Daphnids are fresh water microcrustaceans, many of which follow a cyclically parthenogenetic life cycle. Daphnia species have been well studied in the context of ecology, toxicology, and evolution, but their epigenetics remain largely unexamined even though sex determination, the production of sexual females and males, and distinct adult morphological phenotypes, are determined epigenetically. Here, we report on the characterization of histone modifications in Daphnia. We show that a number of histone H3 and H4 modifications are present in Daphnia embryos and histone H3 dimethylated at lysine 4 (H3K4me2) is present nonuniformly in the nucleus in a cell cycle-dependent manner. In addition, this histone modification, while present in blastula and gastrula cells as well as the somatic cells of adults, is absent or reduced in oocytes and nurse cells. Thus, the epigenetic repertoire of Daphnia includes modified histones and as these epigenetic forces act on a genetically homogeneous clonal population Daphnia offers an exceptional tool to investigate the mechanism and role of epigenetics in the life cycle and development of an ecologically important species. 1. Introduction Daphnids are freshwater crustaceans that hold the distinction of being among the relatively few genera that reproduce parthenogenetically. Under most circumstances conventional oogenesis is modified. The first meiotic division is abortive so only the mitosis-like equational division occurs producing clonal diploid eggs [1, 2]. While homologs do pair in the abortive first meiotic division [2] and many of the same meiotic genes are expressed in parthenogenetic and sexual reproduction [3], there is no cytological [2] or genetic [3, 4] evidence for recombination. As a result, other than rare mitotic recombination, conversion, or mutational events [5], the progeny produced are genetically identical [1, 2, 4]. However, while the offspring are genetically identical to each other and their mother, they are not necessarily epigenetically identical. Under stressful conditions some of these clonal diploid eggs develop as males rather than females [1, 6–8]. Additionally, in many species stressful conditions similarly trigger the restoration of conventional meiosis allowing production of haploid eggs and sperm [1–3, 6, 8]. Importantly, parthenogenetically reproducing females and sexually reproducing females are genetically identical, and both are identical to their mothers [1, 4, 5]. Moreover, parthenogenetically produced males are genetically identical to parthenogenetically produced females [1, 4,
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