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默认岛屿种群的中性遗传变异水平较低。然而，这一观点仅在少数涉及植物类群的案例中得到正式检验，而基于假定中性标记的遗传多样性（Genetic Diversity, GD）估计值所受选择的混淆效应通常被忽视。本研究针对具有岛-陆分布格局的植物类群杠柳（Periploca laevigata），生成了核微卫星与质体DNA序列数据，旨在达成两个研究目标：其一，探究选择是否会影响不同生境下种群的GD估计值；其二，检验“岛屿种群遗传多样性低于大陆对应种群”这一长期存在的学术假说。质体数据显示，对加那利群岛的定殖推动了杠柳（P. laevigata）内部强烈的谱系分化，同时伴随多个核微卫星位点经历选择清除事件。纳入受强歧化选择影响的位点后，大陆谱系的GD估计值出现了显著的负偏倚，但仅当计算中纳入1个以上受选择位点时，这种低估才会达到显著水平（>14%）。当移除受选择影响的位点后，我们未发现证据表明杠柳的岛屿种群GD低于大陆对应种群。通过对全面文献调研获得的数据进行分析，进一步验证了这一结果：在所有纳入统计的植物类群（N=66）中，岛屿种群与大陆种群的GD估计值整体比较并无显著差异，仅分布范围狭窄的岛屿特有种除外。本研究表明，在GD估计中，尤其是在比较不同谱系时，应常规识别并移除潜在受选择影响的分子标记。此外，本研究提供了有力证据，证明“岛屿种群遗传多样性较低”的预期无法推广至所有岛屿植物类群。