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When running a simulation in PopG, with parameters:

  • Population size: 100
  • AA fitness: 1.0
  • Aa fitness: 1.0
  • aa fitness: 1.0
  • Mutation A to a: 1.0E-6
  • Mutation a to A: 1.0E-6
  • Migration rate between populations: 0.001
  • Initial frequency of A: 0.5
  • Generations to run: 1000
  • Populations evolving simultaneously: 100
  • Random number seed: autogenerate

I get a result of 20 populations being fixed and 10 populations being lost. Obviously, as this is a simulation, these results will vary each run; but what I am having trouble understanding is are lost populations just fixation of the recessive a allele?

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  • $\begingroup$ I'm voting to close this question as off-topic because the question was specific to the OP and the OP abandoned the question, has provided no feedback to the answerers as to why their answers were not sufficient, and has had no subsequent activity on the site. $\endgroup$ – AMR Jan 3 '16 at 9:43
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    $\begingroup$ I don't think this is a valid closure reason. As irritating as it is for the work to go seemingly unappreciated by the OP, they have no obligation to feedback, and Fileunderwater appears to have grasped the question and given an answer that suits, which is therefore still useful to the site. $\endgroup$ – rg255 Jan 3 '16 at 9:58
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Yes, 'lost' seems to be referring to fixation of the a allele in this program, where the statements 'fixed' and 'lost' are specifically referring to the A allele. Conceptually, 'fixed' and 'lost' are describing the same thing in this particular case ( since you only have two alleles in the population) - the loss of one allele in a population.

Note that once the plot of the gene frequency curves reaches the right-hand side of the graph, the program prints there the number of populations that fixed for the A allele (ended up with a frequency of 1.0) and the number that lost this allele.

(my emphasis, from http://evolution.gs.washington.edu/popgen/popg.html)

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Lost vs fixed population

I am not sure I understand your question. It seems to be a matter of definition. The term lost and fixed populations sounds quite wrong. I have never used PopG. Is the PopG manual using these terms without defining them?

Probability of loss and probability of fixation

Given your parameters, you will clearly expect that, if fixation occurs, then it is as likely that the allele a fixes than the allele A fixes. In other words, the probability of loss and the probability of fixation for a neutral locus are equal if you start at frequency 0.5.

Did you say recessive allele

Note that there is no recessive allele at least in terms of fitness (but you probably don't have an explicit phenotype that is afterward link to these fitness values anyway) in your simulation as all genotypes have the same fitness.

Extra info: $F_{ST}$

If I understand your parameters correctly, you are simulation an island model with constant migration between any two populations with D=100 populations. In such circumstances, the $F_{ST}$ should be $$F_{ST}=\frac{1}{1+4N(m+\mu)\left(\frac{D}{D-1}\right)^2}$$ which is approximatively equal to $\frac{1}{1+4Nm}$, where $m$ and $\mu$ are the migration and mutation rate respectively.

Because of migration, you wouldn't expect that all population would be fixed for one or another allele at any time point.

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