Support, Ribosomal Sequences and the Phylogeny Of The Eukaryotes

Abstract

Sequences of the small subunit SSU ribosomal RNA are considered useful for reconstructing the tree of life because this molecule is found in all organisms and is large enough not to have become saturated with multiple mutations. However, these data sets are large, difficult to align, and have extreme biases in base compositions which makes their phylogenetic signal ambiguous. Large ambiguous data sets may have many most-parsimonious trees, and finding them all may be impossible using convential phylogenetic methods. To examine the reliability of the number and relationships of eukaryotic kingdoms proposed by previous analyses of the SSU, we calculated trees from aligned sequences from eukaryotes in the Ribosomal Database Project using parsimony jackknifing which uses a resampling procedure to rapidly search large data sets for the branches that are strongly supported and eliminates poorly supported groups. Two separate analyses were carried out: an analysis in which all bases were equally weighted, and one in which transversions only were used. The parsimony jackknife procedure was able to efficiently find trees in which most major groups of eukaryotes were supported and in which some evolutionary hypotheses proposed by previous workers were tested. The relationships of these major groups to each other were largely unresolved, indicating that the SSU data, as represented in this database, is insufficient for answering questions about these deep branches. Interestingly, the analysis of transitions differs from the results of the entire data set, primarily being less resolved. This indicates that transversional mutations are important contributors to the resolved structure of the tree.ᮊ

Phylogenetic analysis identifies the invertebrate pathogen Helicosporidium sp. as a green alga (Chlorophyta).

“…Although the taxonomic position of D. discoideum is subject to debate (Baldauf et al, 2000), it appears basal in conservative rDNA reconstruction (Lipscomb et al, 1998). Our tree is fairly consistent with other previous molecular phylogenetic studies of eukaryotes (Drouin et al, 1995 ;Lipscomb et al, 1998 ;Baldauf et al, 2000), showing that the animal and fungal lineages share a more recent common ancestor than either does with the plant lineage (Baldauf & Palmer, 1993) and that green algae and green plants form a monophyletic group. Due in part to limited sampling, the relationships between protists are not well resolved, Helicosporidium sp.…”

“…Additionally, maximum-parsimony analyses, including jackknifing (100 000 replicates ; Farris et al, 1996), were also performed using *. We chose the latter, conservative approach for its ability to search rapidly a large amount of tree space and to estimate support for an unambiguously resolved group (Lipscomb et al, 1998).…”

Morphology disentangles the systematics of a ubiquitous but elusive meiofaunal group (Kinorhyncha: Pycnophyidae)

“…Continuous characters (total trunk length, maximal sternal width/total trunk length) were coded as categorical by defining six and four consecutive states and analysed as unordered (Kitching et al., ; Wiens, ; Martínez et al., ). Several coding methods for morphological characters have been proposed, all of them with problems related to character linkage, hierarchical dependency, missing values and information content (Pleijel, ; Wilkinson, ; Kitching et al., ; Lipscomb et al., ). The problems associated with the “c‐coding” are the effect of “inapplicable” characters on the tree topology and the hierarchical coding that might inflate the nodal support for certain clades.…”

Cephalic muscles of Cyclostomes (hagfishes and lampreys) and Chondrichthyes (sharks, rays and holocephalans): comparative anatomy and early evolution of the vertebrate head muscles

“…Donoghue & Smith, ; Gess, Coates & Rubidge, ; Near, ; Miyashita, and citations therein), molecular data supporting the cyclostome monophyly have increasingly gained popularity (e.g. Stock & Whitt, ; Lipscomb et al ., ; Kuraku et al ., ; Delarbre et al ., ; Furlong & Holland, ; Takezaki et al ., ; Blair & Hedges, ; Delsuc et al ., ; Kuraku & Kuratani, ; Mallatt & Winchell, ; Near, ; Heimberg et al ., ). Developmental insights appear to reinforce the latter view.…”