Microcrustacean taxa in temporary waters are important contributors to aquatic biodiversity on the landscape scale even though much of the diversity at the molecular level is still undiscovered. Cladoceran species other than Daphnia are not frequently targeted in molecular investigations. We used nuclear allozyme polymorphisms as well as DNA sequence variation in mitochondrial 16 S and COI gene regions to reveal patterns of genetic differentiation among populations of a cladoceran species ? Moina brachiata ? that typically inhabits temporary aquatic habitats. Samples originated from 20 temporary to semi-permanent waterbodies in the Hungarian Great Plain of the Pannonian biogeographic region. We observed strong genetic differentiation in the phylogenetic analyses of the concatenated 16 S and COI genes, based on which M. brachiata was found to represent a complex of four cryptic lineages (A, B, C and D) with, however, one of these (lineage D) detected based on only one individual. Regarding the nuclear markers, diagnostic alleles of the PGM and MDH enzyme loci in complete linkage disequilibrium were observed separating the 'B' lineage from the rest. In addition, indirect evidence was provided by the AAT locus, where the AAT1 allele was found to be potentially diagnostic for lineage 'C'. The three phylogenetically defined lineages ('A', 'B', 'C') could be separated from each other along the first canonical axis of a multivariate analysis of occurrence, and this first axis was strongly correlated with depth and salinity of the ponds. There is a strong association between habitat depth and the occurrence of the 'B' lineage. Our results indicate that habitat depth and associated ecological characteristics driven by differences in hydroperiod likely are responsible for the present distribution of the lineages.
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