Fig. 2.

—Most partners of transposon-redundant enhancer pairs originated independently. (A) Transposon families contribute differently to the evolution of redundant enhancers. The green dots indicate the fraction of transposon enhancers annotated with each transposon family. The green boxplots depict the distribution of the fraction of random genomic sequences annotated with the same transposon family, estimated based on 1,000 random sets. Asterisks indicate FDR-corrected empirical P values. *P < 0.05, **P < 0.01, ***P < 0.001. (B) The scheme depicts the connection of the redundant enhancer, transposon enhancer, and transposon-redundant enhancer sets. The 3,523 enhancers that are significantly correlated to a promoter are referred to as “correlated enhancers.” About 1,686 correlated enhancers annotated as transposons and are referred to as “transposon enhancers.” About 1,280 correlated enhancers form one or more redundant enhancer pairs and are referred to as “redundant enhancers.” Finally, if both partners of a redundant enhancer pair are annotated as transposons, they are referred to as “transposon-redundant enhancers”; these pairs comprise a total of 432 enhancers. (C) In the majority of transposon-redundant enhancer pairs, the partners have different transposon annotation. Depicted are the number of pairs where partners have different, partially identical (i.e., some transposons are identical), or identical transposon species annotation. (D) Redundancy in human transposon-redundant enhancers seems to have originated throughout the evolution of placentals. Shown is the age of transposon-redundant enhancers, estimated based on the insertion times of the transposons with which they are annotated. Redundancy can arise by 1) the evolution of a new (“younger”) enhancer with regulatory activities that are (possibly partially) redundant to those of an already existing (“oldest”) enhancer or 2) by the simultaneous (“contemporaneous”) evolution of two or more enhancers with (possibly partially) regulatory activities.