Recknagel, Friedrich AdolfJennings, John ThomasShiel, Russell JohnMills, ScottSharma, Pranay2014-08-292014-08-292014http://hdl.handle.net/2440/84760The taxonomy of Ceriodaphnia Dana, 1853 has long been uncertain, and their species richness often underestimated due to a lack of good morphological taxonomy. Modern molecular techniques such as genetic barcoding allow the detection of cryptic species. In this study DNA sequences from two mitochondrial DNA (COI and 16s) and one nuclear DNA (28s) gene fragments, were used to investigate Ceriodaphnia diversity in Australia, and is the first molecular analysis of this genus from Australia. A preliminary study using morphology and DNA barcoding of zooplankton diversity, particularly Ceriodaphnia from two South Australian reservoirs: Myponga and South Para and supplemented by specimens from water bodies across Australia, revealed cryptic speciation for Ceriodaphnia. Derived sequences support the recognition of three beaked species in Ceriodaphnia cornuta Sars (1885) complex, C. sp. nov. 1 and C. sp. nov. 2, and three non-beaked species C. dubia Richard, 1894, C. spinata Henry, 1919 and C. sp. nov. 3. We also examined the Folmer primer (LCO 1490 and HCO 2198) region, sourced from 725 complete mitochondrial genomes across 17 animal phyla is universal. The correlation between the frequency of base pair differences in the primer region at different taxonomic levels were analysed using 1-way ANOVA and Fishers Post Hoc analysis. A significant difference in the means of base pair differences from Order to Species and Class to Kingdom levels (ANOVA, F= 8.193, p = 0.00) for LCO 1490 and at the level of Genus (ANOVA, F= 2.538, p = 0.027) for HCO 2198 was detected. This study has demonstrated the potential of DNA barcoding in identifying species in a taxonomically uncertain group like Ceriodaphnia. However, the success of DNA barcoding relies on sequence databases that have been verified taxonomically. This research highlights the importance of an integrative approach required to clarify the taxonomic status of Ceriodaphnia from Australia. It also shows that automated primer sites can be generated for species which have an insufficient numbers of sequences in online genetic databases for which the Universal primers (LCO 1490 and HCO 2198) have been unsuccessful in amplifying the COI gene.invertebrates; Cladocera; Copepoda; mtDNA; GenBank; BOLD; freshwater; AustraliaThesis20140826103540