Tuesday, January 1, 2008

RE Another comment on Hawks et al

Thanks for commenting John.
I think that people do not doubt that the effective population size of humans has increased, what is debatable is when and by how much.

I stand by my comment that effective population sizes can not be estimated from archaeological data. The only way to truly estimate the population genetic parameter Ne is from population genetic data. It is not enough to do some calculations to suggest that Ne could only be some fraction smaller than the census size. Any such calculation can only take approximate account of some of the many factors contributing towards the reduction in Ne from the census size. The effective population size of many large cosmopolitan species is often far, far smaller than anyone would have predicted (which is why people don't predict it, they estimate it). Archaeological data (and simulations based on them) are of use in trying to understand what factors may have played a role in the reduction of the effective population size, but can not be taken as a proxy for it.

I would be interested to know the recent references that show conclusively that Ne increased rapidly around 30k-50kys ago. I think that this is actually a controversial point, as many recent analyses of population genetic data do not support long-term growth (even in African populations where the signal is not complicated by the bottleneck), most analyzes reject strong growth occurring 30-50kyrs (see here , here , here and here ). African populations (Bantu) show a signals of moderate recent growth, i..e. an excess of singletons, but not enough to be compatible with strong long term growth. European populations will probably also show signals of very recent growth, once resequencing nuclear DNA sample sizes are large enough to find the signal in very low frequency polymorphisms (that have been recently introduced). Now undoubted these papers suffer from flaws in their assumptions, but they suggest that you can not assume that the effective population size was increasing dramatically 10's thousand of years ago.

The reason (I think) why a number of analyses ignore recent growth (and use a constant population size of 10,000) is not that the authors do not appreciate that effective population sizes have increased, it is just that the increase is thought to be too recent ( i.e. not 10's thousands of years ago) to affect the estimates of bottlenecks or such.

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