I calculated allele frequency classes and number of alleles (from microsat data) to infer selection/demography of a population. I experienced that intermediate and high frequency alleles are lack. There is no sign of recent bottleneck because I have high numbers at low frequency class. May I experience high geneflow or large scale drift as cause distortion? Please suggest articles on the topic to explain.
Also, what if rapid population size change, drift and/or fluctuating selection prohibits fixation of alleles. Therefore we have lack of intermediate and high frequency alleles..???
Allele frequency largely depend on the choice of your markers per se. It is difficult to make any conclusion without further information on the number of markers you are using, their repartition across the genome, and so on... What about HW disequilibrium?
Echo what Gregoire said: context matters to assess the patterns. How many loci, how were they detected (e.g. fragment analysis of high-throughput sequencing), target species, etc. Be wary about using microsatellites to infer selection, especially if the genomic position is unknown.
Lack of alleles with a frequency >0.4 could be due to a number of factors. It would suggest none are experiencing high selection and may be neutral. Do you have lot of alleles per locus? What is overall and per locus heterozygosity? High diversity and low allele frequency suggests substantial gene slow. However, if individuals are fixed for different alleles and that suppresses allele frequency, that would be something different.
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