TY - JOUR T1 - Homology and the optimization of DNA sequence data JF - Cladistics Y1 - 2001 A1 - Wheeler, Ward SP - S3 EP - S11 KW - direct optimization KW - dna KW - homology KW - molecules KW - phylogenetics KW - poy VL - 17 N1 - PDF ER - TY - JOUR T1 - Optimization alignment: the end of multiple sequence alignment in phylogenetics? JF - Cladistics Y1 - 1996 A1 - Wheeler, Ward C. SP - 1 EP - 9 KW - alignment KW - direct optimization KW - optimization KW - poy N1 - PDF ER - TY - CHAP T1 - Homology and DNA sequence data T2 - The character concept in evolutionary biology Y1 - 2001 A1 - Wheeler, Ward C. ED - Wagner, G. P. SP - 303 EP - 317 KW - direct optimization KW - dynamic homology KW - homology KW - molecular characters KW - poy JF - The character concept in evolutionary biology PB - Academic Press CY - San Diego N1 - PDF ER - TY - JOUR T1 - Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search JF - Cladistics Y1 - 2003 A1 - Wheeler, Ward C. SP - 261 EP - 268 KW - alignment KW - direct optimization KW - implied alignment KW - phylogenetics KW - poy VL - 19 N1 - PDF ER - TY - JOUR T1 - Phylogeny and biogeography of cichlid fishes (Teleostei : Perciformes : Cichlidae) JF - Cladistics Y1 - 2004 A1 - Sparks, J. S. A1 - Smith, W. L. SP - 501 EP - 517 KW - biogeography KW - direct optimization KW - dna KW - evolution KW - fishes KW - phylogeny KW - poy AB - Family level molecular phylogenetic analyses of cichlid fishes have generally suffered from a limited number of characters and/or poor taxonomic sampling across one or more major geographic assemblage, and therefore have not provided a robust test of early intrafamilial diversification. Herein we use both nuclear and mitochondrial nucleotide characters and direct optimization to reconstruct a phylogeny for cichlid fishes. Representatives of major cichlid lineages across all geographic assemblages are included, as well as nearly twice the number of characters as any prior family-level study. In a strict consensus of 81 equally most-parsimonious hypotheses, based on the simultaneous analysis of 2222 aligned nucleotide characters from two mitochondrial and two nuclear genes, four major subfamilial lineages are recovered with strong support. Etroplinae, endemic to Madagascar (Paretroplus) and southern Asia (Etroplus), is recovered as the sister taxon to the remainder of Cichlidae. Although the South Asian cichlids are monophyletic, the Malagasy plus South Asian lineages are not. The remaining Malagasy lineage, Ptychochrominae, is monophyletic and is recovered as the sister group to a clade comprising the African and Neotropical cichlids. The African (Pseudocrenilabrinae) and Neotropical (Cichlinae) lineages are each monophyletic in this reconstruction. The use of multiple molecular markers, from both mitochondrial and nuclear genes, results in a phylogeny that in general exhibits strong support, notably for early diversification events within Cichlidae. Results further indicate that Labroidei is not monophyletic, and that the sister group to Cichlidae may comprise a large and diverse assemblage of percomorph lineages. This hypothesis may at least partly explain why morphological studies that have attempted to place Cichlidae within Percomorpha, or that have tested cichlid monophyly using only "labroid" lineages, have met with only limited success. (c) The Willi Hennig Society 2004. VL - 20 UR - ://000226965400001 N1 - PDFTimes Cited: 3ArticleEnglishCited References Count: 89896wq ER - TY - JOUR T1 - Polyphyly of the mail-cheeked fishes (Teleostei : Scorpaeniformes): evidence from mitochondrial and nuclear sequence data JF - Molecular Phylogenetics and Evolution Y1 - 2004 A1 - Smith, W. L. A1 - Wheeler, W. C. SP - 627 EP - 646 KW - direct optimization KW - evolution KW - mtDNA KW - nuDNA KW - phylogenetics KW - poy KW - taxonomy AB - Mitochondrial and nuclear DNA sequence data for 105 acanthomorph taxa are analyzed to address questions of scorpaeniform monophyly and relationships. The combination of 3425 aligned base pairs from the mitochondrial small subunit rDNA (12S), large subunit rDNA (16S), and tRNA-Val and the nuclear large subunit rDNA (28S), histone H3, and TMO-4c4 loci are analyzed. Representatives of all scorpaeniform suborders and 32 of 36 scorpaeniform families are included with most suborders represented by multiple species. In addition to 69 scorpaeniform taxa, 36 outgroup taxa, including representatives of most families previously conjectured to be related to the Scorpaeniformes, are analyzed due to serious concerns of scorpaeniform monophyly. The traditionally recognized scorpaeniform fishes are recovered as polyphyletic, The 13 representatives of the Atheriniformes, Blennioidei, Gasterosteoidei, Grammatidae, Notothenioidei, Percidae, Trichodontidae, and Zoarcoidei included in the analysis are all nested within the least inclusive clade that includes all traditionally recognized scorpaeniforms. The scorpaenoid lineage is widely polyphyletic, and its intrarelationships differed