Evolutionary relationships among marine cercozoans as inferred from combined SSU and LSU rDNA sequences and polyubiquitin insertions

► Combined SSU and LSU rDNA sequences help resolve the phylogenetic relationships among cercozoan flagellates. ► The presence of amino acid insertions between highly conserved polyubiquitin monomers provides a robust molecular signature for the clade consisting of cercozoans and foraminiferans. ► 2 polyubiquitin amino acid insertions are found in most cercozoans examined so far. ► 1 polyubiquitin amino acid insertion is found in the Foraminifera, the earliest-branching cercozoans, and a derived clade of cercozoans consisting of the Ebriida and Cryomonadida. ► The number of polyubiquitin amino acid insertions has changed from 1 to 2 and back to 1 several times in the evolutionary history of cercozoans.