September 10, 2006

Y chromosome mutation rate

There has been some controversy about the mutation rate of the Y chromosome. Roughly speaking, the rate estimated from recent father-son or male sibling pairs seems to be much "faster" than that estimated from population data. A new letter by Zhivotovsky et al., who advocates the slower rate has just been published by Molecular Biology and Evolution. We need to obtain good estimates of the mutation rate in order to pinpoint in time the common ancestor of a set of Y chromosomes. A factor of 3, especially fore relatively recent events may correspond to a difference between early historical and late Paleolithic events.

Mol Biol Evol. 2006 Sep 6; [Epub ahead of print]

Difference Between Evolutionarily Effective and Germ-line Mutation Rate due to Stochastically Varying Haplogroup Size.

Zhivotovsky LA, Underhill PA, Feldman MW.

Within a Y chromosome haplogroup defined by unique event mutations, variation in microsatellites can accumulate due to their rapid mutation. Estimates based on pedigrees for the Y chromosome microsatellite mutation rate are 3 or more times greater than the same estimates from evolutionary considerations. We show by simulation that the haplogroups that survive the stochastic processes of drift and extinction accumulate microsatellite variation at a lower rate than predicted from corresponding pedigree estimates; in particular, under constant the total population size, the accumulated variance is on average 3-to-4 times smaller.


On a related note, it has been proposed that the cause for the discrepancy between mutation rates as measured in different time spans is due to deleterious mutations. Roughly speaking, such mutations are culled by natural selection, but not immediately. This would tend to reduce the observed mutation rate over larger time spans. For example, if X mutations occur usually between a father and a son, we do not expect 2X mutations to occur between a grandfather and a grandson, but rather some smaller number than 2X. A new letter in the same journal, however, suggests that this effect cannot really explain this phenomenon.

Can Deleterious Mutations Explain the Time Dependency of Molecular Rate Estimates?

Michael Woodhams


It has recently been observed by Ho et al. that apparent rates of molecular evolution increase when measured over short timespans. I investigate whether the data are explainable purely by deleterious mutations. I derive an empirical approximation for the persistence of these mutations in a randomly mating population, and hence derive lower limits on effective population sizes. These limits are high, and get higher if additional reasonable assumptions are made. This casts doubt on whether deleterious mutations are able to explain the apparent rate acceleration.


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