Figure 4.

Evolutionary tree of the 213 subfamilies we identified. (Large nodes) Subfamilies with more than 10,000 elements; (medium nodes) 1000 to 10,000 elements; (small nodes) less than 1000 elements. Subfamilies listed in Repbase Update are colored blue, and the 6 novel subfamilies listed in Figure 2 are colored red. Each of the subfamilies listed in Figure 2 is labeled. A rendition of this tree with every node labeled is available in the Supplementary materials online. The AluJ, AluS, and AluY classes of subfamilies are contained in boxes; not all subfamilies fit into one of these classes. A timeline roughly depicting the average divergence of each subfamily from its consensus sequence and the approximate age obtained by applying a constant scaling factor of 4 million years per 1% divergence from consensus sequence are included at right.