10.5061/DRYAD.6MP65
Campagna, Leonardo
Cornell University
Gronau, Ilan
University of Sao Paulo
Silveira, Luís Fábio
University of Sao Paulo
Siepel, Adam
Cornell University
Lovette, Irby J.
Cornell University
Data from: Distinguishing noise from signal in patterns of genomic
divergence in a highly polymorphic avian radiation
Dryad
dataset
2015
Sporophila bouvreuil
Sporophila cinnamomea
Sporophila pileata
Pleistocene to present
Outlier Analysis
Sporophila hypoxantha
Sporophila melanogaster
Genomic Scan
Sporophila ruficollis
drift
Species Flock
2015-07-22T16:27:26Z
2015-07-22T16:27:26Z
en
https://doi.org/10.1111/mec.13314
20236318177 bytes
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CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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
Neotropics