Data from: Can AFLP genome scans detect small islands of differentiation? The case of shell sculpture variation in the periwinkle Echinolittorina hawaiiensis

Genome scans have identified candidate regions of the genome undergoing selection in a wide variety of organisms, yet have rarely been applied to broadly dispersing marine organisms experiencing divergent selection pressures, where high recombination rates can reduce the extent of linkage disequilibrium and the ability to detect genomic regions under selection. The broadly dispersing periwinkle Echinolittorina hawaiiensis exhibits a heritable shell sculpture polymorphism that is correlated with environmental variation. To elucidate the genetic basis of phenotypic variation, a genome scan using over 1000 AFLP loci was conducted on smooth and sculptured snails from divergent habitats at four replicate sites. Approximately 5% of loci were identified as outliers with Dfdist, while no outliers were identified by BayeScan. Closer examination of the Dfdist outliers supported the conclusion that these loci were false positives. These results highlight the importance of controlling for Type I error by using multiple outlier detection approaches, multitest corrections, and replicate population comparisons. Assuming shell phenotypes have a genetic basis, our failure to detect outliers suggests that the life history of the target species needs to be considered when designing a genome scan.

基因组扫描已在多种生物中鉴定出经历自然选择的基因组候选区域，但此类方法极少应用于面临歧化选择压力的广泛扩散型海洋生物——这类生物的基因组重组率较高，会降低连锁不平衡（linkage disequilibrium）的程度，进而削弱检测受选择基因组区域的能力。广泛扩散的滨螺Echinolittorina hawaiiensis存在可遗传的壳表雕刻多态性，且该多态性与环境变异显著相关。为阐明表型变异的遗传基础，研究人员对来自4个重复采样生境的光滑型和雕刻型滨螺，开展了基于1000余个扩增片段长度多态性（Amplified Fragment Length Polymorphism, AFLP）位点的基因组扫描。通过Dfdist方法鉴定出约5%的位点为异常位点，而BayeScan方法未检测到任何异常位点。对Dfdist检出的异常位点进行细致分析后证实，这些位点均为假阳性结果。上述研究结果凸显了通过采用多种异常位点检测方法、多重检验校正以及重复种群比较策略，来控制I型错误（Type I error）的重要性。若假设壳表表型具有遗传基础，我们未检测到异常位点的结果提示，在设计基因组扫描实验时，需充分考虑目标物种的生活史特征。