Distinguishing North American D. pulex and D. pulicaria
North American D. pulex and D. pulicaria are thought to have recently diverged from a common ancestor and adapted to distinct environments while still experiencing introgression (Omilian and Lynch 2009; Cristescu et al. 2012). Such introgression may cause the D. pulex /pulicaria hybrids to have mtDNA from either D. pulex or D. pulicaria , thus biasing inferences based on trees when derived from mtDNA data (Marková et al. 2013). Although the nuclear-encoded lactate dehydrogenase locus (Ldh) has been used to discriminate D. pulex and D. pulicaria , and was useful in determining the species of NZ Daphnia samples, inferring species solely based on the Ldh locus can still be misinformative due to hybridization and backcrossing (Xu et al. 2013). For example, an Ldh SSDaphnia that derived from crossing between SF D. pulex/pulicaria and SS D. pulex may be erroneously inferred as a non-hybrid clone. To eliminate the limitations of a single nuclear marker to derive inferences, we generated a set of 24,185 D. pulicaria -specific nuclear markers that are monomorphic in every non-hybrid D. pulicaria, and unique with respect to North American D. pulex . These markers will be useful for diagnostic purposes in other future studies involving these two species, including the identification of hybrids. They may also serve as a resource for studying genes involved in potential adaptive divergence betweenD. pulex and D. pulicaria.