EFFECT OF TAXON SAMPLING, CHARACTER WEIGHTING, AND COMBINED DATA ON THE INTERPRETATION OF RELATIONSHIPS AMONG THE HETEROKONT ALGAE¹

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.

Magic bullets and golden rules: Data sampling in molecular phylogenetics

“…The consequences, in terms of accuracy and support for inferred phylogenetic relationships, attributable to the taxonomic sample depend on the details of the biological situation as has been shown in empirical studies involving lemurs (Yoder and Irwin, 1999), land plants (Soltis et al, 1999;Rydin and Kallersjo, 2002), birds (Omland et al, 1999;Saunders and Edwards, 2000;Johnson, 2001;Braun and Kimball, 2002), noctuoid moths (Mitchell et al, 2000), xenarthrans (anteaters, armadillos and sloths) (Delsuc et al, 2002), heterokont algae (Goertzen and Theriot, 2003), and many simulations (Sanderson and Donoghue, 1989;Kim, 1996;Graybeal, 1998;Hillis, 1998;Rannala et al, 1998;Poe and Swofford, 1999;Kumar, 2001, 2003;Pollock et al, 2002;Zwickel and Hillis, 2002;Hillis et al, 2003;Poe, 2003). Some of the results of these studies are apparently contradictory, because of factors relating to different performance measures, interactions with specific inference methods, and the nature of the taxa added or deleted.…”

Molecular phylogeny of advanced snakes (Serpentes, Caenophidia) with an emphasis on South American Xenodontines: a revised classification and descriptions of new taxa

“…However, we feel that some of their formally recognized taxa are only weakly supported by their molecular data, or receive conflicting phylogenetic signals in different data sets. These authors made little attempt to analyze the effects of taxon sampling and long branch attraction (Felsenstein, 1978) or repulsion (Siddall & Whiting 1999) in small molecular data matrices, problems that were acknowledged by Kraus & Brown (1998) and Kelly et al (2008), and supported by simulation and other studies (e.g., Goertzen & Theriot, 2003;Salisbury & Kim, 2001). Vidal et al (2007) argued that the problem of long branch attraction (and repulsion) in more basal nodes was better addressed through gene sampling rather than taxon sampling, but this will only partially solve the issue.…”

Diatoms

“…these taxa have similar pigment composition and use silica in some way to make cell wall coverings, albeit the kinds of coverings differ between diatoms and the other two taxa). However, study of ribosomal DNA (rDNA), the large subunit of the ribulose-bisphosphate carboxylase gene (rbcL) and morphological data suggest that a clade of very poorly known microflagellates are sister to diatoms, including algae presently classified as Bolidophyceae and Parmales (Guillou et al, 1999;Daugbjerg and Guillou, 2001;Goertzen and Theriot, 2003;Ichinomiya et al, 2011).…”