Dear folks,
I'm trying to figure it out what is the maximum number of missing loci allowed to exclude an individual from an genetic analysis (e.g. Geneland, Structure)?
I'll be grateful for any help
Cristian
Hi Cristian. As i am not confident with genetics i am maybe not competent to answer your question from genetic point of view, but your question sounds nevertheless very interesting to me. From my viewpoint what i learn from your question is that genetic information can be used to adress single individuals in a logic that is used for making scientific studies. And you want to determine how to focus on specific collections of genetic material. That seems very interesting. Actually, is genetics about doing magic on people?
I'd say it depends on the number of loci, the average number of alleles among the loci being used, as well as what type of marker you are using. Obviously all of that varies from study to study, so I would recommend in your case you simulate some comparable data to what you think you have in your system and then determine what the maximum number of missing loci can be and still be able to identify the structure you think you have. A quick glance on the web led me to the link I attached - it's a worksheet describing how to simulate some basic microsatellite data in EASYPOP.
http://operorgenetic.com/MolecularAspects/labs/03.pop.sim.pdf
Hi Cristian
It depends on total number of loci you have, population size and relatedness of the individuals for microsatellite data. CERVUS software will tell u whether you have enough loci to perform genetic analysis in the form of a line graph (Probability of identity on Y axis Vs No. of loci on X axis). Also if your population size is less hardly you can allow any missing locus. More related individuals require more scored loci.
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