Fig. 1 Speciation with gene flow and genomic island of divergence. (A) Conceptual diagram showing the early stage of the process of speciation with gene flow from the genic view. When Pop.1 and Pop.2 start to diverge, only a few loci on the chromosome (here only one is shown) are under divergent selection, and the exchange of the alleles at these loci between populations is restricted. The thickness of the double-headed arrows represents the strength of effective gene flow. (B) Variation of the genetic linkage between neutral loci and divergently selected locus and the effective gene flow at neutral sites along the chromosome. (C) Heterogeneous landscape of genomic divergence and genomic island of divergence. Sea level separates the genomic island of divergence and the sea floor. Adapted from Wu (2001), Nosil & Feder (2012), and Aeschbacher et al (2017).

Fig. 2 Illustration of within-population nucleotide diversity (πw), between-population sequence divergence/absolute divergence (πb or dXY), fixation index (FST) and relative node depth (RND). X and Y are two diverging populations or species. The gene tree (grey) of an example gene is contained within the species tree (black). The sizes of species tree and gene tree displayed are both directly proportional to the mutation rate (μ) of the example gene, μ1> μ2. T1 and T3 are the divergence time or speciation time between X and Y, and between O and the ancestor of X and Y, respectively. T2 and T4 are the divergence time of example gene between X and Y, and between O and the ancestor of X and Y, respectively. πwX, πwY, and absolute divergence (dXY) represent the average number of nucleotide differences of pairwise sequences within X, within Y, and between X and Y, respectively. FST is calculated as 1-πw/πb or similar formulas. RND is an estimate of sequence divergence with the effect of μ corrected. dout is the average of absolute divergence between O and X and between O and Y. dXY of gene 1 is the same as that of gene 2, but FST of gene 2 is higher due to lower πw (A and B). There are no differences in FST, T2, T4, and RND between gene 2 and gene 3, but dXY of gene 3 is lower due to lower μ (B and C). Adapted from Cruickshank & Hahn (2014) and Rosenzweig et al (2016).

Fig. 3 Schematic diagram illustrating different evolutionary processes that could lead to the formation of genomic island of divergence. X and Y are two diverging populations or species. Z is a related species, from which some genetic materials are introgressed into X in scenario (B) in contrast to the other four scenarios (A, C, D, E). The gene trees of two example genes are contained within the species tree (black). The colored gene tree represents the locus underlying the corresponding evolutionary process or its tightly linked loci, and the grey gene tree represents the loosely linked or unlinked loci. The graphs below species trees show the difference of FST, dXY (on the assumption of no variation of μ), and RND (without the assumption of no variation of μ) between two kinds of loci under various evolutionary processes. Adapted from Cruickshank & Hahn (2014) and Han et al (2017).

Fig. 4 Flow chart illustrating the logic of discerning the mechanism contributing to genomic islands of divergence. FSTsym and FSTallo are abbreviations for FST of sympatric and allopatric populations of focal sister species, respectively. Here, only the key pieces of evidence are listed (see text for complementary evidence).