| Summary: | Testing among competing demographic models of divergence has become an important component of evolutionary research in model and non-model organisms. However, the effect of unaccounted demographic events on model choice and parameter estimation remains largely unexplored. Using extensive simulations, we demonstrate that under realistic divergence scenarios, failure to account for population size (N-e) changes in daughter and ancestral populations leads to strong biases in divergence time estimates as well as model choice. We illustrate these issues reconstructing the recent demographic history of North Sea and Baltic Sea turbots (Scophthalmus maximus) by testing 16 isolation with migration (IM) and 16 secondary contact (SC) scenarios, modeling changes in N-e as well as the effects of linked selection and barrier loci. Failure to account for changes in N-e resulted in selecting SC models with long periods of strict isolation and divergence times preceding the formation of the Baltic Sea. In contrast, models accounting for N-e changes suggest recent ( Peer reviewed
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