Evaluation of chloroplast genes for resolving ordinal phylogenetic relationships in Chlorophyceae.

Relationships among chlorophycean algae are being resolved with ever increasing frequency due to an abundance of molecular data and phylogenetic methods. Despite the current bulk of data, however, many crucial phylogenetic relationships remain insufficiently resolved. In addition, analyses using different sources of molecular data often obtain incongruent results. Following an initial reliance on relatively few genes (e.g., 18S, rbcL), current studies employ data from several loci simultaneously. With whole chloroplast genome sequences available for a sparse sample of all major Chlorophyceae lineages, we are poised to evaluate the relative utility of various chloroplast genes for resolving phylogenetic relationships, and thus to make informed decisions about the most useful genes to pursue in future phylogenetic studies. To this end, we investigated (1) the ability of nine chloroplast genes (atpA, atpB, psaA, psaB, psbA, psbB, psbC, psbD, rbcL) to resolve ordinal relationships in Chlorophyceae, (2) the effect of increased taxon sampling on the topology and support values for four of these gene regions (psaA, psaB, psbC, rbcL), and (3) the topology achieved by analyzing multiple gene regions simultaneously. Several relationships were recovered in a majority of single-gene analyses (e.g., the monophyly of Chaetopeltidales + Chaetophorales + Oedogoniales and Sphaeropleales + Volvocales), occasionally with high statistical support. Inclusion of additional taxa in single-gene analyses did not appreciably alter branch support for ordinal relationships. Analyses of combined data from multiple genes, however, achieved the highest overall branch support and congruence with expected relationships. Preliminary results support psaA, psaB, and psbC as candidate regions for resolving ordinal relationships in Chlorophyceae, whereas rbcL data produced trees that were less well resolved at deeper nodes and less consistent with the current understanding of chlorophycean phylogenetic relationships.