Ribosomal DNA variation in Daphnia pulex

Variation in the ribosomal DNA (rDNA) gene family was surveyed in five cyclically parthenogenetic populations of Daphnia pulex from central Illinois and in obligately parthenogenetic clones from Illinois and Ontario. A total of 37 distinct rDNA repeat types were identified on the basis of restriction-site and repeat-length polymorphism in a sample of 90 isolates. Repeat-type diversity was high within cyclic populations; however, individuals possessed only a small subset of the repeat-type variation present in each population. The distribution of repeat types within and among individuals suggested that new variants spread within rDNA arrays much faster than arrays carrying the variants spread within populations. This observation is contrary to a model developed by Ohta and Dover for strictly sexual organisms. Previous surveys of isozyme and mitochondrial DNA variation in these populations showed that gene flow among them is limited. Hierarchical analysis of rDNA restriction-site variation was consistent with this observation and showed that genetic divergence accumulates between populations for rDNA almost as rapidly as it does for single-copy nuclear genes (isozymes). Analysis of rDNA variation in obligately parthenogenetic clones provided evidence that both intra- and interchromosomal exchanges occur between rDNA arrays in the absence of meiosis. Moreover, individuals reproducing by obligate parthenogenesis possessed fewer rDNA repeat types, on average, than did individuals from cyclic populations, suggesting that there is a net loss of rDNA repeat-type variability within obligately clonal lineages over time. Preliminary analyses of two additional species, D. pulicaria and D. obtusa, revealed several restriction-site polymorphisms that were found in more than one of the three species. The existence of such shared polymorphisms advises caution in the use of multigene-family variation to infer phylogenies among species when levels of intraspecific variation have not been assessed.