Supplementary material for "Oikopleura dioica, the cosmopolitan appendicularian hides multiple cryptic species around the globe"

18S and ITS sequences used to estimate phylogenetic trees for "Oikopleura dioica, the cosmopolitan appendicularian hides multiple cryptic species around the globe." To identify 18S rDNA genes from genome sequences, we searched genome sequences for the best-hit matches to the Rfam models for the eukaryotic small subunit (SSU; RF01960) and large subunit (LSU; RF02543) using cmsearch of the Infernal package (v.1.1.4). The SSU and LSU models from Rfam were downloaded in April 2021. The internal transcribed spacer (ITS) regions were obtained by extracting the region between SSU and LSU. Multiple sequence alignments for the 18S and ITS regions were created with MUSCLE (v5) within Seaview (v.3.2).