Advances in the methods of detecting interspecific gene introgression and their applications

With the proceeding of lineage sorting, gene flow gradually decays among progeny populations that are derived from splitting of a common ancestral population, and may probably continue till the phase of speciation. The differences between interspecific genome sequences or between interspecific population gene frequencies partially record these dynamics of historical and contemporary demography and occurrences, and hence inferences on these events can be attained from analyses of interspecific genomic sequences or gene frequencies. Here, we systematically discussed the methods of detecting interspecific gene introgression, including the approaches based on the differences among interspecific gene frequencies ( F st , LD, STRUCTURE, AFS, TreeMix) and the differences of interspecific DNA sequences (ABBA-BABA, IM, IIM, ABC). We discussed the principles and limits of these methods. Relaxations of some important assumptions underlying these methods remain open questions in the future, including the effects of recombination, the separate contribution of gamete vs. zygote dispersal to gene introgression, the interaction of mating system with gene flow, and the impediment to speciation arising from introgression of adaptive genes. Clarifications of these effects would aid in our deep understanding of the process of speciation.