Data from: Speciation in sympatry with ongoing secondary gene flow and an olfactory trigger in a radiation of Cameroon cichlids

The process of sympatric speciation in nature remains a fundamental
unsolved problem. Cameroon crater lake cichlid radiations were long
regarded as one of the most compelling examples; however, recent work
showed that their origins were more complex than a single colonization
event followed by isolation. Here, we performed a detailed investigation
of the speciation history of a radiation of Coptodon cichlids from Lake
Ejagham using whole-genome sequencing data. The existence of this
radiation is remarkable since this 0.5 km2 lake offers limited scope for
divergence across a shallow depth gradient, disruptive selection is weak,
and the species are sexually monochromatic. We infer that Lake Ejagham was
colonized by riverine cichlids soon after its formation 9,000 years ago,
yet speciation occurred only in the last 1,000-2,000 years. We show that
secondary gene flow from riverine species has been ongoing, into ancestral
and extant Lake Ejagham lineages, and identify and date river-to-lake
admixture blocks. One of these contains a cluster of olfactory receptor
genes that introgressed close to the time of the first speciation event
and coincides with a higher overall rate of admixture into the recipient
lineages. Olfactory signaling is a key component of mate choice and
species recognition in cichlids. A functional role for this introgression
event is consistent with previous findings that assortative mating appears
much stronger than ecological divergence in Ejagham Coptodon. We conclude
that speciation in this radiation took place in sympatry, yet may have
benefited from ongoing riverine gene flow.