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The use of 18S rDNA sequences for inferring phylogenies, in particular for higher taxonomic level analysis, has a long tradition in phycology. Similar to ITS2, the 18S rDNA displays a conserved secondary structure that could be used simultaneously with the primary sequence to increase the amount of information used when inferring phylogenetic relationships. Sequence-structure phylogenetics is already established for ITS2 research. Secondary structures no longer simply guide alignments and trees but are used simultaneously by encoding the sequence-structure information into a 12-letter alphabet. We used the knowledge gathered from the extensive body of ITS2 research regarding sequence-structure phylogenetics and applied it to 18S rRNA data; we present THESES db, the Algae 18S rDNA Sequence-Structure Database (), which contains sequences and their individual secondary structures for three major groups of algae (Chlorophyta, Bacillariophyta and Rhodophyta). This database was designed to serve as the starting point for future 18S rDNA sequence-structure based phylogenetic analyses that will eventually extend beyond phycology. One hundred phylogenetic trees generated from 18S sequence-only datasets and from parallel 18S sequence-structure datasets were compared for each taxon analyzed in this study (diatoms, green algae and red algae). Half of the comparisons produced trees with different topologies that frequently related to the status of sister genera. Using the lineage information for each species as listed in GenBank, we determined that the sequence-structure approach resolved a genus as monophyletic, while the sequence-only approach failed to do so in comparisons that comprised 3% of the cases examined. The reverse was true for a total of 8.3% of the comparisons that we generated. Future work, both in our labs and among the broader phycological community, will provide additional data to test the accuracy and robustness of a sequence-structure approach at different taxonomic ranks. [ABSTRACT FROM AUTHOR]

The distribution of loroxanthin in chlorophycean flagellates is consistent with their phylogeny as inferred from molecular and organismal characters. Although polarity of this character cannot yet be determined, if the absence of loroxanthin is plasiomorphic for chlorophycean flagellates, the presence of loroxanthin defines a clade that includes the Euchlamydomonas morphological groups, two other species of Chlamydomonas, C. asymmetrica and C. oblonga, and Gonium pectorale. A subsequent reversal to loroxanthin absence is apomorphic for the more complex volvocacean taxa. These results suggest that loroxanthin distribution will be useful for resolving phylogenetic questions in green algae. [ABSTRACT FROM AUTHOR]

Comparative ultrastructural data have shown that atleast two distinct groups exist within Carteria. Similarly, interpretations of variation in gross morphological features have led to the discovery of morphologically distinct groups within the genus. Partial sequences from the nuclear-encoded small and large subunit ribosomal RNA molecules of selected Carteria taxa were studied as a means of 1)testing hypotheses that distinct groups of species exist within the genus and 2)assessing monophyly of the genus. Parsimony analysis of the sequence data suggests that three Carteria species, C.lunzenis, C. crucifera, and C.oliveri, form a monophyletic group that is the basal sister group to all other ingroup flagellate taxa (including species of Chlamydomonas, Haematococcus, Stephanosphaera, Volvox and Eudorina). Two other Carteria taxa, C.radiosa and Carteria sp. (UTEX isolate LB 762), form a clade that is the sister group to a clade that includes Haematococcus spp., Chlamydomonas spp., and Stephanosphaera. Thus, the sequence data support the interpretation of ultrastructural evidence that described two distinct Carteria lineages. Moreover, the sequence data suggest that these two Carteria groups do not form a monophyletic assemblage. Parsimony analysis of a suite of organismal (morphologica, ultrastructural, life history and biochemical) character data also suggest two distinct lineages among the five Carteria taxa; however, the organismal data are ambiguous regarding monopophyly of these Carteria taxa. When the two independent data sets are pooled, monophyly of Carteria is not supported; therefore, the weight of available evidence, both molecular and organismal, fails to support the concept of Carteria as a natural genus. [ABSTRACT FROM AUTHOR]