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Fig. 10. Comparison of context-dependent substitution rates in untranscribed regions between clades not shown in Fig. 3. Each point represents the rates in the two clades for a particular substitution wxy®z. Rates were normalized such that within a clade the average rate, weighted by the observed frequency of the trinucleotides wxy, is 1. Horizontal and vertical bars indicate 95% confidence intervals. The color scheme reflects a grouping of substitutions into 14 types that explain much of the difference among clades (see Table 1).

Fig. 11. Estimated tree based on the untranscribed sequence for all substitution types combined. Branch lengths approximate the expected number of substitutions per site, with 95% confidence intervals as indicated.

Fig. 12. Estimated tree based on the untranscribed sequence for substitution type CTT®C. Branch lengths approximate the expected number of substitutions of this type per CTT site, with 95% confidence intervals as indicated.

Fig. 13. Estimated tree based on the untranscribed sequence for substitution type TTY®C, GTT® C. Branch lengths approximate the average expected number of substitutions of this type per TTY and GTT site (weighted according to the relative frequency of these trinucleotides in the observed sequence), with 95% confidence intervals as indicated.

Fig. 14. Estimated tree based on the untranscribed sequence for substitution type TTR®C, STM®C, ATY®C. Branch lengths approximate the average expected number of substitutions of this type per TTR, STM, and ATY site (weighted according to the relative frequency of these trinucleotides in the observed sequence), with 95% confidence intervals as indicated.

Fig. 15. Estimated tree based on the untranscribed sequence for substitution type ATA®C, VTG® C. Branch lengths approximate the average expected number of substitutions of this type per ATA and VTG site (weighted according to the relative frequency of these trinucleotides in the observed sequence), with 95% confidence intervals as indicated.

Fig. 16. Estimated tree based on the untranscribed sequence for substitution type TTD®A, CTA® A, ATN®A. Branch lengths approximate the average expected number of substitutions of this type per TTD, CTA, and ATN site (weighted according to the relative frequency of these trinucleotides in the observed sequence), with 95% confidence intervals as indicated.

Fig. 17. Estimated tree based on the untranscribed sequence for substitution type TTC®A, CTB® A, GTN®A. Branch lengths approximate the average expected number of substitutions of this type per TTC, CTB, and GTN site (weighted according to the relative frequency of these trinucleotides in the observed sequence), with 95% confidence intervals as indicated.

Fig. 18. Estimated tree based on the untranscribed sequence for substitution type TTH®G, GTC® G. Branch lengths approximate the average expected number of substitutions of this type per TTH and GTC site (weighted according to the relative frequency of these trinucleotides in the observed sequence), with 95% confidence intervals as indicated.

Fig. 19. Estimated tree based on the untranscribed sequence for substitution type TTG®G, MTN® G, GTD®G. Branch lengths approximate the average expected number of substitutions of this type per TTG, MTN, and GTD site (weighted according to the relative frequency of these trinucleotides in the observed sequence), with 95% confidence intervals as indicated.

Fig. 20. Estimated tree based on the untranscribed sequence for substitution type ACA®T. Branch lengths approximate the expected number of substitutions of this type per ACA site, with 95% confidence intervals as indicated

Fig. 21. Estimated tree based on the untranscribed sequence for substitution type BCH®T, ACY® T. Branch lengths approximate the average expected number of substitutions of this type per BCH and ACY site (weighted according to the relative frequency of these trinucleotides in the observed sequence), with 95% confidence intervals as indicated.

Fig. 22. Estimated tree based on the untranscribed sequence for substitution type NCG®T. Branch lengths approximate the average expected number of substitutions of this type per NCG site (weighted according to the relative frequency of these trinucleotides in the observed sequence), with 95% confidence intervals as indicated.

Fig. 23. Estimated tree based on the untranscribed sequence for substitution type NCN®A. Branch lengths approximate the average expected number of substitutions of this type per NCN (weighted according to the relative frequency of these trinucleotides in the observed sequence) site, with 95% confidence intervals as indicated.

Fig. 24. Estimated tree based on the untranscribed sequence for substitution type TCH®G, CCY® G, GCW®G. Branch lengths approximate the average expected number of substitutions of this type per TCH, CCY, and GCW site (weighted according to the relative frequency of these trinucleotides in the observed sequence), with 95% confidence intervals as indicated.

Fig. 25. Estimated tree based on the untranscribed sequence for substitution type TCG®G, CCR®G, ACN®G, GCS® G. Branch lengths approximate the average expected number of substitutions of this type per TCG, CCR, ACN, and GCS site (weighted according to the relative frequency of these trinucleotides in the observed sequence), with 95% confidence intervals as indicated.

Fig. 26. W® S/S®W ratio computed excluding NCG®T. Branch labels are as indicated in Fig. 1; data for internal branches 1, 13, and 15 are omitted because of large variance. Vertical bars indicate 95% confidence intervals. Exclusion of NCG® T does not appear to qualitatively affect the relative ratios compared to Fig. 7B.

Fig. 27. Change in NCG® T/total rate ratio over mammalian evolution. For each internal branch (labeled as indicated in Fig. 1), we computed the difference between the NCG® T/total rate ratio for that branch and the NCG® T/total rate ratio for all descendants of that branch. Vertical bars indicate 95% confidence intervals.