol. Phylogenet. Evol. , 41 : 99 – 117 .
  • Murray , S , Jorgensen , MF , Ho , SYW , Patterson , DJ and Jermiin , LS . 2005 . Improving the analysis of dinoflagellate phylogeny based on rDNA . Protist , 156 : 269 – 286 .
  • Muse , SV and Gaut , BS . 1994 . A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome . Mol. Biol. Evol. , 11 : 715 – 724 .
  • Neustupa , J and Stastny , J . 2006 . The geometric morphometric study of Central European species of the genus Micrasterias (Zygnematophyceae, Viridiplantae) . Preslia , 78 : 253 – 263 .
  • Nixon , KC and Carpenter , JM . 1996 . On simultaneous analysis . Cladistics , 12 : 221 – 241 .
  • Nylander , JAA , Ronquist , F , Huelsenbeck , JP and Nieves-Aldrey , JL . 2004 . Bayesian phylogenetic analysis of combined data . Syst. Biol. , 53 : 47 – 67 .
  • Nylander , JAA , Wilgenbusch , JC , Warren , DL and Swofford , DL . 2007 . AWTY (Are We There Yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics . Bioinformatics , btm388
  • Oakley , TH and Cunningham , CW . 2000 . Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny . Evolution , 54 : 397 – 405 .
  • Pagel , M . 1994 . Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters . Proc. Roy. Soc. B, Biol. Sci. , 255 : 37 – 45 .
  • Pagel , M . 1997 . Inferring evolutionary processes from phylogenies . Zoologica Scripta , 26 : 331 – 348 .
  • Pagel , M . 1999a . Inferring the historical patterns of biological evolution . Nature , 401 : 877 – 884 .
  • Pagel , M . 1999b . The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies . Syst. Biol. , 48 : 612 – 622 .
  • Pagel , M and Meade , A . 2004 . A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data . Syst. Biol. , 53 : 571 – 581 .
  • Pagel , M and Meade , A . 2006 . BayesTraits http://www.evolution.rdg.ac.uk/BayesTraits.html
  • Pagel , M , Meade , A and Barker , D . 2004 . Bayesian estimation of ancestral character states on phylogenies . Syst. Biol. , 53 : 673 – 684 .
  • Paradis , E . 2007 . Analysis of Phylogenetics and Evolution with R , New York, , USA : Springer .
  • Paradis , E , Claude , J and Strimmer , K . 2004 . APE: analyses of phylogenetics and evolution in R language . Bioinformatics , 20 : 289 – 290 .
  • Pardi , F and Goldman , N . 2007 . Resource-aware taxon selection for maximizing phylogenetic diversity . Syst. Biol. , 56 : 431 – 444 .
  • Penny , D , McComish , BJ , Charleston , MA and Hendy , MD . 2001 . Mathematical elegance with biochemical realism: the covarion model of molecular evolution . J. Mol. Evol. , 53 : 711 – 723 .
  • Pérez-Losada , M , Høeg , JT and Crandall , KA . 2004 . Unraveling the evolutionary radiation of the thoracican barnacles using molecular and morphological evidence: a comparison of several divergence time estimation approaches . Syst. Biol. , 53 : 244 – 264 .
  • Philippe , H , Zhou , Y , Brinkmann , H , Rodrigue , N and Delsuc , F . 2005a . Heterotachy and long-branch attraction in phylogenetics . BMC Evol. Biol. , 5 : 50
  • Philippe , H , Delsuc , F , Brinkmann , H and Lartillot , N . 2005b . Phylogenomics . Ann. Rev. Ecol. Evol. Syst. , 36 : 541 – 562 .
  • Phillips , MJ and Penny , D . 2003 . The root of the mammalian tree inferred from whole mitochondrial genomes . Mol. Phylogenet. Evol. , 28 : 171 – 185 .
  • Planet , PJ . 2006 . Tree disagreement: measuring and testing incongruence in phylogenies . J. Biomed. Informat. , 39 : 86 – 102 .
