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A reduced complexity aeolian dune stratification model is developed and applied to explore the role of dune morphodynamics in the creation of synthetic sections of aeolian stratigraphy originating from three sets of environmental forcing: 1) steady wind transport capacity, 2) steady bed aggradation and variable wind transport capacity, and 3) steady wind transport capacity and bed aggradation. In each scenario, the forward motion of initial, highly disorganized dunes generates a significant record exclusively containing autogenic signals that arise from early dune growth, deformation, and merger. However, continued dune growth scours deeply, and shreds all records of early dunes. Afterward, dunes self-organize into quasi-stable groups. Forward motion of dune groups create, truncate, and amalgamate sets and co-sets of cross-strata, quickly forming a second, significantly more robust stratigraphic record, which preserves a comingling of signals sourced from ongoing autogenic processes and each scenario’s specific set of environmental forcings, the allogenic boundary conditions of the sand sea. Although the importance of self-organization on modeled aeolian stratification is clear in the few presented scenarios, self-organization may be throttled via variability within environmental forcings, as thoroughly documented within a companion paper Cardenas et al. (This issue). Therefore, additional work is warranted as this numerical experiment only begins to sample possible sets of environmental forcing, boundary conditions, and initial conditions, geomorphic responses, and consequential preservation possible within the presented surface-stratigraphic dune modeling framework.