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Radiolarians are marine planktonic protists that belong to the eukaryote supergroup Rhizaria together with Foraminifera and Cercozoa. Radiolaria has traditionally been divided into four main groups based on morphological characters; i.e. Polycystina, Acantharia, Nassellaria and Phaeodaria. But recent 18S rDNA phylogenies have shown that Phaeodaria belongs within Cerocozoa, and that the previously heliozoan group Taxopodida should be included in Radiolaria. 18S rDNA phylogenies have not yet resolved the sister relationship between the main Radiolaria groups, but nevertheless suggests that Spumellaria, and thereby also Polycystina, are polyphyletic. Very few sequences other than 18S rDNA have so far been generated from radiolarian cells, mostly due to the fact that Radiolaria has been impossible to cultivate and single cell PCR has been hampered by low success rate. Here we have therefore investigated the mutual evolutionary relationship of the main radiolarian groups by using the novel approach of combining single cell whole genome amplification with targeted PCR amplification of the 18S and 28S rDNA genes. Combined 18S and 28S phylogeny of sequences obtained from single cells shows that Radiolaria is divided into two main lineages: Polycystina (Spumellaria+Nassellaria) and Spasmaria (Acantharia+Taxopodida). Further we show with high support that Foraminifera groups within Radiolaria supporting the Retaria hypothesis.

Polycystine radiolarians are used to reconstruct summer sea surface temperatures (SSSTs) for the Late Pleistocene‐Holocene (600–13,400 14C years BP) in the Norwegian Sea. At 13,200 14C years BP, the SSST was close to the average Holocene SSST (∼12°C). It then gradually dropped to 7.1°C in the Younger Dryas. Near the Younger Dryas‐Holocene transition (∼10,000 14C years BP), the SSST increased 5°C in about 530 years. Four abrupt cooling events, with temperature drops of up to 2.1°C, are recognized during the Holocene: at 9340, 7100 (“8200 calendar years event”), 6400 and 1650 14C years BP. Radiolarian SSSTs and the isotopic signal from the GISP2 ice core are strongly coupled, stressing the importance of the Norwegian Sea as a mediator of heat/precipitation exchange between the North Atlantic, the atmosphere, and the Greenland ice sheet. Radiolarian and diatom‐derived SSSTs display similarities, with the former not showing the recently reported Holocene cooling trend.