02127nas a2200229   4500008004100000245012600041210006900167260000800236300001200244490000700256520145800263653002401721653001401745653001001759653001001769653001801779653000801797653001301805100001801818700002001836856004101856       2004                        eng d00aPolyphyly of the mail-cheeked fishes (Teleostei : Scorpaeniformes): evidence from mitochondrial and nuclear sequence data0 aPolyphyly of the mailcheeked fishes Teleostei Scorpaeniformes ev  cAUG  a627-6460 v323 aMitochondrial 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.10adirect optimization10aevolution10amtDNA10anuDNA10aphylogenetics10apoy10ataxonomy1 aSmith, W., L.1 aWheeler, W., C.  u<u><Go to ISI>://000222732000016</u>01993nas 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<u><Go to ISI>://000231591500017</u>