Data from: Do island plant populations really have lower genetic variation than mainland populations? Effects of selection and distribution range on genetic diversity estimates

Ecological and evolutionary studies largely assume that island populations display low levels of neutral genetic variation. However, this notion has only been formally tested in a few cases involving plant taxa, and the confounding effect of selection on genetic diversity (GD) estimates based on putatively neutral markers has typically been overlooked. Here, we generated nuclear microsatellite and plastid DNA sequence data in Periploca laevigata, a plant taxon with an island-mainland distribution area, to (i) investigate whether selection affects GD estimates of populations across contrasting habitats and (ii) test the long-standing idea that island populations have lower GD than their mainland counterparts. Plastid data showed that colonization of the Canary Islands promoted strong lineage divergence within P. laevigata, which was accompanied by selective sweeps at several nuclear microsatellite loci. Inclusion of loci affected by strong divergent selection produced a significant downward bias in the GD estimates of the mainland lineage, but such underestimates were substantial (>14%) only when more than one loci under selection were included in the computations. When loci affected by selection were removed, we did not find evidence that insular Periploca populations have less GD than their mainland counterparts. The analysis of data obtained from a comprehensive literature survey reinforced this result, as overall comparisons of GD estimates between island and mainland populations were not significant across plant taxa (N=66), with the only exception of island endemics with narrow distributions. This study suggests that identification and removal of markers potentially affected by selection should be routinely implemented in estimates of GD, particularly if different lineages are compared. Furthermore, it provides compelling evidence that the expectation of low GD cannot be generalized to island plant populations.生态学与进化研究大多假定岛屿种群的中性遗传变异水平较低。然而，这一观点仅在少数植物类群的案例中得到正式验证，且基于假定中性标记的遗传多样性（genetic diversity, GD）估算往往忽略了选择所带来的混淆效应。本研究针对具有岛-陆分布格局的植物类群杠柳（Periploca laevigata），获取了核微卫星与质体DNA序列数据，旨在完成两项研究目标：其一，探究选择是否会影响不同生境下种群的GD估算结果；其二，检验“岛屿种群遗传多样性低于陆域种群”这一长期存在的学术假说。质体DNA数据显示，加那利群岛的定殖事件促使杠柳发生了显著的谱系分化，且伴随多个核微卫星位点的选择扫荡现象。若纳入受强烈分化选择影响的位点，会对陆域支系的GD估算造成显著负偏倚，但仅当计算中纳入1个以上受选择位点时，这种低估幅度才会达到14%以上且较为显著。当移除受选择影响的位点后，本研究未发现证据表明岛屿杠柳种群的GD低于陆域种群。对全面文献调研所得数据的分析进一步佐证了这一结果：在涵盖66个植物类群的整体对比中，岛屿与陆域种群的GD估算值并无显著差异，仅分布范围狭窄的岛屿特有类群属于例外。本研究表明，在GD估算工作中应常规开展受选择标记的识别与移除步骤，尤其是在比较不同支系的情况下。此外，本研究提供了强有力的证据，证明“岛屿种群遗传多样性较低”这一预期无法普遍适用于岛屿植物类群。