Figure 3. Allele frequencies of L1Hs alleles in the population.

(a) Genotyping assays: L1s were queried in panels of individuals for their absence (solid grey lines), or presence (red line). Genotyping of 26 elements in the three panels allowed the discovery of population restricted or potentially ‘private’ L1Hs elements. The expected amplicon sizes are diagrammed for element #3-24. (b) Pedigrees showing the inheritance of two elements typed in the ABC10 trio: Genotyping gels show the heritability of #3-31 (African specific) and #3-24 (absent from the HGDP). E and F at the top of the gel image indicate PCR results for empty and filled sites. M, F, and C at the bottom of the image indicate lanes for the mother, father, and child of the trio. (c) Example data sheet for the G248 element #1-5: Empty site: insertion site in the HGR. EN cleavage site: the endonucleolytic cleavage site used by L1 EN to initiate retrotransposition. pA length: the approximate L1 poly (A) tail length; 3′ transductions and interrupted poly (A) tails also are annotated. TSD length: the length of the target site duplication flanking the L1Hs element (underlined lettering). Table S2 contains data sheets for each L1 in this study. Table S3 contains L1Hs insertion locations with respect to genes. Figure S2 displays a non-canonical L1Hs insertion and documents a possible sequence anomaly in the HGR.