Figure 2. Alu subfamily evolution in primates.

The evolution of Alu elements in primate genomes is roughly illustrated. The left panel shows the three major Alu subfamilies AluJ (green), S (blue), and Y (red). The range of their activity and continuous evolution is indicated through a color gradient. The estimated sizes of AluY, S, and J subfamilies, drawn from Wang et al.,¹⁴³ are given at the bottom left. The major Alu subfamily thought to be active at the time of divergence of each lineage is shown at the base of each lineage branch. Lineage specific subfamilies are likely derived from that subfamily. The color gradient within each lineage branch indicates that Alu subfamilies continued to evolve in each lineage and created lineage-specific subfamilies. Each major subfamily contains several subfamilies. Several different Alu subfamilies are commonly active in parallel and often evolve, causing diverged Alu subfamily networks. On the right the evolution of lineage specific Alu subfamilies in the Cercopithecoidea lineage leading to rhesus macaque (M. mulatta) is exemplified. The network was reconstructed with Alu subfamily data from Han et al. with permission from the original publisher (Science).⁵⁹