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.

生态学与进化研究普遍假设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过正式验证，且选择作用对基于假定中性标记的遗传多样性（genetic diversity, GD）估计值的混淆效应通常被忽视。本研究中，我们获取了海岛-大陆分布的植物类群光叶杠柳（Periploca laevigata）的核微卫星与质体DNA序列数据，旨在（i）探究选择作用是否会影响不同生境种群的GD估计值；（ii）验证岛屿种群GD低于大陆种群这一长期存在的观点。质体数据显示，加那利群岛的殖民化促进了光叶杠柳种群内的强烈谱系分化，同时伴随多个核微卫星位点的选择性清除。纳入受强分歧选择影响的位点会导致大陆谱系的GD估计值出现显著的向下偏差，但仅当计算中包含多个受选择位点时，这种低估才会显著（>14%）。当排除受选择位点后，我们未发现岛屿光叶杠柳种群的GD低于大陆种群的证据。通过综合文献调查获取的数据的分析结果进一步支持了这一结论：在66个植物类群中，岛屿与大陆种群的GD估计值总体比较无显著差异，仅分布范围狭窄的岛屿特有种除外。本研究表明，在GD估计中应常规识别并排除可能受选择影响的标记，尤其是在比较不同谱系时。此外，研究提供了有力证据，表明低GD的预期不能推广至所有岛屿植物种群。