Project idea: Estimating different measures of effective population size

[EwersAquaGenomics]

This is a rather specific idea, but one that, as far as I know, is not well implemented in R. Effective population size (Ne) gives an estimate of the number of individuals that contribute alleles into the next generation. Ne plays a role in most areas of population genetics. Ne determines how fast alleles are fixed in a population, how large selection has to be to be effective in a population, and generally the amount of genetic diversity.

It has its issues, but receives most attention in conservation genetics. Populations with small Ne have low genetic diversity, and have been thought to be at a high risk of extinction. Moreover, different measures integrate Ne over different time scales, allowing the comparison between longterm and current Ne. These comparisons can give valuable insight into population decline and expansion.

I would be interested in compiling a R package that can estimate Ne in different ways, and possibly even compare these measures, using microsats, SNPs and sequence data.

[thibautjombart]

Hi Christine,
I like this, and I believe it is actually fairly generic, if you think of
it under the coalescent approach umbrella. Then coalescentMCMC is the ideal
starting point, and people could contribute various population dynamic
models. I suspect a bunch of us, including epidemiologists, might be
interested in this.

On Mon, Mar 9, 2015 at 6:53 PM, Christine Ewers-Saucedo <
notifications@github.com> wrote:

This is a rather specific idea, but one that, as far as I know, is not
well implemented in R. Effective population size (Ne) gives an estimate of
the number of individuals that contribute alleles into the next generation.
Ne plays a role in most areas of population genetics. Ne determines how
fast alleles are fixed in a population, how large selection has to be to be
effective in a population, and generally the amount of genetic diversity.

It has its issues, but receives most attention in conservation genetics.
Populations with small Ne have low genetic diversity, and have been thought
to be at a high risk of extinction. Moreover, different measures integrate
Ne over different time scales, allowing the comparison between longterm and
current Ne. These comparisons can give valuable insight into population
decline and expansion.

I would be interested in compiling a R package that can estimate Ne in
different ways, and possibly even compare these measures, using microsats,
SNPs and sequence data.

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