DOI: 10.5061/dryad.6mp65
title: Data from: Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation

description: Recently diverged taxa provide the opportunity to search for the genetic
 basis of the phenotypes that distinguish them. Genomic scans aim to
 identify loci that are diverged with respect to an otherwise weakly
 differentiated genetic background. These loci are candidates for being
 past targets of selection because they behave differently from the rest of
 the genome that has either not yet differentiated or that may cross
 species barriers through introgressive hybridization. Here we use a
 reduced-representation genomic approach to explore divergence among six
 species of southern capuchino seedeaters, a group of recently radiated
 sympatric passerine birds in the genus Sporophila. For the first time in
 these taxa, we discovered a small proportion of markers that appeared
 differentiated among species. However, when assessing the significance of
 these signatures of divergence, we found that similar patterns can also be
 recovered from random grouping of individuals representing different
 species. A detailed demographic inference indicates that genetic
 differences among Sporophila species could be the consequence of neutral
 processes, which include a very large ancestral effective population size
 that accentuates the effects of incomplete lineage sorting. As these
 neutral phenomena can generate genomic scan patterns that mimic those of
 markers involved in speciation and phenotypic differentiation, they
 highlight the need for caution when ascertaining and interpreting
 differentiated markers between species, especially when large numbers of
 markers are surveyed. Our study provides new insights into the demography
 of the southern capuchino radiation and proposes controls to distinguish
 signal from noise in similar genomic scans.
description: Input file for the
 GPhoCS analysis.Sequence data for 60
 individuals of 6 capuchino species in GPhoCS format.Campagna_Sporophila.gphocs.txtGenotypes in Arlequin formatGenotypes for all SNPs in Arlequin format (as in Figure 1c)Genotypes_ALL_SNPs_Arlequin.arpGenotypes in Arlequin format for the randomized datasetRandomized_ALL_SNPs_Arlequin.arpGenotypes_Structure_Figure1Genotypes in Structure format. One SNP per RAD locus as in Figure 1b.Genotypes_Structure_Figure4Gentoypes in Structure format. One SNP per RAD locus as in Figure 4c.Restriction Site Associated DNA dataCompressed file containing quality-filtered and demultiplexed reads for each individual in the study. Files are identified by species name followed by sample number as shown in Table S1.demultiplexed_ddRAD_data.tar.gzFst estimates for each locus - RANDOMIZED datasetSpecies are coded as follows: 1-S. bouvreuil; 2-S. pileata; 3-S. hypoxantha; 4-S. melanogaster; 5-S. palustris; 6-S. ruficollis.FST_randomized_data.zipFst estimates for each locusSpecies are coded as follows: 1-S. bouvreuil; 2-S. pileata; 3-S. hypoxantha; 4-S. melanogaster; 5-S. palustris; 6-S. ruficollis.FST_species_data.zipOutput from Stacks assemblyThis folder contains the Stacks output from the RAD assembly (M=n=5). There are four files per sample (72 samples in total) plus three catalog files (291 files in total). Samples are identified by species name followed by collection number as indicated in Table S1.RAD_assembly.tar.gzInter-species average PhiST matrixInter-species average PhiST matrix displayed in a Neighbor-joining tree built in PHYLIP (Figure 1a)PhiST_tree.zipStacks output with identified variants in VCF formatVariants identified by Stacks. Assembly parameters M=n=5.Stacks_variants.vcf