LAUSR

Abstract The saline-alkaline Rift Valley lakes of Kenya are isolated habitats supporting emergent halophytes on the shorelines. Cyperus laevigatus L. (Smooth flatsedge) is common to these endorheic lakes suggesting connectivity over long distances. The main objective of this study was to assess the amount and pattern of genetic diversity in C. laevigatus populations in wetlands and along shorelines of lakes of the Eastern Rift Valley in Kenya. The clonal, allelic and gene diversity, population genetic structure and fine-scaled spatial genetic structure were assessed on 204 C. laevigatus individuals from nine populations, using thirteen newly developed microsatellites. Cyperus laevigatus populations maintained high levels of clonal and allelic diversity, though with significant within-population inbreeding. No or only restricted local clonal growth over few metres could be found along shorelines of most lakes. A fine-scaled spatial genetic structure was revealed on sheltered populations indicating contemporary local dispersal from repeated seedling recruitment. Significant differentiation and isolation-by-distance was observed, supporting a stepping-stone model. A north to south gradient, as revealed from pairwise FST, PCoA, Structure and a Barrier analysis, included barriers between some lakes, with Lake Magadi fully separated. Bayesian clustering of individuals revealed a gene pool corresponding to the Great Nakuru-Elementaita basin. Historical hydrological connectivity during Holocene as well as geographical distances between Rift Valley lakes were proposed as major driving forces explaining the contemporary genetic structure.