Data from: Genotypic diversity and differentiation among populations of two benthic freshwater diatoms as revealed by microsatellites

Given their large population sizes and presumed high dispersal capacity, protists are expected to exhibit homogeneous population structure over large spatial scales. On the other hand, the fragmented and short-lived nature of the lentic freshwater habitats that many protists inhabit promotes strong population differentiation. We used microsatellites in two benthic freshwater diatoms, Eunotia bilunaris “robust” and Sellaphora capitata and sampled from within a pond and connected ponds, through isolated ponds from the same region to western Europe to determine the spatial scale at which differentiation appears. Because periods of low genotypic diversity contribute to population differentiation, we also assessed genotypic diversity. While genotypic diversity was very high to maximal in most samples of both species, some had a markedly lower diversity, with up to half (Eunotia) and over 90% (Sellaphora) of the strains having the same multilocus genotype. Population differentiation showed an isolation-by-distance pattern with very low standardized FST values between samples from the same or connected ponds but high values between isolated ponds, even when situated in the same region. Partial rbcL sequences in Eunotia were consistent with this pattern since isolated ponds in the same region could differ widely in haplotype composition. Populations identified by Structure corresponded to the source ponds, confirming that ‘pond’ is the main factor structuring these populations. We conclude that freshwater benthic diatom populations are highly fragmented on a regional scale, reflecting either less dispersal than is often assumed or reduced establishment success of immigrants, so that dispersal does not translate into gene flow.鉴于原生生物（protists）种群规模庞大且被认为具有较强的扩散能力，学界通常推测其在大空间尺度下会呈现均一的种群结构。另一方面，许多原生生物所栖息的静水淡水生境（lentic freshwater habitats）具有碎片化且存续周期较短的特性，这反而会显著促进种群分化。本研究针对两种底栖淡水硅藻——菱面弯楔藻"粗壮型"（Eunotia bilunaris "robust"）和头状壳缝藻（Sellaphora capitata）——利用微卫星（microsatellites）标记进行基因分型，采样范围涵盖单个池塘、连通池塘以及同一区域内的孤立池塘直至西欧地区，旨在明确种群分化出现的空间尺度。由于基因型多样性较低的时期会加剧种群分化，本研究同时对基因型多样性进行了评估。尽管两个物种的多数样本均表现出极高乃至最高的基因型多样性，但部分样本的多样性显著偏低：其中菱面弯楔藻样本中最高有半数菌株拥有完全一致的多位点基因型（multilocus genotype），头状壳缝藻该比例更是超过90%。种群分化呈现距离隔离模式（isolation-by-distance）：同一或连通池塘的样本间标准化FST（standardized FST）数值极低，而孤立池塘间的标准化FST数值则较高，即便这些孤立池塘处于同一区域亦是如此。菱面弯楔藻的rbcL基因部分序列分析结果也印证了这一模式：同一区域内的孤立池塘在单倍型组成上可能存在显著差异。经Structure聚类软件鉴定得到的种群分组与采样池塘一一对应，证实了"池塘"是塑造这些种群结构的核心因素。综上，本研究认为底栖淡水硅藻种群在区域尺度上存在高度碎片化现象，这要么反映出其实际扩散能力弱于普遍认知，要么意味着外来迁入者的定殖成功率较低，最终导致扩散并未转化为基因交流（gene flow）。