Phylogenetic tree of human KRAB-A motifs. This neighbor-joining phylogenetic tree represents 418 human KRAB-A nucleotide sequences from KRAB-ZNF and SCAN-KRAB-ZNF genes (including some with noncanonical structures). Gene designations are removed from this unrooted phylogram for clarity; a list of the genes including location and aligned KRAB sequences is presented in Supplemental Table S2. Genes from several major physical clusters are colored to show comparisons between physical location and sequence similarity. Loci within a highlighted phylogenetic group that do not map to the same physical cluster as related genes appear as superimposed circles in the appropriate color (or in white for genes that do not belong to any labeled cluster). Genes that also encode SCAN, KRAB-b, KRAB-BL, or KRAB-C motifs are indicated as follows: SCAN, red circles; KRAB-b, orange triangles; KRAB-BL, blue squares; and KRAB-C, green diamonds. The green arrow notes the position of the Xenopus Xfin KRAB sequence, added as a potential outgroup, although the tree is shown unrooted.
