Fig. 3

The rRNA phylogeny of Diphyllatea. The topology was reconstructed with the GAMMA-GTR model in RAxML v8.0.26. and inferred with 64 taxa and 3983 characters. The inference has been collapsed at varying taxonomic levels for easier visualisation, with blue representing the in-group. The numbers on the internal nodes are ML bootstrap values (BP, inferred by RAxML v8.0.26. under then GAMMA-GTR model) and posterior probabilities (PP, inferred by MrBayes v3.2.2 under the GTR + GAMMA+Covarion model), ordered; RAxML/MrBayes. Black circles indicate BP > 90% and PP 1.00, values with BP < 50% are not shown. Asterisk (*) denotes environmental OTUs sequenced in this study, with “N” representing the number of reads included in each OTU. § depicts rRNA from cultured Diphyllatea amplified in this study. The clonal Å85 Sanger sequence and Årungen PacBio OTU are represented as a single taxon as they shared a 100% identity. Abbreviations for countries: CN = China, FR = France, JP = Japan, MY = Malaysia, NL = Netherlands, NO = Norway, TH = Thailand, and VN = Vietnam. See Additional file 1: Figure S2 for 18S rRNA inference of Diphyllatea