DOI: 10.5061/dryad.bnzs7h470
title: Selection on a small genomic region underpins differentiation in multiple color traits between two warbler species

description: Speciation is one of the most important processes in biology, yet the
 study of the genomic changes underlying this process is in its infancy.
 North American warbler species Setophaga
 townsendi and S. occidentalis hybridize in a
 stable hybrid zone, following a period of geographic separation. Genomic
 differentiation accumulated during geographic isolation can be homogenized
 by introgression at secondary contact, while genetic regions that cause
 low hybrid fitness can be shielded from such introgression. Here we
 examined the genomic underpinning of speciation by investigating: (1) the
 genetic basis of divergent pigmentation traits between species, (2)
 variation in differentiation across the genome, and (3) the evidence for
 selection maintaining differentiation in the pigmentation genes. Using
 tens of thousands of single nucleotide polymorphisms (SNPs) genotyped in
 hundreds of individuals within and near the hybrid zone, genome-wide
 association mapping revealed a single SNP associated with cheek, crown,
 breast coloration, and flank streaking, reflecting pleiotropy (one gene
 affecting multiple traits) or close physical linkage of different genes
 affecting different traits. This SNP is within an intron of the RALY gene,
 hence we refer to it as the RALY SNP. We then examined between-species
 genomic differentiation, using both genotyping-by-sequencing and whole
 genome sequencing. We found that the RALY SNP is within one of the highest
 peaks of differentiation, which contains three genes known to influence
 pigmentation: ASIP, EIF2S2, and RALY (the ASIP-RALY gene block).
 Heterozygotes at this gene block are likely of reduced fitness, as the
 geographic cline of the RALY SNP has been narrow over two decades.
 Together, these results reflect at least one barrier to gene flow within
 this narrow (~200kb) genomic region that modulates plumage difference
 between species. Despite extensive gene flow between species across the
 genome, this study provides evidence that selection on a
 phenotype-associated genomic region maintains a stable species
 boundary. 
description: To make Figure 1 & 3, please use this file. <br>
 -RALY.genopheno.EV.csv            <br> This data table has the
 following columns used for figure 1:<br> genomic.EV1 (genomic
 eigenvector 1);<br> genomic.EV2 (genomic eigenvector 2); <br>
 W (longitude); <br> N (latitude).<br> This data table has the
 following columns used for figure 3:<br> genomic.EV1 (genomic
 eigenvector 1);<br> genomic.EV2 (genomic eigenvector 2); <br>
 crown.b.agecr    (crown coloration, age-corrected)<br> cheek.b.agecr
 (cheek coloration, age-corrected)<br> breast.y.b.agecr (breast
 coloration, age-corrected)<br> flank.int.agecr (flank streaking,
 age-corrected)
 -Individual.background.genotype.phenotype.csv        <br>
 This data table has the following column used for figure 1: <br>
 plumage.hybridindex (mean plumage hybrid index of the eight plumage
 landmark scores). <br> In addition, this table has the
 "plateID" correspond to the .vcf file. <br> For sampling
 location of each individual, please use the coordinates specified in the N
 and W columns.  Figure 2<br> The following csv
 files contain the GWAS scans of 7 phenotypes for figure 2. <br>
 RIGHT.cheek.b_association.full.jun.2020.csv<br>
 back.a_association.full.jun.2020.csv<br>
 bib.b.association.full.jun.2020.csv<br>
 breast.y.b_association.full.jun.2020.csv<br>
 breast.y.ext_association.full.jun.2020.csv<br>
 crown.b_association.full.jun.2020.csv<br>
 flank.int_association.full.jun.2020.csv In each of the
 files above (corresponds with the association of each phenotype with
 genotype), there are a few columns involved in making Figure 2: <br>
 1, CHROM (chromozome);<br> 2, Position (base position along the
 chromosome);<br> 3, A1 (allele 1 at this position);<br> 4, A2
 (allele 2 at this position);<br> 5, Pc1df (p-value after correcting
 for genomic control). Figure 4<br>
 -WGSslidingwindow.csv            <br> In this data table, the
 columns used to generate figure 4 is: <br> CHROM
 (chromosome);<br> midPos (mid point position of the sliding
 window);<br> Fst (Weir & Cockerham fixation index)
 -HEWA.TOWA.SNP.FST.csv        463.55 kB    Submitted  
  <br> In this data table, the columns used to generate figure 4
 is: <br> CHROM (chromosome);<br> POS (base position of the
 SNP);<br> WEIR_AND_COCKERHAM_FST (SNP-specific Fixation
 Index).  Figure 5<br>
 -boot.raly.w2.100000.aug.201...       <br>
 -boot.plum.w2.100000.csv        2.52 MB    Submitted    <br>
 -boot.nu.pc1.w2.100000.july....<br> Each of the above data table
 corresponds the 100,000 bootstrap scores of change in the squared cline
 (RALY SNP cline, plumage cline, genomic cline) width between the two
 sampling periods. -TOWA.HEWA.hybridzone.plate1...      
  245.26 MB    Submitted    <br> VCF file for all analysis. Please
 use the plateID of the Individual.background.genotype.phenotype.csv file
 to match background information of each individual.