Table 1.

Publications on ‘speciation with gene flow’ since 2005.

	Taxa	Species	Main research focus	Inferred stage of speciation	Reference
1	Anopheles	A. gambiae	Genomic islands of speciation in Anopheles gambiae	Early stage. Reason: the materials are two sympatric, partially isolated subtaxa known as M form and S form of A. gambiae	Turner et al., 2005
2	Mus	M. musculus and M. m. domesticus	Genomic islands of differentiation between house mouse subspecies	Early stage. Reason: the materials are subspecies, although there seems to be partial RI associated with the X	Harr, 2006
3	Ficedula	F. albicollis and F. hypoleuca	The genomic landscape of species divergence in Ficedula flycatchers	Uncertain. Reason: although the age of divergence is said to be >1 Myrs, the fixed differences seem low (see their table 2)	Ellegren et al., 2012
4	Heliconius	H. melpomene, H. cydno and H. timareta	Genome-wide evidence for speciation with gene flow in Heliconius butterflies	Uncertain. Reason: the case is commented in the main text. The density of speciation genes seems low	Martin et al., 2013
5	Helianthus	H. petiolaris, H. debilis, H. annuus and H. argophyllus	Genomic islands of divergence are not affected by geography of speciation in sunflowers	Early stage. Reason: the materials are four recently diverged pairs of sunflower species with low pair FST. There are far fewer fixed changes than polymorphic ones (see their table 2)	Renaut et al., 2013
6	Mimulus	M. guttatus and M. nasutus	Speciation and introgression between Mimulus nasutus and Mimulus guttatus	Uncertain. Reason: these two sister species are 200 000–500 000 years apart	Brandvain et al., 2014
7	Oryctolagus	O. cuniculus algirus and O. c. cuniculus	The genomic architecture of population divergence between subspecies of the European Rabbit	Early stage. Reason: the materials are two subspecies of rabbits in the early stages of divergence	Carneiro et al., 2014
8	Anopheles	A. gambiae species pair (A. coluzzii and A. gambiae sensu stricto)	Adaptive introgression between Anopheles sibling species eliminates a major genomic island but not reproductive isolation	Early stage. Reason: the materials are the M form and S form of A. gambiae	Clarkson et al., 2014
9	Corvus	C. (corone) corone and C. (corone) cornix	The genomic landscape underlying phenotypic integrity in the face of gene flow in crows	Early stage. Reason: the two species show only a small number of narrow genomic islands across the whole genome	Poelstra et al., 2014
10	Anopheles	An. gambiae complex	Extensive introgression in a malaria vector species complex revealed by phylogenomics	Early stage. Reason: it is evident that the introgressions in these species are earlier-stage events (see their Fig. 1C)	Fontaine et al., 2015
11	Multiple taxa	All Darwin's finch species and two tanagers, Tiaris bicolor and Loxigilla noctis	Evolution of Darwin's finches and their beaks revealed by genome sequencing	Early stage. Reason: they find extensive evidence for interspecific gene flow throughout the radiation which represents the early stages of diversification when phenotypic transitions between species	Lamichhaney et al., 2015
12	Astatotilapia	Two cichlid fish ecomorphs	Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake	Early stage. Reason: this study is about the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish	Malinsky et al., 2015
13	Vermivora	V. chrysoptera and V. cyanoptera	Plumage genes and little else distinguish the genomes of hybridizing warblers	Early stage. Reason: the two species show extremely low differentiation: only six small genomic regions exhibit strong differences	Toews et al., 2016
14	Xiphophorus	Three hybrid pops between sister species of X. birchmanni and X. malinche	Natural selection interacts with recombination to shape the evolution of hybrid genomes	Early stage. Reason: they studied three replicate hybrid populations that formed naturally between two sister swordtail fish species	Schumer et al., 2018
15	Heliconius	Many Heliconius butterflies species	Genomic architecture and introgression shape a butterfly radiation	Early stage. Reason: introgressions happened during the process of adaptive radiation	Edelman et al., 2019