Does anyone have experience with calculating relatedness coeffiecintes for male-female pairs in Kingroups software?
When I calculated coefficeintes (males impited as diploids, Queller-Goodnight method), the from mother-son dyads I obtained relatedness around 0.6. In the contrast, mother-daughter relatedness were around 0.5, as I supposed. I hear about possible correction to dividing coefficents to 2, but after it I provide coefficents 0.3, which also do not have much sense.
When I impotuped males only as haploids (one alelle), I obtained low mother-son coefficients (about 0.3).
Therefore, I am not sure, what is the best way how imput male data for obtianing relatedness coefficients in kingroup or if kingroup is able calculate mother-son relatedness coefficients properly.
If you can give me some advice how to fix this or which alternative software can I use for calculating relatedness coefficeintes for male-female dyads for haplodiploids, I will be grateful.
We had the same problem with Kingroup and couldn't get around it. Queller and Goodnight's Kinship program will do the trick (and allow you to specify all kinds of neat null hypotheses). However, it has a limit of about 60 loci, but won't tell you when you have exceeded the limit, though it will still deliver (spurious) results. Therefore if you are using msat data you will probably be ok, but if using SNPs you'll need to prune back the number of loci very substantially.
Thank you very much for response! When I saw the number, I thought that there is the problem, but I was not nure. I will try use Kinship (I hope that will be able do this, I have no experience with Mac-bsed programs. I have 14 msats, therefore number of markers is not too high
We now use COLONY because it calculates relationships for haplodiploids. However, we have not explicitly compared relationships with Kingroup, which we ought to do sometime...
Thank you for information! I also use Colony and for some purposes is surely better (e.g. becuase tests directly maternity/paternity and do not show only relatedness coefficients). However, colony do not show relatedness coefficitnes and sometimes results demendent of settings of initial parametres, which I can guess but not know. Therefore, I would like compare results from more programs.
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