DOI: 10.5061/dryad.4s5dm31
title: Data from: Speciation in sympatry with ongoing secondary gene flow and an olfactory trigger in a radiation of Cameroon cichlids

description: 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.
description: 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.txt