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.Merged output from all G-PhoCS runs.Merged output from all G-PhoCS runs. Columns: Sample=sampling step; var=parameter name; val=parameter value; cval=converted parameter value; pop=focal population (species); migfrom=migration from; migto=migration to; rep=repeat ID of identical run; migRun=migration from source population to target population in format source2target; migfromRun=migration source population; migtoRun= migration target population; phyl = can be ignored; cn = can be ignored; migfromType=type of source population(s) for migration; migtoType=type of target population(s) for migration; migtoType2=type of target population(s) for migration; migtoType3=type of target population(s) for migration; theta.mean=mean value of theta.gphocs_mergedOutput.txtRAXML output.RAXML output -- see readme file for details.raxml.zipSaguaro outputsaguaro.zipSaguaro outputsaguaro.zipSNPable mask.Mask created by SNPable. See SNPable documentation for background and format: http://lh3lh3.users.sourceforge.net/snpable.shtml.SNPable_mask_l50_r50.faAdmixture blocks.Admixture blocks -- see readme file for details.admixblocks.txtPer-window Fd statistics.Per-window Fd statistics -- see readme file for details.fd_EjaC.Dstat.DP5.GQ20.MAXMISS0.5.MAF0.01.txtInput files for analyses.Input files for analyses -- see readme file for details.analyses_input.zipFinal VCF file.EjaC.Ckot.Dstat.DP5.GQ20.MAXMISS0.5.MAF0.01.vcf.gzOutput for admixtools and DFOIL.Output for admixtools and DFOIL. See readme for details.admixstats.zipOutput from phylogenetic programs ASTRAL, MP-EST, Phylonet, and Splitstree.Output from phylogenetic programs ASTRAL, MP-EST, Phylonet, and Splitstree. See readme for details.other_trees.zipSequenced individuals and corresponding metadata.Sequenced individuals and corresponding metadata. Each row is an individual. Columns: ID = individual ID (e.g. used in VCF file); genus = genus of focal individual; species = species of focal individual; abbreviation = abbreviation used for focal species; R1 = name of fastq file with forwards reads; R2 = = name of fastq file with reverse reads.individuals.tx