Data from: Genetic architecture of skeletal evolution in European lake and stream stickleback

Advances in genomic techniques are greatly facilitating the study of molecular signatures of selection in diverging natural populations. Connecting these signatures to phenotypes under selection remains challenging, but benefits from dissections of the genetic architecture of adaptive divergence. We here perform quantitative trait locus (QTL) mapping using 488 F2 individuals and 2011 single nucleotide polymorphisms (SNPs) to explore the genetic architecture of skeletal divergence in a lake-stream stickleback system from Central Europe. We find QTL for gill raker, snout, and head length, vertebral number, and the extent of lateral plating (plate number and height). Although two large-effect loci emerge, QTL effect sizes are generally small. Examining the neighborhood of the QTL-linked SNPs identifies several genes involved in bone formation, which emerge as strong candidate genes for skeletal evolution. Finally, we use SNP data from the natural source populations to demonstrate that some SNPs linked to QTL in our cross also exhibit striking allele frequency differences in the wild, suggesting a causal role of these QTL in adaptive population divergence. Our study paves the way for comparative analyses across other (lake-stream) stickleback populations, and for functional investigations of the candidate genes.

基因组学技术的迅猛发展，极大推动了分化型自然种群选择分子特征的相关研究。将此类分子特征与受选择作用的表型建立关联仍颇具挑战，而解析适应性分化的遗传架构则可为该领域研究提供关键助力。本研究利用488个F2个体与2011个单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点，开展数量性状基因座（quantitative trait locus, QTL）定位分析，以探究中欧湖-溪棘鱼系统中骨骼特征分化的遗传架构。研究共定位到与鳃耙长度、吻长、头长、脊椎骨数量以及侧骨板发育程度（含骨板数量与高度）相关的QTL。尽管本研究发现了两个效应值较大的基因座，但绝大多数QTL的效应值普遍偏小。通过对与QTL连锁的SNPs侧翼区域进行分析，本研究筛选出多个参与骨骼形成的基因，这些基因可作为骨骼演化研究的强力候选基因。最后，本研究借助来自自然源种群的SNP数据证实：本研究杂交群体中与QTL连锁的部分SNPs，在野生种群中同样呈现出显著的等位基因频率差异，这表明此类QTL在适应性种群分化中发挥了因果性作用。本研究为后续针对其他湖-溪棘鱼种群的比较分析，以及候选基因的功能验证研究奠定了坚实基础。