Microsatellite size homoplasy, SSCP, and population structure: A case study in the freshwater snail Bulinus truncatus

The extent of microsatellite size homoplasy, as well as its effect on sever al population genetics statistics, was investigated in natural populations using the single-strand conformation polymorphism (SSCP) method. The analys is was conducted using 240 individuals from 13 populations of the freshwate r snail Bulinus truncatus at a GT(n)CT(m) compound microsatellite locus. We showed that SSCP can be used to uncover, at least partly, size homoplasy i n the core sequence of this category of loci. Eight conformers (SSCP varian ts) were detected among the three size variants (electromorphs). Sequencing revealed that each conformer corresponded to a different combination of re peats in the GT(n) and CTm arrays, part of this additional variability was detected within populations, resulting in a substantial increase in gene di versity in four populations. Additional variability also changed the values of parameters used to analyze population differentiation among populations : pairwise tests of differentiation were significant much more often with c onformers than with electromorphs. On the other hand, pairwise estimates of F-st were either smaller or larger with conformers than with electromorphs , depending on whether or not electromorphs were shared among populations. However, estimates of F-st (or analogs) over all populations were very simi lar, ranging between 0.66 and 0.75. Our results were consistent with the th eoretical prediction that homoplasy should not always lead to stronger popu lation structure. Finally, conformer sequences and electromorph size distri bution suggested that single-point and/or stepwise mutations occurring simu ltaneously in the different repeated arrays of compound microsatellites pro duce sequence variation without size variation and hence generate more size homoplasy than expected under a simple stepwise mutation model.