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3
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85027741514
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(1975)
Am. Zool.
, vol.15
, pp. 391
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18
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0000311591
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Total genomic DNA was isolated by standard techniques and amplified with the polymerase chain reaction (PCR) D. M. Hillis and C. Moritz, Eds. (Sinauer, Sunderland, MA PCR fragments were then either sequenced directly (with Sequenase version 2.0, U.S. Biochemical) or cloned into a plasmid vector before sequencing. In both cases, replicates of the PCR amplification were sequenced. A list of the PCR and sequencing oligonucleotides and a description ofthe PCR conditions are available from K.M.H. and A.A.A. by way of e-mail (halanych@utxvms.cc.utexas.edu and aguinald@uclaue.mbi.ucla.edu). The following organisms were used in this study. The sequences for Glottidia pyramidata (inarticulate, GenBank accession number U12647), Phoronis vancouverensis (phoronid, U12648), Plumatella repens (bryozoan, U12649), Terebratalia transversa (articulate, Ul2650), and Glycera americana (polychaete, U19519) were collected by the authors
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(1990)
Molecular Systematics
, pp. 318-370
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Hillis, D.M.1
Larson, A.2
Davis, S.K.3
Zimmer, E.A.4
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19
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0001311362
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Sequences for Anemonia sulcata (anthozoan, X53498), Tripedalia cystophora (scyphozoan, L10829), Artemia salina (crustacean, X01723), Eurypelma californica (chelicerate, X13457), Placopecten magellanicus (bivalve, X53899), Acanthopleura japonica (chiton, X702), Antedon serrata (echinoderm, D14357), Lampetra aepyptera (vertebrate, M97573), and Branchiostoma floridae (cephalochordate, M97571) were extracted from GenBank release 81.0. Sequences were aligned with the program Clustal V and were then proofread by hand. Regions that could not be readily aligned were excluded from the analyses. The alignments and position of the excluded regions are available at the Internet address given above for K.M.H.
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(1992)
CABIOS
, vol.8
, pp. 189
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Higgings, D.G.1
Bleasby, A.J.2
Fuchs, R.3
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23
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0004248459
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The sequence alignment of the 14-terminal taxa included 1605 unambiguously aligned nucleotide positions, of which 502 are variable and 294 are phylogenetically informative (that is, parsimony sites). D. L. Swofford's program PAUP version 3.1.2d5 Smithsonian Institution, Washington, DC was used for the parsimony analyses. The program package PHYLIP version 3.5 (J. Felsenstein, Department of Genetics, University of Washington) was used for the neighbor-joining and maximum likelihood analyses. A revision of the PHYLIP maximum likelihood program, fastDNAml version 1.0 (G. J. Olsen, University of Illinois at Urbana-Champaign), was also used
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(1993)
Phylogenetic Analysis Using Parsimony
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27
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85027753476
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in preparation] was used. The parsimony and Kimura analyses incorporated a transversion-transition ratio of 1.4:1. We obtained this ratio by determining the number of unambiguous transition and transversion events of 10 randomly selected trees and calculating the average ratio. The maximum likelihood score is also maximized atthis ratio. Analyses with transversion-transition ratios of 1:1 to 3:1 did not alter our conclusions. Bootstrap analyses
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Lake, J.A.1
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29
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12044253190
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Empirical studies of bootstrap analyses indicate that bootstrap values represent highly conservative estimates of phylogenetic accuracy. Typically, bootstrap proportions of ≥70% correspond to a probability of ≥95% that the respective lade is an historical lineage
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(1993)
Syst. Biol.
, vol.42
, pp. 182
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Hillis, D.M.1
Bull, J.J.2
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30
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84960612286
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The topology-dependent cladistic permutation tail probability (T-PTP) test determines whether the difference in length between the shortest tree supporting the monophyly of this clade (997 steps) and the shortest tree not supporting monophyly (1003 steps) is significantly different from the difference in length expected from randomized data. If the difference in length between the monophyly and nonmonophyly trees is outside 95% of the distribution based on randomized data, it can be concluded that the data significantly support monophyly of the lade
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(1991)
Syst. Zool.
, vol.40
, pp. 366
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Faith, D.P.1
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31
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0026746685
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We used 200 randomized data sets that were created with the program Shuffle (J. P. Huelsenbeck, University of Texas at Austin) and were analyzed by means of the parsimony criterion
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(1992)
Science
, vol.258
, pp. 1345
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Ballard, J.W.O.1
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