Figure 1.
Temporal Variation of Subfamily Sequence Variation π and IPL
Results for three expansion models are shown, in which retrotransposition activity was instantaneous (M0) or lasted for 3 (M3) or 6 (M6) myrs. Variation in π (A) is slowed during retrotransposition, but increases immediately upon the cessation of retrotransposition. Rate of IPL decay (B) is attenuated during retrotransposition activity but increases once retrotransposition ends.
Figure 2.
Distribution of Subfamily Sequence Variation π (x-Axis) versus IPL (y-Axis)
Expectations based on 1,000 replicates of expansion models M0–M6. Shaded area in each plot indicates 95% of resulting values for each model. Observed (π and IPL) values for ten recent human Alu subfamilies are shown as black diamonds. These results are based on a generation time of 25 y and an effective population size of 10,000 individuals.
Table 1.
Alu Subfamily Diversity (π) and IPL Parameters and Their Age under Different Models of Amplification
Figure 3.
Estimation of the Age of the Ya5a2 Alu Subfamily under Simulation M4
In M4, Ne is 10,000 and generation time is 25 y. Data are based on observed subfamily sequence variation π and IPL parameters. Time estimates consistent with π and IPL values are indicated in boxes. The bold double arrow indicates age estimates concordant with both parameters.
Figure 4.
Impact of Subfamily Copy Number (n) on the Sequence Variation π Parameter
Increasing subfamily size beyond 100 copies had little effect on between-replicate variation.