Supplement: Thousands of human mobile element fragments undergo strong purifying selection near developmental genes

S1 pan-boreoeutherian mobile elements Mobile elements, as annotated by Repbase [1] and RepeatMasker [2], have a hierarchical naming convention where they are first broken down into classes, then families, and finally subfamilies. In the main text we define “pan-boreoeutherian” subfamilies to be the subfamilies that are present in primates (human, chimp, or rhesus), rodents (rat or mouse), and carnivores (dog). Having a presence in all three of the subtrees means that the mobile element subfamily either predated, or was alive at the time of the boreoeutherian ancestor. These were the only subfamilies used in our study since mobile elements would have to be this old to deposit conserved nonexonic elements (CNEs) that were present in the boreoeutherian ancestor. Figure S1 may aid in visualizing the location of the boreoeutherian ancestor in relation to sequenced extant species. All these pan-boreoeutherian subfamilies can be grouped at the family and class level to show which types of mobile elements are contributing the most (Table S1). LINEs and SINEs appear to be contributing the majority of the CNEs. This data set can also be shown at the subfamily level and in Table S2 we show the 50 subfamilies that have contributed the most CNEs in our survey. In Table S3 we show the top 50 subfamilies, ranked by how many CNEs they have contributed, in relation to their overall genomic abundance. These subfamilies tend to be older, since this allows for their neutral copies to have drifted far enough from the consensus to be unrecognizable in the extant species.