I use the 'vegan' function in the R package 'diveRsity' to calculate the Inbreeding coefficient of populations with SSR data. However, ten of twenty-six values are negative. If there is something wrong with analyze. Many thanks for your help.
If the number of observed heterozygotes is larger than the number of expected heterozygotes, then, you can find negative FIS. There are populations, such as in Populus tremuloides in Mexico, that reach an FIS of almost -1. This means an almost maximum heterozygote excess in these populations.
Calling Fis inbreeding coefficient is often misleading. The fixation coefficient Fis is basically a metrix of HW departure, which can be negative, in case of excess of heterozygosity (as underlined above).
Reason for excess of heterozygosity with microsatellites, may be related to different phenomena, such as randomness (you may check if your Fis are significantly different from 0), inbreeding avoidance, or small effective population size in species with sexual differentiation.
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