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 Setophaga 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, whereas 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 (∼200 kb) 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.

中文翻译：

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对小基因组区域的选择支持两种莺物种之间多种颜色性状的分化

物种形成是生物学中最重要的过程之一，但对该过程背后的基因组变化的研究还处于起步阶段。北美莺种Setophaga Townsendi和Setophaga occidentalis经过一段时间的地理隔离后，在稳定的杂交区杂交。在地理隔离期间积累的基因组分化可以通过二次接触时的基因渗入来均质化，而导致低杂交适应度的遗传区域可以免受这种基因渗入。在这里，我们通过研究（1）物种之间不同色素沉着性状的遗传基础，（2）整个基因组分化的变化，以及（3）选择维持色素沉着基因分化的证据来检查物种形成的基因组基础。使用在杂交区域内和附近的数百个个体中对数以万计的单核苷酸多态性 (SNP) 进行基因分型，全基因组关联作图揭示了与脸颊、冠部、乳房颜色和侧翼条纹相关的单个 SNP，反映了多效性（一个基因影响多个性状）或影响不同性状的不同基因的紧密物理联系。该 SNP 位于 RALY 基因的内含子内，因此我们将其称为 RALY SNP。然后，我们使用测序基因分型和全基因组测序检查了物种间基因组差异。我们发现 RALY SNP 位于分化的最高峰之一，其中包含已知影响色素沉着的三个基因：ASIP、EIF2S2 和 RALY（ASIP-RALY 基因块）。由于 RALY SNP 的地理谱线在过去二十年里一直在缩小，因此该基因块上的杂合子的适应性可能会降低。总之，这些结果反映了这一狭窄（~200 kb）基因组区域内基因流动的至少一个障碍，该区域调节物种之间的羽毛差异。尽管跨基因组的物种之间存在广泛的基因流动，但这项研究提供了证据，表明对表型相关基因组区域的选择维持了稳定的物种边界。