  • Poe , S . 2003 . Evaluation of the strategy of long-branch subdivision to improve the accuracy of phylogenetic methods . Syst. Biol. , 52 ( 3 ) : 423 – 428 .
  • Poe , S and Swofford , DL . 1999 . Taxon sampling revisited . Nature , 398 : 300 – 301 .
  • Pol , D and Siddall , ME . 2001 . Biases in maximum likelihood and parsimony: a simulation approach to a 10-taxon case . Cladistics , 17 : 266 – 281 .
  • Pollock , DD , Zwickl , DJ , McGuire , JA and Hillis , DM . 2002 . Increased taxon sampling is advantageous for phylogenetic inference . Syst. Biol. , 51 : 664 – 671 .
  • Pombert , JF , Otis , C , Lemieux , C and Turmel , M . 2005 . The chloroplast genome sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) reveals unusual structural features and new insights into the branching order of chlorophyte lineages . Mol. Biol. Evol. , 22 : 1903 – 1918 .
  • Posada , D and Buckley , TR . 2004 . Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests . Syst. Biol. , 53 : 793 – 808 .
  • Rambaut , A and Drummond , AJ . 2007 . Tracer. v1.4. http://beast.bio.ed.ac.uk/tracer
  • Rodríguez-Ezpeleta , N , Brinkmann , H , Roure , B , Lartillot , N , Lang , BF and Philippe , H . 2007a . Detecting and overcoming systematic errors in genome-scale phylogenies . Syst. Biol. , 56 : 389 – 399 .
  • Rodríguez-Ezpeleta , N , Philippe , H , Brinkmann , H , Becker , B and Melkonian , M . 2007b . Phylogenetic analyses of nuclear, mitochondrial, and plastid multigene data sets support the placement of Mesostigma in the Streptophyta . Mol. Biol. Evol. , 24 : 723 – 731 .
  • Rokas , A , Williams , BL , King , N and Carroll , SB . 2003 . Genome-scale approaches to resolving incongruence in molecular phylogenies . Nature , 425 : 798 – 804 .
  • Ronquist , F and Huelsenbeck , JP . 2003 . MrBayes 3: bayesian phylogenetic inference under mixed models . Bioinformatics , 19 : 1572 – 1574 .
  • Rosenberg , MS and Kumar , S . 2001 . Incomplete taxon sampling is not a problem for phylogenetic inference . Proc. Natl. Acad. Sci. USA , 98 : 10751 – 10756 .
  • Rosenberg , MS and Kumar , S . 2003 . Heterogeneity of nucleotide frequencies among evolutionary lineages and phylogenetic inference . Mol. Biol. Evol. , 20 : 610 – 621 .
  • Ruano-Rubio , V and Fares , MA . 2007 . Artifactual phylogenies caused by correlated distribution of substitution rates among sites and lineages: the good, the bad, and the ugly . Syst. Biol. , 56 : 68 – 82 .
  • Ruiz-Trillo , I , Riutort , M , Littlewood , DTJ , Herniou , EA and Baguna , J . 1999 . Acoel flatworms: earliest extant bilaterian metazoans, not members of Platyhelminthes . Science , 283 : 1919 – 1923 .
  • Rutschmann , F . 2006 . Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times . Divers. Distrib. , 12 : 35 – 48 .
  • Sanderson , MJ . 1997 . A nonparametric approach to estimating divergence times in the absence of rate constancy . Mol. Biol. Evol. , 14 : 1218 – 1231 .
  • Sanderson , MJ . 2002 . Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach . Mol. Biol. Evol. , 19 : 101 – 109 .
  • Sanderson , MJ . 2003 . r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock . Bioinformatics , 19 : 301 – 302 .
  • Sanderson , MJ , Thorne , JL , Wikström , N and Bremer , K . 2004 . Molecular evidence on plant divergence times . Am. J. Bot. , 91 : 1656 – 1665 .
