00639nas a2200181 4500008004100000245009500041210006900136300001200205490000700217653001400224653001500238653001800253653000800271653001600279653001200295100002200307856012800329 1995 eng d00aSequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data0 aSequence alignment parameter sensitivity and the phylogenetic an a321-3310 v4410aalignment10acongruence10aphylogenetics10apoy10asensitivity10asupport1 aWheeler, Ward, C. uhttps://pterioidea.myspecies.info/content/sequence-alignment-parameter-sensitivity-and-phylogenetic-analysis-molecular-data00725nas a2200205 4500008004100000245007800041210006900119300001200188490000700200653002700207653002500234653001800259653001600277653001900293100002200312700002600334700001800360700002600378856011500404 2006 eng d00aPartition-free congruence analysis: implications for sensitivity analysis0 aPartitionfree congruence analysis implications for sensitivity a a256-2630 v2210acombined data analyses10amolecular characters10aphylogenetics10asensitivity10atotal evidence1 aWheeler, Ward, C.1 aRamírez, Martín, J.1 aAagesen, Lone1 aSchulmeister, Susanne uhttps://pterioidea.myspecies.info/content/partition-free-congruence-analysis-implications-sensitivity-analysis02479nas a2200265 4500008004100000245010000041210006900141260000800210300001200218490000700230520173500237653001401972653001501986653002402001653001502025653001002040653001702050653001802067653000802085653001602093100002102109700002002130700002202150856004102172 2002 eng d00aSimultaneous analysis of the basal lineages of Hymenoptera (Insecta) using sensitivity analysis0 aSimultaneous analysis of the basal lineages of Hymenoptera Insec cOCT a455-4840 v183 aThe 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.10aalignment10acongruence10adirect optimization10amorphology10amtDNA10aoptimization10aphylogenetics10apoy10asensitivity1 aSchulmeister, S.1 aWheeler, W., C.1 aCarpenter, J., M. u://00017906150000100964nas a2200265 4500008004100000245019000041210006900231300001200300490000700312653001500319653001300334653001400347653001800361653001400379653000800393653001600401653001300417100002500430700002500455700002500480700000500505700002400510700002500534856013900559 2008 eng d00aThe phylogeny of termites (Dictyoptera: Isoptera) based on mitochondrial and nuclear markers: implications for the evolution of the worker and pseudergate castes, and foraging behaviors0 aphylogeny of termites Dictyoptera Isoptera based on mitochondria a615-6270 v4810aarthropoda10abehavior10amolecules10aphylogenetics10aphylogeny10apoy10asensitivity10atermites1 aLegendre, Frédéric1 aWhiting, Michael, F.1 aBordereau, Christian1 a1 aEvans, Theodore, A.1 aGrandcolas, Philippe uhttps://pterioidea.myspecies.info/content/phylogeny-termites-dictyoptera-isoptera-based-mitochondrial-and-nuclear-markers-implications00875nas a2200241 4500008004100000245013600041210006900177300001000246490000700256653001500263653001700278653002700295653002000322653003100342653001400373653000800387653001600395653001500411100002100426700001900447700002800466856013900494 2003 eng d00aSpeciation on a conveyor belt: sequential colonization of the Hawaiian Islands by Orsonwelles spiders (Araneae, Linyphiidae)0 aSpeciation on a conveyor belt sequential colonization of the Haw a70-880 v5210aarthropoda10abiogeography10acombined data analyses10amolecular clock10apartitioned bremer support10aphylogeny10apoy10asensitivity10aspeciation1 aHormiga, Gustavo1 aArnedo, Miquel1 aGillespie, Rosemary, G. uhttps://pterioidea.myspecies.info/content/speciation-conveyor-belt-sequential-colonization-hawaiian-islands-iorsonwellesi-spiders-aran00627nas a2200181 4500008004100000245008200041210006900123300001400192490000700206653001500213653001800228653001600246653001400262653001200276100001700288700002200305856011800327 2003 eng d00aData exploration in phylogenetic inference: scientific, heuristic, or neither0 aData exploration in phylogenetic inference scientific heuristic a379–4180 v1910aphilosophy10aphylogenetics10asensitivity10astability10asupport1 aGrant, Taran1 aKluge, Arnold, G. uhttps://pterioidea.myspecies.info/content/data-exploration-phylogenetic-inference-scientific-heuristic-or-neither00540nas a2200181 4500008004100000245004800041210004600089300001400135490000700149653001500156653001800171653001600189653001400205653001200219100001700231700002200248856008800270 2005 eng d00aStability, sensitivity, science and heurism0 aStability sensitivity science and heurism a597–6040 v2110aphilosophy10aphylogenetics10asensitivity10astability10asupport1 aGrant, Taran1 aKluge, Arnold, G. uhttps://pterioidea.myspecies.info/content/stability-sensitivity-science-and-heurism01867nas a2200217 4500008004100000245021300041210006900254260000800323300001200331490000700343520111800350653001401468653001801482653000801500653001601508100002201524700002601546700001701572700001901589856004101608 2001 eng d00aPhylogenetics of the lizard genus Tropidurus (Squamata : Tropiduridae : Tropidurinae): Direct optimization, descriptive efficiency, and sensitivity analysis of congruence between molecular data and morphology0 aPhylogenetics of the lizard genus Tropidurus Squamata Tropidurid cDEC a352-3710 v213 aBy 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.10aalignment10aphylogenetics10apoy10asensitivity1 aFrost, Darrel, R.1 aRodrigues, Miguel, T.1 aGrant, Taran1 aTitus, Tom, A. u://00017325130000301993nas a2200241 4500008004100000245006200041210006000103260000800163300001200171490000700183520137700190653002401567653000801591653001401599653000801613653001501621653001801636653000801654653001601662653001401678100001801692856004101710 2005 eng d00aDirect optimization, affine gap costs, and node stability0 aDirect optimization affine gap costs and node stability cSEP a641-6530 v363 aThe 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.10adirect optimization10adna10aevolution10agap10amorphology10aphylogenetics10apoy10asensitivity10astability1 aAagesen, Lone u://000231591500017