Demography alone explains the polymorphic profiles on highly diverged loci between cultivated and wild rice

Abstract The confounding effects of demography have hampered the efforts on mapping the causal genes of artificial selection during the domestication of animals and plants. It is challenging to distinguish selection from demography, especially for those derived populations subject to the effect of bottleneck. In this study, to examine whether highly diverged loci were subject to artificial selection during domestication, we developed a new statistical test and genotyped 45 InDel (insertion/deletion) loci in two subspecies of Asian cultivated rice (Oryza sativa ssp. japonica and Oryza sativa ssp. indica) and their wild progenitor (O. rufipogon / O. nivara). Among them, 17 loci are highly diverged (FST > 0.4) between rice cultivars and their ancestor. We performed coalescent-based simulations on neutral demographic scenarios and found that neutral demography alone could explain the polymorphic profiles on those highly diverged loci between cultivated and wild rice. Therefore, more signatures of selection should be considered when detecting artificial selection in rice.