I need to calculate the statistical power of my mtDNA marker (i.e. beta, probability of rejecting the null hypothesis when it is true). The reason is that I want to know the minimum sampling size required to testing genetic differentiation among populations (e.g. exact test and Chi-square tests), considering the haplotype diversity found among all my samples for my marker. I have checked POWSIM (Ryman&Palm 2006, Molecular Ecology), that is exactly what I want but it seems designed only for diploid markers (like SNPs or microsatellites). Any idea of how to do it for haploid markers like those in the mtDNA?
Hi Carlos
I think Powermarker software be suitable,because it can be used for 3 states of alleles e.g: AA, AB and BB.
Answering my own question (as I see a few question followers):
*An interesting reference comparing organelle vs nuclear markers using POWSIM: Larsson, L.C., Charlier, J., Laikre, L., Ryman, N. (2009): Statistical power for detecting genetic divergence-organelle versus nuclear markers. Conserv. Genet. 10: 1255-1264.
*An alternative method to calculate statistic power, online and that allows you to make some tests prior to your experiment (e.g. to assess how many markers or samples do you expect to need before starting the project): SPOTG http://www.congressgenetics.eu/page.aspx?SP=Simulator_Start The reference is: Hoban, S., Gaggiotti, O., Bertorelle, G., Con, G.C. (2013): Sample Planning Optimization Tool for conservation and population Genetics (SPOTG): a software for choosing the appropriate number of markers and samples. Methods in Ecology and Evolution 4: 299-303.
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