THE ORIGIN AND EVOLUTION OF VARIABLE-REGION HELICES IN V4 AND V7 OF THE SMALL-SUBUNIT RIBOSOMAL-RNA OF BRANCHIOPOD CRUSTACEANS

We sequenced the V4 and V7 regions of the small-subunit ribosomal RNA (SSU rRNA) from 38 species of branchiopod crustaceans (e.g., Artemia, Daphnia, Triops) representing all eight extant orders. Ancestral large -bodied taxa in the orders Anostraca, Notostraca, Laevicaudata, and Sp inicaudata (limnadiids and cyzicids) possess the typical secondary str ucture in these regions, whereas the spinicaudatan Cyclestheria and al l of the cladocerans (Anomopoda, Ctenopoda, Onychopoda, and Haplopoda) possess three unique helices. Although the lengths and primary sequen ces of the distal ends of these helices are extremely variable, their locations, secondary structures, and primary sequences at the proximal end are conserved, indicating that they are homologous. This evidence supports the classical view that Cladocera is a monophyletic group an d that the cyclestheriids are transitional between spinicaudatans and cladocerans. The single origin and persistence since the Permian of th e unique cladoceran helices suggests that births and deaths of variabl e region helices have been rare. The broad range of sequence divergenc es observed among the cladoceran helices permitted us to make inferenc es about their evolution. Although their proximal ends are very CC-bia sed, there is a significant negative correlation between length and GC content due to an increasing proportion of U at their distal ends. Sl ippage-like processes occurring at unpaired nucleotides or bulges, whi ch are very U-biased, are associated with both helix origin and runawa y length expansion. The overall GC contents and lengths of V4 and V7 a re highly correlated. More surprisingly, the lengths of these SSU rRNA variable regions are also highly correlated with the length of the la rge-subunit rRNA expansion segment, D2, indicating that mechanisms aff ecting length variation do so both across single genes and across gene s in the rRNA gene family.