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Do direct and phylogenetic estimates of the mutation rate agree?

Posted by AdamEyreWalker on 26 Aug 2009 at 12:15 GMT

The data given by Haag-Liautard et al. allow one to ask whether the direct and phylogenetic estimates of the mutation rate agree for Drosophila mtDNA.

We can directly estimate the mutation rate for 4-fold degenerate sites from the data of Haag-Liautard et al. by multiplying the mutation rates per base from their table 4 (I used the approx estimates and averaged the Florida and Madrid estimates) by the base composition of those sites (40% T, 54% A, 4% C and 1.6% G - note that sites from genes on the minor strand were complimented); this yields an estimate of 1.4 x 10-8 (standard error = 0.5 x 10-8), substantially below the estimate for the whole genome (6.2 x 10-8).

To be obtain a phylogenetic estimate I used the divergence at 4-fold synonymous sites between D.melanogaster and D.simulans (again complimenting sites on the minor strand). Using the method of Tamura and Nei (1993 - MBE) I estimate there have been 0.25 synonymous substitutions per site (SE = 0.06) if we assume equal rates of substitution across sites, and 0.64 (0.64) substitutions per site if we allow the substitution rate to vary exponentially between sites.

This yields estimates of the mutation of 0.2 x 10-8 (0.05 x 10-9) and 0.6 x 10-8 (0.6 x 10-8) for the equal and exponential models respectively if we assume 10 generations per year and a time of divergence of 5.4 MYR (Tamura et al. (2004) MBE). These are 7 and 2.3 fold lower then the direct estimate. The first estimate is significantly lower, but the second estimate is not. Frustratingly it is therefore difficult to determine if the phylogenetic and direct estimates are different or not, particularly given uncertainties about the generation time in Drosophila.

No competing interests declared.