Fig. 2.

—Genetic relationships among individuals estimated from Alu, LINE-1, and SVA mobile element insertion polymorphisms. PCA was used to visualize the genetic distance estimates among 296 individuals from world populations. Points are color-coded by each of the seven major population groups in the SGDP. (a) Nonreference Alu markers (n = 2,561) separate Africans and non-Africans along PC1 and non-Africans populations are distributed along PC2. A hypothetical ancestral individual lacking Alu elements at all loci is located centrally. (b) Nonreference LINE-1 insertions (n = 310) produce genetic distance estimates similar to Alu elements, but there is substantially greater dispersion among Africans. (c) Genetic relationships based on SVA insertions (n = 96) are less structured than for Alus and LINE-1s, which may be attributable to a small number (65) of common SVA markers. (d) The genetic relationships among individuals in the SGDP based on SNPs (n = 347,532; CpG sites excluded) are highly congruent with Alu and LINE-1 polymorphic insertions. All sites used in each analysis are unlinked (r² ≤ 0.2), have an overall minor allele frequency of ≥0.02, and have <10% missing data by sample and locus.