Soil micro-organisms drive the global carbon and nutrient cycles that underlie essential ecosystem functions. Yet, we are only beginning to grasp the drivers of terrestrial microbial diversity and biogeography, which presents a substantial barrier to understanding community dynamics and ecosystem functioning. This is especially true for soil protists, which despite their functional significance have received comparatively less interest than their bacterial counterparts. Here, we investigate the diversification of Pinnularia borealis, a rare biosphere soil diatom species complex, using a global sampling of >800 strains. We document unprecedented high levels of species-diversity, reflecting a global radiation since the Eocene/Oligocene global cooling. Our analyses suggest diversification was largely driven by colonization of novel geographic areas and subsequent evolution in isolation. These results illuminate our understanding of how protist diversity, biogeographical patterns, and members of the rare biosphere are generated, and suggest allopatric speciation to be a powerful mechanism for diversification of micro-organisms.

British Antarctic Survey High Cross Madingley Rd Cambridge CB3 0ET UK Natural History Museum of Denmark Øster Farimagsgade 5 Building 7 DK 1353 Copenhagen Denmark

Department of Ecology Charles University Viničná 7 128 44 Prague 2 Czech Republic Stream Biofilm and Ecosystem Research Laboratory École Polytechnique Fédérale Lausanne GR B0 422 CH 1015 Lausanne Switzerland

Laboratory of Protistology and Aquatic Ecology Ghent University Krijgslaan 281 S8 9000 Gent Belgium

Laboratory of Protistology and Aquatic Ecology Ghent University Krijgslaan 281 S8 9000 Gent Belgium Meise Botanic Garden Nieuwelaan 38 1860 Meise Belgium Ecosystem Management Research Group University of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium Department of Biological Sciences University of Arkansas 850 W Dickson St SCEN 601 Fayetteville AR 72701 1201 USA

Laboratory of Protistology and Aquatic Ecology Ghent University Krijgslaan 281 S8 9000 Gent Belgium Natuurpunt Michiel Coxiestraat 11 2800 Mechelen Belgium

Meise Botanic Garden Nieuwelaan 38 1860 Meise Belgium

Meise Botanic Garden Nieuwelaan 38 1860 Meise Belgium Ecosystem Management Research Group University of Antwerp Universiteitsplein 1 2610 Wilrijk Belgium

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