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We consider a stochastic model for the evolution of a discrete population structured by a trait with values on a finite grid of the torus, and with mutation and selection. Traits are vertically inherited unless a mutation occurs, and influence the birth and death rates. We focus on a parameter scaling where population is large, individual mutations are small but not rare, and the grid mesh for the trait values is much smaller than the size of mutation steps. When considering the evolution of the population in a long time scale, the contribution of small sub-populations may strongly influence the dynamics. Our main result quantifies the asymptotic dynamics of sub-population sizes on a logarithmic scale. We establish that under the parameter scaling the logarithm of the stochastic population size process, conveniently normalized, converges to the unique viscosity solution of a Hamilton-Jacobi equation. Such Hamilton-Jacobi equations have already been derived from parabolic integro-differential equations and have been widely developed in the study of adaptation of quantitative traits. Our work provides a justification of this framework directly from a stochastic individual based model, leading to a better understanding of the results obtained within this approach. The proof makes use of almost sure maximum principles and careful controls of the martingale parts.