Data from: Genetic architecture in a marine hybrid zone: comparing outlier detection and genomic clines analysis in the bivalve Macoma balthica

The role of natural selection in speciation has received increasing attention and support in recent years. Different types of approaches have been developed that can detect genomic regions influenced by selection. Here we address the question whether two highly different methods - Fst outlier analysis and admixture analysis - detect largely the same set of non-neutral genomic elements or, instead, complementary sets. We study genetic architecture in a natural secondary contact zone where extensive admixture occurs. The marine bivalves Macoma balthica rubra and M. b. balthica descend from two independent trans-Arctic invasions of the north Atlantic and hybridize extensively where they meet, for example in the Kattegat - Danish Straits - Baltic Sea region. The Kattegat - Danish Straits region forms a steep salinity cline and is the only entrance to the recently (ca 8000 years ago) established brackish water basin the Baltic Sea. Salinity along the contact zone drops from 30‰ (Skagerrak, M.b.rubra) to 3‰ (Baltic, M.b.balthica). Both outlier analysis and genomic clines analysis suggest that large parts of the genome are influenced by non-neutral effects. Contrasting samples from well outside the hybrid zone, outlier analysis detects 16 of 84 amplified fragment length polymorphism (AFLP) markers as significant Fst outliers. Genomic clines analysis detects 31 out of 84 markers as non-neutral inside the hybrid zone. Remarkably, only three markers are detected by both methods. We conclude that the two methods together identify a suite of markers that are under the influence of non-neutral effects.

近年来，自然选择在物种形成过程中的作用愈发受到学界关注与认可。目前已开发出多种可检测受选择作用影响的基因组区域的研究方法。本研究旨在探讨两个差异显著的分析方法——Fst离群值分析（Fst outlier analysis）与群体混合分析（admixture analysis）——究竟能否检出高度重合的非中性基因组元件，抑或二者所检出的为互补的基因组元件集合。
本研究以一处发生广泛遗传混合的自然次生接触带为研究对象，解析其遗传结构。研究涉及的海洋双壳类生物红色白樱蛤（Macoma balthica rubra）与白樱蛤指名亚种（M. b. balthica）源自两次独立的跨北极入侵北大西洋事件，二者在相遇区域（如卡特加特海峡—丹麦海峡—波罗的海区域）发生广泛杂交。卡特加特海峡—丹麦海峡区域存在显著的盐度梯度，同时也是距今约8000年前形成的咸淡水混合水体盆地——波罗的海的唯一入海口。该接触带的盐度从斯卡格拉克海域的30‰（栖息有红色白樱蛤）降至波罗的海海域的3‰（栖息有白樱蛤指名亚种）。
离群值分析与基因组梯度分析（genomic clines analysis）均表明，基因组的大片区域均受到非中性进化作用的影响。以杂交带外的对照样本为参照，离群值分析在84个扩增片段长度多态性（amplified fragment length polymorphism, AFLP）标记中检出16个为显著Fst离群值；而在杂交带内，基因组梯度分析则在84个标记中检出31个为非中性标记。值得注意的是，两种方法仅能共同检出3个标记。本研究最终得出结论：两种方法联合使用可鉴定出一套受非中性进化作用影响的标记集合。