Copy number variation of ribosomal RNA genes and the Pokey DNA transposon in the Daphnia pulex species complex

There are two full length variants of the Pokey DNA transposon, PokeyA and PokeyB, and two MITEs, mPok1 and mPok2. Pokey inserts into ribosomal DNA (rDNA) and other genomic locations within the genomes of Daphnia species. I used qPCR to estimate haploid rDNA and Pokey copy number in five Daphnia pulex complex species. In general, rDNA number ranges from ~100 to 500. In four species, low numbers of PokeyA and PokeyB in rDNA and the rest of the genome suggest these elements have low transposition rates, high deletion rates, and/or strong purifying selection against them at the host level. Further, PokeyA may have a higher transposition rate than PokeyB. In these species, mPok1 was not found, and mPok2 is likely inactive. In comparison, the fifth species, D. arenata, which may be a hybrid, has higher Pokey numbers. Higher Pokey numbers could be due to release from epigenetic repression following hybridization.