A comparison of RAPD versus microsatellite DNA markers in population studies of the massasauga rattlesnake

We compared genetic differentiation among populations of the threatened mas sasauga rattlesnake (Sistrurus c. catenatus) using two types of nuclear mol ecular markers: randomly amplified polymorphic DNA (RAPD) markers and micro satellites. Analyses of molecular variance (AMOVA) and G(ST) and F-ST analy ses Indicated that levels of among-population differentiation between regio nal populations (>100 km) were comparable for both markers. However, micros atellites were superior in population assignment tests and at discerning fi ne-scale genetic differentiation between subpopulations separated by tens o f kilometers. These results argue that both types of markers are suitable f or defining broad-scale genetic structures in snake populations and can pro vide important inputs into conservation Initiatives of focal taxa. However, our analyses suggest that microsatellites are better for detecting structu re at limited spatial scales.