EFFECT OF TAXON SAMPLING, CHARACTER WEIGHTING, AND COMBINED DATA ON THE INTERPRETATION OF RELATIONSHIPS AMONG THE HETEROKONT ALGAE

Authors: Goertzen L.R.; Theriot E.C.

Source: Journal of Phycology, Volume 39, Number 2, April 2003 , pp. 423-443(21)

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Abstract:

Nuclear ribosomal small subunit and chloroplast rbcL sequence data for heterokont algae and potential outgroup taxa were analyzed separately and together using maximum parsimony. A series of taxon sampling and character weighting experiments was performed. Traditional classes (e.g. diatoms, Phaeophyceae, etc.) were monophyletic in most analyses of either data set and in analyses of combined data. Relationships among classes and of heterokont algae to outgroup taxa were sensitive to taxon sampling. Bootstrap (BS) values were not always predictive of stability of nodes in taxon sampling experiments or between analyses of different data sets. Reweighting sites by the rescaled consistency index artificially inflates BS values in the analysis of rbcL data. Inclusion of the third codon position from rbcL enhanced signal despite the superficial appearance of mutational saturation. Incongruence between data sets was largely due to placement of a few problematic taxa, and so data were combined. BS values for the combined analysis were much higher than for analyses of each data set alone, although combining data did not improve support for heterokont monophyly.

Keywords: bootstrap support; Chromista; combined data; heterokont algae; molecular phylogeny; rbcL; ribosomal DNA; stramenopiles; taxon sampling

Document Type: Research article

DOI: http://dx.doi.org/10.1046/j.1529-8817.2003.01238.x

Publication date: 2003-04-01