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 -