Fig. 4

The origin of the human-specific subfamily SVA_F. a Alignment of the consensus sequences of pt_SVA_DRb and hs_SVA_Fa sub-groups and SVA_F. Only variant positions are shown. The chromosome 6 element included represents the source element of pt_SVA_DRb_3 still lacking a sub-group-specific additional 13 bp deletion (not included in the alignment) in the Alu-like region. CA_1–3 represent the inferred sequences of the common ancestors of the entire cluster (CA_1); the pt_SVA_DRb_1/pt_SVA_DRb_3/SVA_F group (CA_2, top panel) and the pt_SVA_DRb_2/hs_SVA_Fa group (CA_3, bottom panel). pt_SVA_DRb_4 and hs_SVA_Fa_1 are the sub-groups containing the elements shared between gorilla/chimpanzee and chimpanzee/human, respectively. Substitutions leading to CA_1 are highlighted in yellow; those leading from CA_1 to CA_2 in purple and those resulting in CA_3 in red. N represents the junction between the Alu-like and SINE-R domains. Substitutions in the chr6 element not present in any of the consensus sequences were assumed to represent random mutation and disregarded. Some of the pt_SVA_DRb_4 elements in chimpanzee represent an additional G → C mutation absent from the gg-pt shared chr6 element and the pt-hs shared chr2 element in humans – it was, therefore, considered to represent a chimpanzee-specific mutation and excluded from the pt_SVA_DRb_4 consensus. b A scenario for the emergence of the human-specific SVA_F and related subfamilies. The 11 bp deletion in the SVA Alu-like domain to become the hallmark of human SVA_F elements occurred in the hominine common ancestor. The resulting gg-pt-shared element on chromosome 6 gave then rise to the pt-hs-shared chr2 element in the chimpanzee-human common ancestor. Either one of the two shared elements currently present in chimpanzee could have been the precursor of a common ancestor (CA_1) that subsequently gave rise to two distinct lineages founded by CA_2 and CA_3. After the chimpanzee-human split species-specific amplification starting from these two founders and the shared elements occurred in both humans and chimpanzees. The gg-pt-shared chr6 element has been lost in the human lineage. gg – gorilla; pt – chimpanzee; hs – human; CA – common ancestor; chr6 148 k – pt_DRb3 precursor lacking the 13 bp additional deletion