Fig. 7.

—Median-joining network of active Alu subfamilies. A median-joining network of full-length Alu elements discovered from 296 fully sequenced genomes illustrates their relationships and relative proportions in this diverse set of world populations. The star-like topologies for the AluYa5 and AluYb8 indicate recent rapid expansion of these subfamilies. The highly variable middle A-rich region and poly(A) tail were masked for each sequence prior to clustering. Each node represents an Alu haplotype that was found in at least ten independent loci. The number of segregating loci identified is proportional to a node’s radius. Additional mutational changes from each known subfamily are specified at the nodes, and most are transitions at CpG sites (red). Some AluYb8 nodes have mutations within a diagnostic indel. These mutation locations are based on the AluYb8 consensus (blue) rather than the AluY consensus (black). A node may also contain haplotypes with additional mutations within the masked middle A-rich region for the haplotype assignment, and these are indicated parenthetically. Edges represent one classifying mutational step unless otherwise specified. The Y node located in the center is the AluY consensus sequence.