Data from: Complex histories of repeated gene flow in Cameroon crater lake cichlids cast doubt on one of the clearest examples of sympatric speciation

One of the most celebrated examples of sympatric speciation in nature are
monophyletic radiations of cichlid fishes endemic to Cameroon crater
lakes. However, phylogenetic inference of monophyly may not detect complex
colonization histories involving some allopatric isolation, such as double
invasions obscured by genome-wide gene flow. Population genomic approaches
are better suited to test hypotheses of sympatric speciation in these
cases. Here we use comprehensive sampling from all four sympatric crater
lake cichlid radiations in Cameroon and outgroups across Africa combined
with next-generation sequencing to genotype tens of thousands of SNPs. We
find considerable evidence of gene flow between all four radiations and
neighboring riverine populations after initial colonization. In a few
cases, some sympatric species are more closely related to outgroups than
others, consistent with secondary gene flow facilitating their speciation.
Our results do not rule out sympatric speciation in Cameroon cichlids, but
rather reveal a complex history of speciation with gene flow, including
allopatric and sympatric phases, resulting in both reproductively isolated
species and incipient species complexes. The best remaining non-cichlid
examples of sympatric speciation all involve assortative mating within
microhabitats. We speculate that this feature may be necessary to complete
the process of sympatric speciation in nature.