TY - JOUR T1 - Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data JF - Systematic Biology Y1 - 1995 A1 - Wheeler, Ward C. SP - 321 EP - 331 KW - alignment KW - congruence KW - phylogenetics KW - poy KW - sensitivity KW - support VL - 44 N1 - PDF ER - TY - JOUR T1 - Partition-free congruence analysis: implications for sensitivity analysis JF - Cladistics Y1 - 2006 A1 - Wheeler, Ward C. A1 - Ramírez, Martín J. A1 - Aagesen, Lone A1 - Schulmeister, Susanne SP - 256 EP - 263 KW - combined data analyses KW - molecular characters KW - phylogenetics KW - sensitivity KW - total evidence VL - 22 N1 - PDF 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 - The phylogeny of termites (Dictyoptera: Isoptera) based on mitochondrial and nuclear markers: implications for the evolution of the worker and pseudergate castes, and foraging behaviors JF - Molecular Phylogenetics and Evolution Y1 - 2008 A1 - Legendre, Frédéric A1 - Whiting, Michael F. A1 - Bordereau, Christian A1 - Cancello, Eliana, M. A1 - Evans, Theodore A. A1 - Grandcolas, Philippe SP - 615 EP - 627 KW - arthropoda KW - behavior KW - molecules KW - phylogenetics KW - phylogeny KW - poy KW - sensitivity KW - termites VL - 48 N1 - PDF ER - TY - JOUR T1 - Speciation on a conveyor belt: sequential colonization of the Hawaiian Islands by Orsonwelles spiders (Araneae, Linyphiidae) JF - Systematic Biology Y1 - 2003 A1 - Hormiga, Gustavo A1 - Arnedo, Miquel A1 - Gillespie, Rosemary G. SP - 70 EP - 88 KW - arthropoda KW - biogeography KW - combined data analyses KW - molecular clock KW - partitioned bremer support KW - phylogeny KW - poy KW - sensitivity KW - speciation VL - 52 N1 - PDF ER - TY - JOUR T1 - Data exploration in phylogenetic inference: scientific, heuristic, or neither JF - Cladistics Y1 - 2003 A1 - Grant, Taran A1 - Kluge, Arnold G. SP - 379–418 KW - philosophy KW - phylogenetics KW - sensitivity KW - stability KW - support VL - 19 N1 - PDF ER - TY - JOUR T1 - Stability, sensitivity, science and heurism JF - Cladistics Y1 - 2005 A1 - Grant, Taran A1 - Kluge, Arnold G. SP - 597–604 KW - philosophy KW - phylogenetics KW - sensitivity KW - stability KW - support VL - 21 N1 - PDF ER - TY - JOUR T1 - Phylogenetics of the lizard genus Tropidurus (Squamata : Tropiduridae : Tropidurinae): Direct optimization, descriptive efficiency, and sensitivity analysis of congruence between molecular data and morphology JF - Molecular Phylogenetics and Evolution Y1 - 2001 A1 - Frost, Darrel R. A1 - Rodrigues, Miguel T. A1 - Grant, Taran A1 - Titus, Tom A. SP - 352 EP - 371 KW - alignment KW - phylogenetics KW - poy KW - sensitivity AB - By use of the technique of direct optimization the phylogenetics of the cis-Andean lizard genus Tropidurus were examined on the basis of both molecular (ca. 1.04 kb of sequences from 12S rDNA, valine tDNA, and 16S rDNA) and morphological (93 characters) data. Although equal weighting of all parsimony cost functions logically must maximize descriptive efficiency and explanatory power of all evidence, a sensitivity analysis demonstrated that equal weighting of indels, transitions, transversions, and morphological change provided the most congruent solution between the molecular and the morphological data partitions. The position of Uranoscodon is resolved as the sister taxon of the remaining members of the Tropidurinae. Plica, Uracentron, and Strobilurus, previously considered synonyms of Tropidurus, are resurrected; the group of these three genera form the sister taxon of the former Tropidurus nanuzae group (herein named Eurolophosaurus) plus Tropidurus sensu stricto (composed of the T. bogerti, T. semitaeniatus, T. spinulosus, and T. torquatus groups, herein diagnosed). (C) 2001 Elsevier Science. VL - 21 UR - ://000173251300003 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 -