TY - JOUR T1 - Nucleic acid sequence phylogeny and random outgroups JF - Cladistics Y1 - 1990 A1 - Wheeler, W. C. SP - 363–367 KW - outgroup KW - phylogenetics VL - 6 N1 - DO NOT HAVE ER - TY - JOUR T1 - Measuring topological congruence by extending character techniques JF - Cladistics Y1 - 1999 A1 - Wheeler, W. C. SP - 131–135 KW - congruence KW - phylogenetics VL - 15 N1 - DO NOT HAVE ER - TY - CHAP T1 - Optimization alignment: down, up, error, and improvements T2 - Techniques in molecular systematicsand evolution Y1 - 2002 A1 - Wheeler, W. C. ED - DeSalle, Rob ED - Giribet, G. ED - Wheeler, W. C. SP - 55 EP - 69 KW - poy JF - Techniques in molecular systematicsand evolution PB - Birkhäuser CY - Basel N1 - DO NOT HAVE ER - TY - BOOK T1 - Dynamic homology and phylogenetic systematics: a unified approach using POY Y1 - 2006 A1 - Wheeler, W. C. A1 - Aagesen, Lone A1 - Arango, Claudia P. A1 - Faivovich, Julián A1 - Grant, Taran A1 - D'Haese, Cyrille A1 - Janies, Daniel A1 - Smith, W. L. A1 - Varón, A. A1 - Giribet, G. SP - 365 KW - homology KW - molecular characters KW - phylogenetics PB - American Museum of Natural History CY - New York N1 - book ER - TY - JOUR T1 - Mitochondrial intergenic spacer in fairy basslets (Serranidae: Anthiinae) and the simultaneous analysis of nucleotide and rearrangement data JF - American Museum Novitates Y1 - 2009 A1 - Smith, W. L. A1 - Smith, K. R. A1 - Wheeler, W. C. SP - 1 EP - 10 KW - dna rearrangement KW - molecular characters KW - mtDNA KW - poy VL - 3652 N1 - PDF 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 - Genomic analysis and geographic visualization of the spread of avian influenza (H5N1) JF - Systematic Biology Y1 - 2007 A1 - Janies, Daniel A1 - Hill, Andrew W. A1 - Guralnick, Robert A1 - Habib, Farhat A1 - Waltari, Eric A1 - Wheeler, W. C. SP - 321 EP - 329 KW - biogeography KW - phylogenetics KW - poy KW - supermap VL - 56 N1 - PDF ER - TY - JOUR T1 - Triploblastic relationships with emphasis on the acoelomates and the position of Gnathostomulida, Cycliophora, Plathyhelminthes, and Chaetognatha: a combined approach of 18S rDNA sequences and morphology JF - Systematic Biology Y1 - 2000 A1 - Giribet, G. A1 - Distel, Daniel L. A1 - Polz, M. A1 - Sterrer, W. A1 - Wheeler, W. C. SP - 539 EP - 562 VL - 49 N1 - DO NOT HAVE ER -