This is all the data I have for PCR products of 102 samples for this specific locus. I'm not sure if I should be counting the fragments on that range (more that 175 bp) because it is too far from the original one reported for the microsatellite. How do I know if the articles that have been published for my species actually use alleles that amplify over the top range number?
Pamela Rubí Cejudo Nevarez, the two peaks within 130-155 bp range look like two distinct alleles for me. Remaining fragments look like stutters, I would not count them unless same sample (individual) shows distinct peaks (instead of stutters) consistently at two or more loci.
Don't assume that previous studies have completely captured all the genetic variation possible for a species. Our lab routinely tests microsatellites in which we find alleles out of the supposed "range" (still happens with loci we have used for a decade). Have others tested these microsatellites on this population or geographically proximate ones? Is there the potential for introgression?
Unfortunately studies do not typically list the alleles they observe per locus. Maybe check for an allele frequency table. 175 really is not that far off from the reported range and those peaks look like real alleles to me, especially since they have been observed in multiple individuals. The peaks look just like those of the smaller alleles. Have you tried re-running the samples to confirm? If you really want to test it you could run the sample on agarose, cut out the alleles, and then sequence them.
Madhav Nepal and Justin H. Bohling Thanks for taking the time to answer my question. Justin H. Bohling I just found one report that shows variation even further from the range that I mentioned. I did not say it before but these are actually results from two species of the same genus and I will also be testing for hybridization of both species. It has been reported there is introgression. The alleles on the ~175 bp range are mostly represented on one of the species.
Pamela Rubí Cejudo Nevarez , one thing I did not bring up was that recent allopolyploid might possess the alleles of that nature ( make sure that they are not the stutters), which can be verified by the consistencies across multiple markers or of course by looking at the sequence variation.
Madhav Nepal thanks for your answer. My samples belong to a diploid species so I'm supposed to have two alleles per sample.
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