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  1. An important goal of conservation genetics is to determine if the viability of small populations has been compromised by genetic drift leading to loss of adaptive variation. Here, we assessed the impact of drift and selection on direct measures of adaptive variation (toxin loci encoding venom proteins) in the Eastern Massasauga rattlesnake (Sistrurus catenatus), a threatened snake that exists in small populations. We estimated levels of individual polymorphism in 46 toxin loci and 1467 control loci across 12 populations of this species, and compared the results with patterns of selection on the same loci following speciation of S. catenatus and its closest relative, the Western Massasauga (S. tergeminus). Multiple lines of evidence suggest that both drift and selection have had observable impacts on standing adaptive variation. In support of drift effects, we found little evidence for selection on toxin variation within populations and a significant positive relationship between current levels of adaptive variation and long-term and short-term estimates of effective population size. However, we also observed levels of directional selection on toxin loci among populations that are broadly similar to patterns predicted from interspecific selection analyses that predate the effects of recent drift, and that functional variation in these locimore »persists despite small short-term effective sizes. We suggest that much of the adaptive variation present in populations may represent an example of “drift debt,” a non-equilibrium state where present-day measures overestimate the amount of functional genetic diversity that will be present in these populations in the future.« less