I am interested in the use of microsatellites and how they're used to identify a species. Especially if you have a population of an indeterminate species and would like to compare it with two possible options of nearby populations.
There are many examples of where microsatellites have been used to determine the taxonomic identify of a population. One recent example where the use of microsatellites directly matched the results of DNA bar coding is: DNA Barcoding and Microsatellites Help Species Delimitation and Hybrid Identification in Endangered Galaxiid Fishes by Vanhaecke et al. (2012) in the journal PLOS ONE:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0032939#pone-0032939-g004.
Microsatellites can help determine the identify of an individual when you have the genetic profiles of the two suspected populations. Once the microsatellite profiles are created, statistical programs can help identify which population the individual belongs to, if any. In the past, many have used programs like STRUCTURE, which is a Bayesian clustering software, though now, many are doing multiples types of analyses in conjunction with STRUCTURE, as done in the attached article.
I agree with Karl. Bayesian statistic is a good choice (Structure, Genland or BAPS), you can perform admixture analyses or population grouping/subdivision. These methods were for ex. sucesfully used in a wide ranging and diverse species of turtles. You need of course a database for populations you want to compare. Standard procedure is to complement microsatellite analyses with mtDNA analysis, I mean a species specific mtDNA region.
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