significantly from previous hypotheses. The cottoid lineage is paraphyletic with only the presence of the Trichodontidae, as the sister-taxon of the Cottoidei, disrupting the traditional subordinal hypothesis of relationships. (C) 2004 Elsevier Inc. All rights reserved. VL - 32 UR - ://000222732000016 N1 - PDFTimes Cited: 8ReviewEnglishCited References Count: 118838ry ER - TY - JOUR T1 - Simultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis JF - Cladistics Y1 - 2002 A1 - Schulmeister, S. A1 - Wheeler, W. C. A1 - Carpenter, J. M. SP - 455 EP - 484 KW - alignment KW - congruence KW - direct optimization KW - morphology KW - mtDNA KW - optimization KW - phylogenetics KW - poy KW - sensitivity AB - The first simultaneous analysis of molecular and morphological data of basal hymenopterans that includes exemplars from all families is presented. DNA sequences (of approximately 2000-2700 by for each taxon) from the nuclear genes 18S and 285 and the mitochondrial genes 16S and CO1 have been sequenced for 39 taxa (four outgroup taxa, 29 symphytans, and six apocritans). These DNA sequences and 236 morphological characters from Vihelmsen [Zool. J. Linnean Soc. 131 (2001) 393] were analyzed separately as well as simultaneously. All analyses were performed on unaligned sequences, using the optimization alignment (= direct optimization) method. Sensitivity analysis sensu Wheeler [Syst. Biol. 44 (1995) 321] was applied by analyzing the data under nine different combinations of analysis parameter values. The superfamily level relationships of basal hymenopterans as proposed by Vilhelmsen [Zool. J. Linnean Soc. 131 (2001) 393] and Ronquist et al. [Zool. Scr. 28 (1999) 13] are mostly confirmed, except that Pamphilioidea is the sister group to Tenthredinoidea s.l. and that Anaxyelidae (i.e., Syntexis libocedrii) and Siricidae are supported as a monophyletic group, partly reestablishing the traditional concept of Siricoidea. The resulting hypothesis that best represents the combined evidence from morphology and DNA. sequences is (Xyeloidea (Tenthredinoidea s.l. Pamphilioidea) (Cephoidea (Siricoidea (Xiphydrioidea (Orussidae Apocrita))))), with Siricoidea = Anaxyelidae + Siricidae. The phylogenetic system within Tenthredinoidea s.l., derived from the combined evidence, is (Blasticotomidae (Tenthredinidae including Diprionidae (Cimbicidae (Argidae Pergidae)))). (C) 2002 Elsevier Science (USA). All rights reserved. VL - 18 UR - ://000179061500001 N1 - PDFTimes Cited: 18ArticleEnglishCited References Count: 88612el ER - TY - JOUR T1 - Efficiency of parallel direct optimization JF - Cladistics Y1 - 2001 A1 - Janies, Daniel A. A1 - Wheeler, Ward C. SP - S71 EP - S82 KW - direct optimization KW - phylogenetics KW - poy VL - 17 N1 - PDF ER - TY - JOUR T1 - Exploring the behavior of POY, a program for direct optimization of molecular data JF - Cladistics Y1 - 2001 A1 - Giribet, Gonzalo SP - S60 EP - S70 KW - direct optimization KW - phylogenetics KW - poy VL - 17 N1 - PDF ER - TY - JOUR T1 - Generating implied alignments under direct optimization using POY JF - Cladistics Y1 - 2005 A1 - Giribet, Gonzalo SP - 396 EP - 402 KW - direct optimization KW - implied alignment KW - phylogenetics KW - poy VL - 21 N1 - PDF ER - TY - JOUR T1 - Direct optimization, affine gap costs, and node stability JF - Molecular Phylogenetics and Evolution Y1 - 2005 A1 - Aagesen, Lone SP - 641 EP - 653 KW - direct optimization KW - dna KW - evolution KW - gap KW - morphology KW - phylogenetics KW - poy KW - sensitivity KW - stability AB - The outcome of a phylogenetic analysis based on DNA sequence data is highly dependent on the homology-assignment step and may vary with alignment parameter costs. Robustness to changes in parameter costs is therefore a desired quality of a data set because the final conclusions will be less dependent on selecting a precise optimal cost set. Here, node stability is explored in relationship to separate versus combined analysis in three different data sets, all including several data partitions. Robustness to changes in cost sets is measured as number of successive changes that can be made in a given cost set before a specific clade is lost. The changes are in all cases base change cost, gap penalties, and adding/removing/changing affine gap costs. When combining data partitions, the number of clades that appear in the entire parameter space is not remarkably increased, in some cases this number even decreased. However, when combining data partitions the trees from cost sets including affine gap costs were always more similar than the trees were from cost sets without affine gap costs. This was not the case when the data partitions were analyzed independently. When data sets were combined similar to 80% of the clades found under cost sets including affine gap costs resisted at least one change to the cost set. (c) 2005 Elsevier Inc. All rights reserved. VL - 36 UR - ://000231591500017 N1 - PDFTimes Cited: 0ArticleEnglishCited References Count: 57960lh ER -