  • Saunders , GW , Chiovitti , A and Kraft , GT . 2002 . Small-subunit rDNA sequences from representatives of selected families of the Gigartinales and Rhodymeniales (Rhodophyta). 3. Delineating the Gigartinales sensu stricto . Can. J. Bot. , 82 : 43 – 74 .
  • Schluter , D . 1997 . ANCML: ancestor states for continuous traits using maximum likelihood http://www.zoology.ubc.ca/∼schluter/ancml.html
  • Schluter , D , Price , T , Mooers , AO and Ludwig , D . 1997 . Likelihood of ancestor states in adaptive radiation . Evolution , 51 : 1699 – 1711 .
  • Schmidt , HA , Strimmer , K , Vingron , M and von Haeseler , A . 2002 . TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing . Bioinformatics , 18 : 502 – 504 .
  • Schöniger , M and von Haeseler , A . 1994 . A stochastic model for the evolution of autocorrelated DNA sequences . Mol. Phylogenet. Evol. , 3 : 240 – 247 .
  • Schöniger , M and von Haeseler , A . 1995 . Performance of the maximum likelihood, neighbor joining, and maximum parsimony methods when sequence sites are not independent . Syst. Biol. , 44 : 533 – 547 .
  • Shalchian-Tabrizi , K , Skanseng , M , Ronquist , F , Klaveness , D , Bachvaroff , TR , Delwiche , CF , Botnen , A , Tengs , T and Jakobsen , KS . 2006 . Heterotachy processes in rhodophyte-derived secondhand plastid genes: implications for addressing the origin and evolution of dinoflagellate plastids . Mol. Biol. Evol. , 23 : 1504 – 1515 .
  • Shapiro , B , Rambaut , A and Drummond , AJ . 2006 . Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences . Mol. Biol. Evol. , 23 : 7 – 9 .
  • Shavit , L , Penny , D , Hendy , MD and Holland , BR . 2007 . The problem of rooting rapid radiations . Mol. Biol. Evol , 24 : 2400 – 2411 .
  • Shimodaira , H . 2002 . An approximately unbiased test of phylogenetic tree selection . Syst. Biol. , 51 : 492 – 508 .
  • Shimodaira , H and Hasegawa , M . 1999 . Multiple comparisons of log-likelihoods with applications to phylogenetic inference . Mol. Biol. Evol. , 16 : 1114 – 1116 .
  • Shimodaira , H and Hasegawa , M . 2001 . CONSEL: for assessing the confidence of phylogenetic tree selection . Bioinformatics , 17 : 1246 – 1247 .
  • Shpak , M and Churchill , GA . 2000 . The information content of a character under a Markov model of evolution . Mol. Phylogenet. Evol. , 17 : 231 – 243 .
  • Siddall , ME . 1998 . Success of parsimony in the four-taxon case: long-branch repulsion by likelihood in the Farris Zone . Cladistics , 14 : 209 – 220 .
  • Siemer , BL , Stam , WT , Olsen , JL and Pedersen , PM . 1998 . Phylogenetic relationships of the brown algal orders Ectocarpales, Chordariales, Dictyosiphonales, and Tilopteridales (Phaeophyceae) based on RUBISCO large subunit and spacer sequences . J. Phycol. , 34 : 1038 – 1048 .
  • Simmons , MP , Zhang , LB , Webb , CT and Reeves , A . 2006 . How can third codon positions outperform first and second codon positions in phylogenetic inference? An empirical example from the seed plants . Syst. Biol. , 55 : 245 – 258 .
  • Smith , AB . 1994 . Rooting molecular trees: problems and strategies . Biol. J. Linn. Soc. , 51 : 279 – 292 .
  • Soltis , PS and Soltis , DE . 2003 . Applying the bootstrap in phylogeny reconstruction . Stat. Sci. , 18 : 256 – 267 .
  • Stamatakis , A . 2006 . RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models . Bioinformatics , 22 : 2688 – 2690 .
  • Stefankovic , D and Vigoda , E . 2007 . Pitfalls of heterogeneous processes for phylogenetic reconstruction . Syst. Biol. , 56 : 113 – 124 .
