Files in this data supplement:

• Supporting Information: Figures S1-S3, Files S1-S6, and Tables S1-S3 (PDF, 135 KB)
• Figure S1: Distributions of dN (A), dS (B), and dN/dS (C) among intermediate WGD duplicates. (PDF, 100 KB)
• Figure S2: Relationship between log expression level and GC content of caudatum genes. (PDF, 31 KB)
• Figure S3: Relationship between evolutionary rate (dN computed between P. caudatum / P. multimicronucleatum orthologs) and post-recent-WGD retention rate in three P. aurelia species. (PDF, 13 KB)
• File S1: Excel file containing orthologous blocks between caudatum genes and recreated pre-recent WGD aurelia segments. (.xls, 3 MB)
• File S2: Excel file containing orthologous blocks between caudatum genes and recreated pre-intermediate WGD aurelia segments. (.xls, 2 MB)
• File S3: Excel file containing number of intermediate WGD duplicates vs. single-copy genes in each GO term functional category and P-values. (.xls, 23 KB)
• File S4: Excel file containing candidates for neofunctionalization from biaurelia, tetraurelia, and sexaurelia. (.xls, 32 KB)
• File S5: Excel file containing paralogous blocks within caudatum from the ancient WGD. (.xls, 132 KB)
• File S6: Excel file containing number of ancient WGD duplicates vs. single-copy genes in each GO term functional category and P-values. (.xls, 17 KB)
• Table S1: Genome assembly and annotation statistics for P. caudatum, as compared to biaurelia (McGrath et al., submitted), tetraurelia (Aury et al. 2006) and sexaurelia (McGrath et al., submitted). (PDF, 7 KB)
• Table S2: Divergent resolutions of intermediate WGD duplicates between aurelia species. (PDF, 8 KB)
• Table S3: Average GC content and log expression level for duplicated vs. single-copy caudatum genes from the ancient WGD. (PDF, 7 KB)