Ribosomal DNA evolution at the population level: nucleotide variation in intergenic spacer arrays of Daphnia pulex

Nucleotide variation was surveyed in 21 subrepeat arrays from the ribosomal DNA intergenic spacer of three Daphnia pulex populations. Eighteen of these arrays contained four subrepeats. Contrary to expectations, each of the four positions within the array had a different consensus sequence. However, gene conversion, involving sequences less than the length of a subrepeat, had occurred between subrepeats in different positions. Three arrays had more than four subrepeats and were undoubtedly generated by unequal crossing over between standard-length arrays. The data strongly suggested that most unequal exchanges between arrays are intrachromosomal and that they occur much less frequently than unequal exchanges at the level of the entire rDNA repeat. Strong associations among variants at different positions allowed the recognition of five groups of arrays, two of which were found in more than one population. Five of the seven individuals surveyed had arrays from more than one group. Analysis of the distribution of nucleotide variation suggested that the populations were quite divergent, a result that is concordant with previous surveys of allozyme and mitochondrial DNA variation. It was suggested that some of the subrepeat array types are quite old, at least predating the recolonization of pond habitats in the midwestern United States after the last glaciation.