  • Strimmer , K and von Haeseler , A . 1996 . Quartet puzzling: a quartet maximum-likelihood method for reconstructing tree topologies . Mol. Biol. Evol. , 13 : 964 – 969 .
  • Strimmer , K and von Haeseler , A . 1997 . Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment . Proc. Natl. Acad. Sci. USA , 94 : 6815 – 6819 .
  • Struck , TH , Purschke , G and Halanych , KM . 2006 . Phylogeny of Eunicida (Annelida) and exploring data congruence using a partition addition bootstrap alteration (PABA) approach . Syst. Biol. , 55 : 1 – 20 .
  • Suchard , MA , Weiss , RE and Sinsheimer , JS . 2001 . Bayesian selection of continuous-time Markov chain evolutionary models . Mol. Biol. Evol. , 18 : 1001 – 1013 .
  • Sullivan , J and Joyce , P . 2005 . Model selection in phylogenetics . Ann. Rev. Ecol. Evol. Syst. , 36 : 445 – 466 .
  • Sung , GH , Sung , JM , Hywel-Jones , NL and Spatafora , JW . 2007 . A multi-gene phylogeny of Clavicipitaceae (Ascomycota, Fungi): identification of localized incongruence using a combinational bootstrap approach . Mol. Phylogenet. Evol. , 44 : 1204 – 1223 .
  • Swofford , DL . 2003 . PAUP*: phylogenetic Analysis Using Parsimony (* and other methods). v4.0b10 ,
  • Swofford , DL , Olsen , GJ , Waddell , PJ and Hillis , DM . 1996 . “ Phylogenetic inference ” . In Molecular Systematics , Edited by: Hillis , DM , Moritz , C and Mable , BK . 407 – 514 . Sunderland, , USA : Sinauer .
  • Swofford , DL , Waddell , PJ , Huelsenbeck , JP , Foster , PG , Lewis , PO and Rogers , JS . 2001 . Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods . Syst. Biol. , 50 : 525 – 539 .
  • Tajima , F . 1993 . Simple methods for testing the molecular evolutionary clock hypothesis . Genetics , 135 : 599 – 607 .
  • Talavera , G and Castresana , J . 2007 . Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments . Syst. Biol. , 56 : 564 – 577 .
  • Tanabe , AS . 2007 . Kakusan: a computer program to automate the selection of a nucleotide substitution model and the configuration of a mixed model on multilocus data . Mol. Ecol. Notes , 7 : 962 – 964 .
  • Telford , MJ , Wise , MJ and Gowri-Shankar , V . 2005 . Consideration of RNA secondary structure significantly improves likelihood-based estimates of phylogeny: examples from the bilateria . Mol. Biol. Evol. , 22 : 1129 – 1136 .
  • Thorne , JL and Kishino , H . 2002 . Divergence time and evolutionary rate estimation with multilocus data . Syst. Biol. , 51 : 689 – 702 .
  • Thorne , JL and Kishino , H . 2003 . Mutidivtime , http://statgen.ncsu.edu/thorne/multidivtime.html
  • Thorne , JL , Kishino , H and Painter , IS . 1998 . Estimating the rate of evolution of the rate of molecular evolution . Mol. Biol. Evol. , 15 : 1647 – 1657 .
  • Townsend , JP . 2007 . Profiling phylogenetic informativeness . Syst. Biol. , 56 : 222 – 231 .
  • Verbruggen , H , De Clerck , O , Kooistra , W and Coppejans , E . 2005 . Molecular and morphometric data pinpoint species boundaries in Halimeda section Rhipsalis (Bryopsidales, Chlorophyta) . J. Phycol. , 41 : 606 – 621 .
  • Verbruggen , H , Leliaert , F , Maggs , CA , Shimada , S , Schils , T , Provan , J , Booth , D , Murphy , S , De Clerck , O , Littler , DS , Littler , MM and Coppejans , E . 2007 . Species boundaries and phylogenetic relationships within the green algal genus Codium (Bryopsidales) based on plastid DNA sequences . Mol. Phylogenet. Evol. , 44 : 240 – 254 .
