Internal Transcribed Spacer 2 (nu ITS2 rRNA) Sequence-Structure Phylogenetics: Towards an Automated Reconstruction of the Green Algal Tree of Life

L). Some have advocated the use of the nuclear-encoded, internal transcribed spacer two (ITS2) as an alternative to the traditional chloroplast markers. However, the ITS2 is broadly perceived to be insufficiently conserved or to be confounded by introgression or biparental inheritance patterns, precluding its broad use in phylogenetic reconstruction or as a DNA barcode. A growing body of evidence has shown that simultaneous analysis of nucleotide data with secondary structure information can overcome at least some of the limitations of ITS2. The goal of this investigation was to assess the feasibility of an automated, sequence-structure approach for analysis of IT2 data from a large sampling of phylum Chlorophyta.Sequences and secondary structures from 591 chlorophycean, 741 trebouxiophycean and 938 ulvophycean algae, all obtained from the ITS2 Database, were aligned using a sequence structure-specific scoring matrix. Phylogenetic relationships were reconstructed by Profile Neighbor-Joining coupled with a sequence structure-specific, general time reversible substitution model. Results from analyses of the ITS2 data were robust at multiple nodes and showed considerable congruence with results from published phylogenetic analyses.Our observations on the power of automated, sequence-structure analyses of ITS2 to reconstruct phylum-level phylogenies of the green algae validate this approach to assessing diversity for large sets of chlorophytan taxa. Moreover, our results indicate that objections to the use of ITS2 for DNA barcoding should be weighed against the utility of an automated, data analysis approach with demonstrated power to reconstruct evolutionary patterns for highly divergent lineages

Characterisation of microsatellite loci in the habitat-forming kelp, Ecklonia radiata (Phaeophyceae, Laminariales)

The original publication can be found at www.springerlink.comHabitat forming algae play an important role in the ecology of temperate reefs worldwide. Despite this, our understanding of levels of gene flow within and among populations of algae is largely limited to studies on intertidal species; we know comparatively little about important habitat-forming subtidal algae. Here, we develop eight polymorphic microsatellite markers for the characterisation of population genetic diversity and structure in the subtidal kelp, Ecklonia radiata. This large macroalga is the most abundant habitat-forming kelp on the subtidal rocky reefs of temperate Australia and New Zealand where it forms extensive forests that support an astounding diversity of associated taxa.G. Dolman and M. A. Colema