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（Genome scans）已在各类生物中鉴定出处于选择作用下的基因组候选区域，但此类研究极少应用于面临歧化选择压力的广扩散海洋生物类群——这类类群的高重组率会降低连锁不平衡（linkage disequilibrium）的程度，同时削弱对受选择基因组区域的检测能力。广扩散的夏威夷滨螺（Echinolittorina hawaiiensis）存在可遗传的壳纹多态性，且该多态性与环境变异相关联。为阐明表型变异的遗传基础，研究人员针对四个重复样地内来自歧化生境的光滑型与具雕刻纹型滨螺，利用超过1000个扩增片段长度多态性（Amplified Fragment Length Polymorphism, AFLP）位点开展了基因组扫描。通过Dfdist方法鉴定出约5%的位点为异常位点，但BayeScan方法未检测到任何异常位点。对Dfdist异常位点的进一步分析证实，这些位点均为假阳性结果。本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来控制一类错误（Type I error）的重要性。若假定壳表表型具有遗传基础，则本研究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。