Data from: High levels of effective long-distance dispersal may blur ecotypic divergence in a rare terrestrial orchid

Background: Gene flow and adaptive divergence are key aspects of metapopulation dynamics and ecological speciation. Long-distance dispersal is hard to detect and few studies estimate dispersal in combination with adaptive divergence. The aim of this study was to investigate effective long-distance dispersal and adaptive divergence in the fen orchid (Liparis loeselii (L.) Rich.). We used amplified fragment length polymorphism (AFLP)-based assignment tests to quantify effective long-distance dispersal at two different regions in Northwest Europe. In addition, genomic divergence between fen orchid populations occupying two distinguishable habitats, wet dune slacks and alkaline fens, was investigated by a genome scan approach at different spatial scales (continental, landscape and regional) and based on 451 AFLP loci. Results: We expected that different habitats would contribute to strong divergence and restricted gene flow resulting in isolation-by-adaptation. Instead, we found remarkably high levels of effective long-distance seed dispersal and low levels of adaptive divergence. At least 15% of the assigned individuals likely originated from among-population dispersal events with dispersal distances up to 220 km. Six (1.3%) ‘outlier’ loci, potentially reflecting local adaptation to habitat-type, were identified with high statistical support. Of these, only one (0.22%) was a replicated outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence. Signals of adaptation in response to habitat type were most evident at the scale of individual populations. Conclusions: The findings of this study suggest that the homogenizing effect of effective long-distance seed dispersal may overwhelm divergent selection associated to habitat type in fen orchids in Northwest Europe.研究背景：基因流（Gene flow）与适应性分化（adaptive divergence）是集合种群动态（metapopulation dynamics）与生态物种形成（ecological speciation）的核心环节。长距离扩散（long-distance dispersal）难以被直接检测，且目前鲜有研究同时估算扩散水平与适应性分化程度。本研究以沼兰（fen orchid，*Liparis loeselii* (L.) Rich.）为研究对象，旨在探究其有效长距离扩散与适应性分化情况。我们采用基于扩增片段长度多态性（amplified fragment length polymorphism, AFLP）的归属分析（assignment tests），对欧洲西北部两个不同区域的有效长距离扩散水平进行定量分析。此外，我们通过覆盖不同空间尺度（大陆、景观、区域）的基因组扫描（genome scan）方法，基于451个AFLP位点，对栖息于两种可区分生境——湿沙丘洼地（wet dune slacks）与碱沼（alkaline fens）——的沼兰种群间的基因组分化展开研究。 研究结果：我们最初推测，不同生境将驱动强烈的种群分化与受限的基因流，进而形成适应性隔离（isolation-by-adaptation）。但实际研究结果显示，有效长距离种子扩散水平显著偏高，而适应性分化水平却较低。至少15%的经归属分析的个体极有可能来自种群间扩散事件，其扩散距离可达220 km。我们以较高统计学显著性鉴定出6个（占比1.3%）离群位点（outlier loci），这些位点可能反映了对特定生境类型的局部适应。其中仅1个（占比0.22%）在多组独立的沙丘洼地-碱沼种群对比中均表现为离群位点，因此其可能代表真正的平行分化（parallel divergence）。针对生境类型的适应信号在单个种群尺度上最为显著。 研究结论：本研究结果表明，在欧洲西北部的沼兰种群中，有效长距离种子扩散所带来的均质化效应（homogenizing effect）可能抵消了与生境类型相关的分化选择压力。