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 - A phylogeny of extant penguins (Aves: Sphenisciformes) combining morphology and mitochondrial sequences
JF - Cladistics
Y1 - 2005
A1 - Bertelli, Sara
A1 - Giannini, Norberto P.
SP - 209
EP - 239
KW - aves
KW - biogeography
KW - character evolution
KW - combined data analyses
KW - molecules
KW - morphology
KW - mtDNA
KW - phylogeny
KW - poy
VL - 21
N1 - PDF
ER -