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，极大推动了分化自然种群中选择作用分子特征的研究。将此类分子特征与选择压力下的表型建立关联仍具挑战，但通过解析适应性分化的遗传架构，可有效破解这一难题。本研究依托488个F2代个体与2011个单核苷酸多态性（single nucleotide polymorphisms, SNPs）标记开展数量性状位点（quantitative trait locus, QTL）定位分析，旨在解析中欧湖-溪棘鱼系统中骨骼性状分化的遗传架构。研究共检测到与鳃耙长度、吻长、头长、椎骨数目以及侧骨板发育程度（含板数与板高）相关的QTL。尽管鉴定出两个效应显著的位点，但绝大多数QTL的效应量普遍偏小。对QTL连锁SNPs侧翼区域的筛查发现了多个参与骨形成的基因，这些基因可作为骨骼演化研究的核心候选基因。最后，本研究利用自然源种群的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，表明此类QTL在适应性种群分化过程中可能发挥了因果性作用。本研究为后续开展其他湖-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基础。