Genomic island of divergence during speciation and its underlying mechanisms

Background & Aims Understanding the mechanisms underlying the formation of species is a major task of ecological and evolutionary studies. Aided by the rapid development of sequencing technologies during the last two decades, a growing body of research has revealed a heterogeneous genomic landscape of divergence with the existence of genomic islands of divergence between closely related taxa. This pattern was interpreted as evidence for the speciation-with-gene-flow model, and genomic islands in divergence landscape were hypothesized to be caused by divergent selection in the face of gene flow. However, genomic islands can also arise from other evolutionary processes, such as introgression, divergent sorting of ancient polymorphisms, and linked selection. Previous empirical studies often focused on part of evolutionary processes when discerning the mechanism governing the formation of genomic islands. Therefore, this paper aims to clarify genomic island of divergence and related concepts, summarize the pros and cons of different methods of identifying genomic islands, compare the predicted properties of genomic islands of divergence under different evolutionary processes, and propose a research route for discerning the mechanism contributing to genomic islands during speciation. This paper may provide a guide for future studies on genomic islands and their underlying mechanisms. Progress In recent years, various empirical and model-based approaches have been proposed to identify genomic islands. After comparing the pros and cons of these approaches, we think the significance test on observed FST using the null distribution of FST under different recombination rate according to the inferred best-fitting demographic model is the most reasonable. Based on similarities and differences of the predicted properties of genomic islands of divergence under different evolutionary processes, we point out the necessity of exploiting multiple indicators, such as introgression level, absolute divergence (dXY), relative node depth (RND), and recombination rate, when discerning the mechanism contributing to genomic islands during speciation. Prospects We suggest more attention should be paid to the ecological and genetic basis of reproductive isolation after discerning the mechanism underlying the formation of genomic islands. Meanwhile, future researches should be standardized to facilitate integrative analysis in a comparative framework, thus improving our understandings of the frequency of speciation with gene flow in the natural world.