Rate acceleration and long-branch attraction in a conserved gene of cryptic daphniid (Crustacea) species.

The nuclear large subunit (LSU) rRNA gene is a rich source of phylogenetic characters because of its large size, mosaic of slowly and rapidly evolving regions, and complex secondary structure variation. Nevertheless, many studies have indicated that inconsistency, bias, and gene-specific error (e.g., within-individual gene family variation, cryptic sequence simplicity, and sequence coevolution) can complicate animal phylogenies based on LSU rDNA sequences. However, most of these studies sampled small gene fragments from expansion segments--among animals only five nonchordate complete LSU sequences are published. In this study, we sequenced near-complete nuclear LSU genes from 11 representative daphniids (Crustacea). The daphniid expansion segment V6 was larger and showed more length variation (90-351 bp) than is found in all other reported LSU V6 sequences. Daphniid LSU (without the V6 region) phylogenies generally agreed with the existing phylogenies based on morphology and mtDNA sequences. Nevertheless, a major disagreement between the LSU and the expected trees involved a positively misleading association between the two taxa with the longest branches, Daphnia laevis and D. occidentalis. Both maximum parsimony (MP) and maximum likelihood (ML) optimality criteria recovered this association, but parametric simulations indicated that MP was markedly more sensitive to this bias than ML. Examination of data partitions indicated that the inconsistency was caused by increased nucleotide substitution rates in the branches leading to D. laevis and D. occidentalis rather than among-taxon differences in base composition or distribution of sites that are free to vary. These results suggest that lineage-specific rate acceleration can lead to long-branch attraction even in the conserved genes of animal species that are almost morphologically indistinguishable.