Marine population genomics based on 1,246 samples. Heatmaps showed hierarchical clustering of PanPhlAn profiles for the rarely sequenced Roseobacter species (a) Pelagibaca bermudensis (1 ref. genome), (b) Roseovarius nubinhibens (1 ref. genome), (c) Roseovarius TM1035 (1 ref. genome), and (d) Sulfitobacter (3 ref. genomes); and two better characterized marine species (e) Prochlorococcus marinus (17 ref. genomes) and (f) Pelagibacter ubique (5 ref. genomes). Different marine regions are marked by different colours. Strains of all species showed a broad presence in many marine regions, partly as regional cluster of strain-specific gene content, especially for locally isolated areas like Baltic Sea and North Sea. (g) PCoA plot based on PanPhlAn profiles of Pelagibacter ubique highlights differences between strains from different marine regions. Strains present in the Baltic Sea could be clearly distinguished from North Sea strains, and also strains detected in samples of the Trondheimsfjord in Norway clustered together.