The examination of molecular phylogenies of cyanobacteria and other micro-organisms is increasing dramatically. The use of a single locus in these studies leaves the resulting phylogenies unconfirmed. In this study, the partial sequences of two loci containing segments of protein-encoding genes, the hetR and the phycocyanin locus (PC-IGS), were examined. Laboratory strains and natural populations of the heterocyst-forming cyanobacteria Anabaena, Aphanizomenon and Nodularia from the Baltic Sea were used, in total 41 sequences were determined and their phylogenies were analysed with maximum-likelihood methods. The hetR phylogenies suggested that the planktonic Aphanizomenon and Nodularia each comprise one species, while there were numerous Anabaena species present in the Baltic Sea. In the case of Nodularia, the PC-IGS phylogenies were incongruent with this and suggested that several lineages of Nodularia plankton species existed. In the hetR phylogeny, the floating and nodularin-producing strains of Nodularia were grouped together. For both the hetR and PC-IGS loci of cultured species of Nodularia their molecular phylogeny did not correspond well with the affiliation suggested by morphology. In sequences derived from species of Anabaena and Aphanizomenon the PC-IGS and hetR phylogenies were congruent, suggesting that Aphanizomenon sp. from the Baltic Sea is genetically distinct from both Aphanizomenon flos-aquae from lakes and Aphanizomenon sp. TR183 from the Baltic Sea. In both Nodularia and Anabaena/Aphanizomenon, the PC-IGS sequences showed a significant degree of either recombination events or selection, while none was detected within the hetR sequences. This is the first study comprising the phylogenies of multiple loci from all heterocystous cyanobacteria from the Baltic Sea and shows that earlier results using the PC-IGS locus should be interpreted cautiously in the absence of a confirmation using a second locus.


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