Strong isolation by distance revealed among Cyperus papyrus populations in the Rift Valley lakes, Lake Victoria, and isolated wetlands of Kenya

• Eight SSRs revealed 60 alleles in 14 papyrus locations.
• Papyrus in Lakes Victoria–Naivasha showed higher gene diversity than isolated papyrus wetlands.
• AMOVA revealed a significant overall high genetic differentiation among populations.
• Strong isolation-by-distance and one-dimensional distribution model was found among populations.
• Monoclonal patches suggested founder effects, while Bayesian grouped populations based on drainage basins.

Many aquatic plant populations occur in isolated habitats surrounded by land masses which can act as barriers to gene flow, unless other mechanisms exist to facilitate connectivity. This isolation together with life history processes influences greatly genetic diversity and structure among populations of aquatic species. We assessed clonal diversity, genetic variation, and genetic structure of Cyperus papyrus that occur in large geographical scale in freshwater wetlands of Kenya using eight nuclear microsatellite markers. A total of 60 alleles were found across 14 populations. The genetic diversity measures varied widely among populations, with both Lakes Naivasha and Victoria displaying higher allelic and gene diversity than isolated wetlands. C. papyrus maintained relatively high levels of clonal diversity and gene diversity at species level (PP = 79%, AT = 25, HE = 0.41, HO = 0.40) comparable to other clonal aquatic plants. Whereas, two monoclonal wetlands suggested recent founder effects, we attributed variation in clonal diversity to different levels of sexual reproduction and perennation among populations. AMOVA revealed overall high genetic differentiation among populations (FST = 0.250, p = 0.001) which varied from very low (FST = 0.014) within lakes to very high (FST = 0.565) among Lake Victoria–Rift Valley lakes and isolated wetlands. Lack of genetic differentiation among populations within Lakes Victoria and Naivasha implicated hydrochorous dispersal. A Mantel test showed significant isolation-by-distance among populations whereas a PCoA and Bayesian analysis of individuals grouped populations according to drainage basins. We hypothesized that connectivity among distant isolated locations could be by migratory waterfowl or large herbivores (through both endozoochory and epizoochory) and historical inter-basin connection.