Phylogenetics of Flowering Plants Based on Combined Analysis of Plastid atpB and rbcL Gene Sequences

Following (1) the large-scale molecular phylogeny of seed plants based on plastid rbcL gene sequences (published in 1993 by Chase et al., Ann. Missouri Bot. Gard. 80:528-580) and (2) the 18S nuclear phylogeny of flowering plants (published in 1997 by Soltis et al., Ann. Missouri Bot. Gard. 84:1-49),...

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Veröffentlicht in:Systematic biology 2000-06, Vol.49 (2), p.306-362
Hauptverfasser: Savolainen, Vincent, Chase, Mark W., Hoot, Sara B., Morton, Cynthia M., Soltis, Douglas E., Bayer, Clemens, Fay, Michael F., de Bruijn, Anette Y., Sullivan, Stuart, Qiu, Yin-Long
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container_end_page 362
container_issue 2
container_start_page 306
container_title Systematic biology
container_volume 49
creator Savolainen, Vincent
Chase, Mark W.
Hoot, Sara B.
Morton, Cynthia M.
Soltis, Douglas E.
Bayer, Clemens
Fay, Michael F.
de Bruijn, Anette Y.
Sullivan, Stuart
Qiu, Yin-Long
description Following (1) the large-scale molecular phylogeny of seed plants based on plastid rbcL gene sequences (published in 1993 by Chase et al., Ann. Missouri Bot. Gard. 80:528-580) and (2) the 18S nuclear phylogeny of flowering plants (published in 1997 by Soltis et al., Ann. Missouri Bot. Gard. 84:1-49), we present a phylogenetic analysis of flowering plants based on a second plastid gene, atpB, analyzed separately and in combination with rbcL sequences for 357 taxa. Despite some discrepancies, the atpB-based phylogenetic trees were highly congruent with those derived from the analysis of rbcL and 18S rDNA, and the combination of atpB and rbcL DNA sequences (comprising ∼3000 base pairs) produced increased bootstrap support for many major sets of taxa. The angiosperms are divided into two major groups: noneudicots with inaperturate or uniaperturate pollen (monocots plus Laurales, Magnoliales, Piperales, Ceratophyllales, and Amborellaceae-Nymphaeaceae-Illiciaceae) and the eudicots with triaperturate pollen (particularly asterids and rosids). Based on rbcL alone and atpB/rbcL combined, the noneudicots (excluding Ceratophyllum) are monophyletic, whereas in the atpB trees they form a grade. Ceratophyllum is sister to the rest of angiosperms with rbcL alone and in the combined atpB/rbcL analysis, whereas with atpB alone, Amborellaceae, Nymphaeaceae, and Illiciaceae/Schisandraceae form a grade at the base of the angiosperms. The phylogenetic information at each codon position and the different types of substitutions (observed transitions and transversions in the trees vs. pairwise comparisons) were examined; taking into account their respective consistency and retention indices, we demonstrate that third-codon positions and transitions are the most useful characters in these phylogenetic reconstructions. This study further demonstrates that phylogenetic analysis of large matrices is feasible.
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source MEDLINE; JSTOR Archive Collection A-Z Listing; Oxford University Press Journals All Titles (1996-Current)
subjects Angiosperms
Base Sequence
Botany
Classification
Codon - genetics
Datasets
DNA, Plant - genetics
Evolution
Flowering plants
Flowers & plants
Genes
Genetics
Magnoliopsida - classification
Magnoliopsida - genetics
Microbiology
Phylogenetics
Phylogeny
Plant Proteins - genetics
Plants
Plastids
Plastids - genetics
Ribosomal DNA
Ribulose-Bisphosphate Carboxylase - genetics
Taxa
title Phylogenetics of Flowering Plants Based on Combined Analysis of Plastid atpB and rbcL Gene Sequences
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