Population structuring in the monogonont rotifer Synchaeta pectinata: high genetic divergence on a small geographical scale

Summary Like many other zooplankton species, individual species of planktonic freshwater rotifers often possess a cosmopolitan distribution despite inhabiting isolated habitats (e.g. ponds or lakes) that present little opportunity for direct gene flow. This ‘everything is everywhere’ distribution is typically ascribed to aspects of the life history of these animals (heterogonic reproductive strategy) in combination with the high dispersal capabilities presented by a dormant stage (resting eggs). Recent molecular analyses indicate the presence of strong population structuring in many rotifer species, including both phylogeographic structuring and the potential for cryptic speciation. Building on these studies, we investigated the intraspecific genetic structuring in the mitochondrial barcoding marker cytochrome c oxidase subunit I (COI) among mid‐European populations of the cosmopolitan rotifer Synchaeta pectinata (Rotifera, Monogononta). These data were analysed using a combination of phylogenetic analysis and haplotype networks as well as population‐genetic methods to assess the degree of population and geographic structuring. Gene flow among four neighbouring populations in north‐west Germany (126 individuals; regional scale) and between them and a set of populations from northern Italy (an additional 48 individuals based on literature data; mid‐European scale) was generally low. Paradoxically, however, higher genetic similarity occurred across the broader mid‐European scale than within the regional scale. Nevertheless, no significant correlation with spatial distance was detected at the former scale, rejecting an isolation‐by‐distance model for population differentiation. Most populations comprised several distinct haplotype clusters, each corresponding to ancient mitochondrial lineages of S. pectinata. Although it is common to infer cryptic speciation from results such as these, the pattern we observed can also arise through historical colonisation events and/or persistent founder effects (Monopolization hypothesis) and we present potential arguments against the default assumption that S. pectinata comprises a complex of cryptic species.