Dear RG community,
I am currently analyzing a microsatellite dataset with individuals from two different species. Some of the individuals from both species are sharing a few alleles at one/several markers. I am trying to discriminate putative hybrids from individuals sharing alleles because of homoplasy. Does anybody know a way to do that?
Many thanks in advance,
Alex
Assuming the dataset was generated using traditional fragment analysis with capillary electrophoresis, then unfortunately there is no real way to do that. Since alleles are scored based on size, there's no way to definitive tell anything about the descent of those alleles.
What is the discrepancy in allele frequencies between your species? How many loci and how many alleles do the species share? Homoplasy does happen, but it should be rare. If your species have substantially different allele frequencies and you have reason to suspect hybridization is on-going, shared alleles are more likely to be due to hybridization than homoplasy. If they share alleles, it could also mean they just aren't that far diverged or introgression has occurred in the past.
Ultimately the only way to know would be to sequence the actual microsatellite alleles. Some program, especially coalescent methods, can incorporate mutational models to account for this uncertainty as well.
Hope this helps. Best of luck!
You may try sequencing the alleles, maybe what appear to be of equal length are two different sequences.
Thank you for you answers!
Unfortunately, I do not have the DNA samples with me anymore... So no sequencing possible.
The two species share alleles at most markers I used, with some alleles being frequent (10-90%) in one group and rare (
Maybe these papers can help you:
Article Hybridization, Introgression, and the Nature of Species Boundaries
Article Introgression of wing pattern alleles and speciation via hom...