I am using AFLPs to perform population genetic surveys of several threatened plant species, and ideally would like to have a measure of inbreeding to compare amongst populations. I would like some advice on which approach most people are using to estimate Fis. I have seen papers by Foll et al (2008), Holsinger et al (2002) and Dasmahapatra et al (2007). Are any of these methods favored? I understand it is problematic to estimate Fis from dominant data - are there any other metrics that people use to infer levels of inbreeding instead (e.g. mean relatedness)?
I find this paper by Markert et al. BMC Evolutionary Biology 2010 illuminating on the issue as well as this one by Dasmahapatra Heredity (2008) 100, 286–295.
You can find some additional information on the method of Foll in Fisher et al. (2011) Molecular Ecology 20, 1450–1462. I do not think there is one favored approach. Both methods, of Dasmahapatra and Foll, have their drawbacks and are based on some assumptions. I have used both and obtained quite different estimates.
We published a paper on estimating inbreeding in Taxus based (Heredity, 06/2011; 107(6):589-600; take a look at my profile) on AFLP and SSRs. Igor Chybicki has developed the software which helps to estimatie inbreeding based on AFLPs. It is available from his website: http://www.ukw.edu.pl/pracownicy/strona/igor_chybicki/software_ukw/
Thanks all for your responses. I have just downloaded I4A from Igor Chybicki's website and found it very easy to use. So far it has given me reasonable/believable estimates of F, which show the patterns amongst populations that I would expect. I will explore I4A further and perhaps try the other methods for comparison. Thank you Jaroslaw for drawing my attention to your paper and the software.
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