IES conservation in ohnologs produced by the different WGDs.

The identification of ohnologs and the reconstitution of the pre-duplication genomes is described in [1]. For the most recent WGD, which preceded the appearance of the P. aurelia complex of 15 sibling species [95], 51% of the pre-duplication genes are still present in 2 copies. For the intermediate duplication, 24% of pre-duplication genes are still present in 2 or more copies. For the ancient duplication, which preceded the divergence of Paramecium and Tetrahymena, 8% of pre-duplication genes are still present in 2 or more copies. The significance of the column headers is as follows. Genes with ohnolog: the number of present day genes with at least one ohnolog from the indicated WGD event. IESs: the number of IESs found in the genes with at least one ohnolog from the indicated WGD event. Conserved IESs: number of IESs found at the same position in at least one other ohnolog, as determined by sequence alignment. The identification of ohnologs is described in [1] and the data are available through ParameciumDB [90]. Note that this analysis only concerns IESs that are within paralogous genes and not IESs found in intergenic regions.