Data from: Don’t throw out the sympatric speciation with the crater lake water: fine-scale investigation of introgression provides equivocal support for causal role of secondary gene flow in one of the clearest examples of sympatric speciation

Genomic data has revealed complex histories of colonization and repeated
gene flow previously unrecognized in some of the most celebrated examples
of sympatric speciation and radiation. However, much of the evidence for
secondary gene flow into these radiations comes from summary statistics
calculated from sparse genomic sampling without knowledge of which
specific genomic regions introgressed. This tells us little about how gene
flow potentially influenced sympatric diversification. Here we
investigated whole genomes of Barombi Mbo crater lake cichlids for
fine-scale patterns of introgression with neighboring riverine cichlid
populations. We found evidence of secondary gene flow into the radiation
scattered across < 0.24% of the genome; however, from our analyses
it is not clear if the functional diversity in these regions contributed
to the ecological, sexual, and morphological diversity found in the lake.
Unlike similar studies, we found no obvious candidate genes for adaptive
introgression and we cannot rule out that secondary gene flow was
predominantly neutral with respect to the diversification process. We also
found evidence for differential assortment of ancestral polymorphisms
found in riverine populations between sympatric sister species, suggesting
the presence of an ancestral hybrid swarm. Although the history of gene
flow and colonization is more complicated than previously assumed, the
lack of compelling evidence for secondary gene flow’s role in species
diversification suggests that we should not yet rule out one of the most
celebrated examples of sympatric speciation in nature without a more
thorough investigation of the timing and functional role of each
introgressed region.