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# Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution

Hwang and Green. 10.1073/pnas.0404142101. |

## Supporting Information

#### Files in this Data Supplement:

Supporting TextSupporting Table 2

Supporting Figure 10

Supporting Figure 11

Supporting Figure 12

Supporting Figure 13

Supporting Figure 14

Supporting Figure 15

Supporting Figure 16

Supporting Figure 17

Supporting Figure 18

Supporting Figure 19

Supporting Figure 20

Supporting Figure 21

Supporting Figure 22

Supporting Figure 23

Supporting Figure 24

Supporting Figure 25

Supporting Figure 26

Supporting Figure 27

Supporting Figure 10

**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).

Supporting Figure 11

**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.

Supporting Figure 12

**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.

Supporting Figure 13

**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.

Supporting Figure 14

**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.

Supporting Figure 15

**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.

Supporting Figure 16

**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.

Supporting Figure 17

**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.

Supporting Figure 18

**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.

Supporting Figure 19

**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.

Supporting Figure 20

**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

Supporting Figure 21

**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.

Supporting Figure 22

**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.

Supporting Figure 23

**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.

Supporting Figure 24

**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.

Supporting Figure 25

**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.

Supporting Figure 26

**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. 7*B*.

Supporting Figure 27

**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.