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 - JOUR T1 - Iterative pass optimization of sequence data JF - Cladistics Y1 - 2003 A1 - Wheeler, Ward C. SP - 254 EP - 260 KW - optimization KW - phylogenetics KW - poy VL - 19 N1 - PDF ER - TY - JOUR T1 - Evaluating the performance of a successive-approximations approach to parameter optimization in maximum-likelihood phylogeny estimation JF - Molecular Biology and Evolution Y1 - 2005 A1 - Sullivan, Jack A1 - Abdo, Zaid A1 - Joyce, Paul A1 - Swofford, David L. SP - 1386–1392 KW - likelihood KW - ML KW - model selection KW - optimization KW - phylogenetics VL - 22 N1 - PDF ER - TY - JOUR T1 - Phylogeny and biogeography of the Malagasy and Australasian rainbowfishes (Teleostei : Melanotaenioidei): Gondwanan vicariance and evolution in freshwater JF - Molecular Phylogenetics and Evolution Y1 - 2004 A1 - Sparks, J. S. A1 - Smith, W. L. SP - 719 EP - 734 KW - atherinomorpha KW - bedotia KW - bedotiidae KW - cladistic biogeography KW - fishes KW - gondwana KW - madagascar KW - melanotaeniidae KW - molecular phylogeny KW - multiple-sequence alignment KW - northeastern madagascar KW - optimization KW - paleogeographic evolution KW - parsimony analysis KW - rheocles KW - single-origin KW - systematics AB - Phylogenetic relationships of the Malagasy and Australasian rainbowfishes are investigated using 4394 characters derived from five mitochondrial genes (12S, 16S, tRNA-Valine, ND5, and COI), three nuclear genes (28S, histone H3, and TMO-4c4), and 102 morphological transformations. This study represents the first phylogenetic analysis of the endemic Malagasy family Bedotiidae and includes a nearly complete taxonomic review of all nominal species, as well as numerous undescribed species. Simultaneous analysis of the molecular and morphological datasets results in two equally most parsimonious trees. Results indicate that Bedotiidae (Bedotia + Rheocles) and Bedotia are monophyletic, whereas Rheocles is paraphyletic with the inclusion of two recently described species from northeastern Madagascar, R. vatosoa, and R. derhami. Rheocles vatosoa and R. derhami are sister taxa, and this clade is recovered as the sister group to Bedotia. The remaining species of Rheocles are not sexually dimorphic and comprise a clade that is recovered as the sister group to Bedotia + (R. derhami + R. vatosoa), all of which are sexually dichromatic, and sexually dimorphic for pigmentation and fin development. Three geographically distinct clades are recovered within Bedotia, one comprising species with distributions ranging from mid- to southeastern Madagascar, another including species restricted to eastern drainages north of the Masoala Peninsula, and a third comprising taxa with distributions extending from the Masoala Peninsula south to the Ivoloina River. The Australian/New Guinean melanotaeniids are monophyletic and are recovered as the sister group to Bedotiidae. The Australasian Telmatherinidae and Pseudomugilidae comprise a clade that is recovered as the sister group to the Melanotaeniidae-Bedotiidae clade. This sister-group relationship between Malagasy bedotiids and a clade restricted to Australia-New Guinea, and the absence of a close relationship between bedotiids and African or Mascarene atheriniforms, is congruent with the break-up of Gondwana, not a scenario reliant on Cenozoic trans-oceanic dispersal. Finally, results of the phylogenetic analysis indicate that Atheriniformes is polyphyletic and further corroborate recent morphological hypotheses, which have recovered Bedotiidae in a derived position within Atherinoidei. (C) 2004 Elsevier Inc. All rights reserved. VL - 33 UR - ://000225206700015 N1 - Times Cited: 0ArticleEnglishCited References Count: 81872ks 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 -