  • Welch , JJ and Bromham , L . 2005 . Molecular dating when rates vary . Trends Ecol. Evol. , 20 : 320 – 327 .
  • Whelan , S . 2007 . New approaches to phylogenetic tree search and their application to large numbers of protein alignments . Syst. Biol. , 56 : 727 – 740 .
  • Whelan , S , Lio , P and Goldman , N . 2001 . Molecular phylogenetics: state-of-the-art methods for looking into the past . Trends Genet. , 17 : 262 – 272 .
  • White , WT , Hills , SF , Gaddam , R , Holland , BR and Penny , D . 2007 . Treeness triangles: visualizing the loss of phylogenetic signal . Mol. Biol. Evol. , 24 : 2029 – 2039 .
  • Wiens , JJ , Kuczynski , CA , Duellman , WE and Reeder , TW . 2007 . Loss and re-evolution of complex life cycles in marsupial frogs: does ancestral trait reconstruction mislead? . Evolution , 61 : 1886 – 1899 .
  • Withall , RD and Saunders , GW . 2006 . Combining small and large subunit ribosomal DNA genes to resolve relationships among orders of the Rhodymeniophycidae (Rhodophyta): recognition of the Acrosymphytales ord. nov. and Sebdeniales ord. nov . Eur. J. Phycol. , 41 : 379 – 394 .
  • Xia , X and Xie , Z . 2001 . DAMBE: software package for data analysis in molecular biology and evolution . J. Hered. , 92 : 371 – 373 .
  • Xia , XH , Xie , Z , Salemi , M , Chen , L and Wang , Y . 2003 . An index of substitution saturation and its application . Mol. Phylogenet. Evol. , 26 : 1 – 7 .
  • Yang , Z . 1994a . Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods . J. Mol. Evol. , 39 : 306 – 314 .
  • Yang , Z . 1994b . Estimating the pattern of nucleotide substitution . J. Mol. Evol. , 39 : 105 – 111 .
  • Yang , Z . 1996 . Among-site rate variation and its impact on phylogenetic analyses . Trends Ecol. Evol. , 11 : 367 – 372 .
  • Yang , Z . 1998 . On the best evolutionary rate for phylogenetic analysis . Syst. Biol. , 47 : 125 – 133 .
  • Yang , Z . 2006 . Computational Molecular Evolution , Oxford, UK : Oxford University Press .
  • Yang , Z . 2007 . PAML 4: phylogenetic Analysis by Maximum Likelihood . Mol. Biol. Evol. , 24 : 1586 – 1591 .
  • Yang , Z and Rannala , B . 2005 . Branch-length prior influences Bayesian posterior probability of phylogeny . Syst. Biol. , 54 : 455 – 470 .
  • Yang , ZH , Nielsen , R , Goldman , N and Pedersen , AMK . 2000 . Codon-substitution models for heterogeneous selection pressure at amino acid sites . Genetics , 155 : 431 – 449 .
  • Yang , ZH and Yoder , AD . 2003 . Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species . Syst. Biol. , 52 : 705 – 716 .
  • Yap , VB and Speed , T . 2005 . Rooting a phylogenetic tree with nonreversible substitution models . BMC Evol. Biol. , 5 : 2
  • Yesson , C and Culham , A . 2006 . Phyloclimatic modeling: combining phylogenetics and bioclimatic modeling . Syst. Biol. , 55 : 785 – 802 .
  • Yoder , AD and Yang , ZH . 2000 . Estimation of primate speciation dates using local molecular clocks . Mol. Biol. Evol. , 17 : 1081 – 1090 .
  • Zwickl , DJ . 2006 . Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion , http://www.bio.utexas.edu/faculty/antisense/garli/Garli.html
  • Zwickl , DJ and Hillis , DM . 2002 . Increased taxon sampling greatly reduces phylogenetic error . Syst. Biol. , 51 : 588 – 598 .

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