Figure 1.
Two species estimation of integration time.
Estimation of insertion times based on multi-species phylogenetic data. LTR insertion date can be estimated through phylogenetic data by adding known speciation times of species pairs where those LTRs are known to be present (T1). Calculating the substitution rates for each separate species along T1 (bold blue line, bold green line) and LTR along T2 (dashed lines) as shown in the figure will allow the implementation of a final corrected estimation date (bottom formula).
Table 1.
Integration times estimated from independent LTR substitution rates and phylogenies, compared with MCMC estimations.
Table 2.
Integration times from traditional LTR divergence analysis.
Figure 2.
Comparison of substitution rates between 5′ and 3′ LTRs. In blue, pairwise rates for loci estimated to be less than 25 million years old; in red, rates for loci estimated to be more than 25 million years old. The black dashed line represents identical rates between 5′ and 3′ LTRs.
Table 3.
Variation of 3′ LTR and 5′ LTR substitution rates.