October 31, 2008

Time-dependent evolutionary mutation rate? Adélie Penguins say no

I have been a vocal critic of the applicability of the evolutionary mutation rate for human Y-chromosomes. Now, a new ancient mtDNA study on Antarctic penguins shows that the evolutionary and germline mutation rates over a period of 37,000 years are not significantly different.

This is an important discovery, since the mutation rate is a basic component of the molecular clock method. A molecular clock infers the amount of time necessary to accumulate the observed present-day variation if this variation accumulates according to a particular rate.

A "slow" evolutionary rate, allegedly supported by fossils in some species, or motivated by the presence of bottlenecks in humans, leads to an overestimation of ages.

From the paper:
Therefore, in order to compare molecular rates accurately over different time periods and within a single species, the following are required: extant natural populations from which large numbers of pedigree samples can be collected, along with large numbers of ancient samples of the same species from an undisturbed environment. Adélie penguins meet these requirements and therefore represent an ideal model for resolving disparate views about the time dependency of molecular rates. Using this species, it is possible to estimate both mutation and evolutionary rates for the same region of the genome precisely.

PLoS Genetics doi: 10.1371/journal.pgen.1000209

Mutation and Evolutionary Rates in Adélie Penguins from the Antarctic

Craig D. Millar et al.


Precise estimations of molecular rates are fundamental to our understanding of the processes of evolution. In principle, mutation and evolutionary rates for neutral regions of the same species are expected to be equal. However, a number of recent studies have shown that mutation rates estimated from pedigree material are much faster than evolutionary rates measured over longer time periods. To resolve this apparent contradiction, we have examined the hypervariable region (HVR I) of the mitochondrial genome using families of Adélie penguins (Pygoscelis adeliae) from the Antarctic. We sequenced 344 bps of the HVR I from penguins comprising 508 families with 915 chicks, together with both their parents. All of the 62 germline heteroplasmies that we detected in mothers were also detected in their offspring, consistent with maternal inheritance. These data give an estimated mutation rate (μ) of 0.55 mutations/site/Myrs (HPD 95% confidence interval of 0.29–0.88 mutations/site/Myrs) after accounting for the persistence of these heteroplasmies and the sensitivity of current detection methods. In comparison, the rate of evolution (k) of the same HVR I region, determined using DNA sequences from 162 known age sub-fossil bones spanning a 37,000-year period, was 0.86 substitutions/site/Myrs (HPD 95% confidence interval of 0.53 and 1.17). Importantly, the latter rate is not statistically different from our estimate of the mutation rate. These results are in contrast to the view that molecular rates are time dependent.


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