DOI: 10.5061/dryad.712kj7v
title: 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

description: 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 &lt; 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.
description: Example_simulated_fd_run_scriptsBarombiMbo_corrected_dxy_piSliding window values of pairwise Dxy and Pi, corrected for missing invariant sites in the vcf, for Barombi Mbo cichlids and riverine outgroupsBmbo.MAF0.05.MaxMiss0.9.DP5.GQ20.recode.vcfFiltered vcf of Sarotherodon Barombi Mbo species, riverine outgroups and Coptodon outgroupBarombiMbo_treemixoutput.tarTreemix output of genome-wide estimates of migration events into Barombi Mbo from riverine outgroupsBarombiMbo_fd_50kslide_and_simulation_output.tarCsv file output of the fd tests of introgression for the empirical Barombi Mbo data and the sequences simulated under a model of no migrationBarombiMbo_Saguaro_SNP_filtered_outputSaguaro output files containing the segments assigned to 75 cacti. This folder contains three versions of SNP filtering: with segments with less than 1, 10 and 20 SNPs removed.BarombiMbo_Saguaro_SNP_filter_output.tar.gzBarombiMbo_Saguaro_tree_files.tar.TRE for all 75 topologies assigned across genome using SaguaroBarombiMbo_raxml_runs.tarRaxml analyses input and output for largest region assigned to introgression topologies focused on in the manuscript (FigS2-S4).BarombiMbo_msmc_output_scriptsScripts used to run msmc, output, and figuresBmbo.MAF0.05.DP5.GQ20.genoGeno formated file for using ABBABABA.py and popGenWindows.py from https://github.com/simonhmartin/genomics_general.