Data from: Demographic modelling reveals a history of divergence with gene flow for a glacially tied stonefly in a changing post-Pleistocene landscape

Aim: Climate warming is causing extensive loss of glaciers in mountainous regions, yet our understanding of how glacial recession influences evolutionary processes and genetic diversity is limited. Linking genetic structure with the influences shaping it can improve understanding of how species respond to environmental change. Here, we used genome-scale data and demographic modelling to resolve the evolutionary history of Lednia tumana, a rare, aquatic insect endemic to alpine streams. We also employed a range of widely used data filtering approaches to quantify how they influenced population structure results.
Location: Alpine streams in the Rocky Mountains of Glacier National Park, Montana, USA.
Taxon: Lednia tumana, a stonefly (Order Plecoptera) in the family Nemouridae.
Methods: We generated single nucleotide polymorphism data through restriction-site associated DNA sequencing to assess contemporary patterns of genetic structure for 11 L. tumana populations. Using identified clusters, we assessed demographic history through model selection and parameter estimation in a coalescent framework. During population structure analyses, we filtered our data to assess the influence of singletons, missing data and total number of markers on results.
Results: Contemporary patterns of population structure indicate that L. tumana exhibits a pattern of isolation-by-distance among populations within three genetic clusters that align with geography. Mean pairwise genetic differentiation (FST) among populations was 0.033. Coalescent-based demographic modelling supported divergence with gene flow among genetic clusters since the end of the Pleistocene (~13-17 kya), likely reflecting the south-to-north recession of ice sheets that accumulated during the Wisconsin glaciation.
Main conclusions: We identified a link between glacial retreat, evolutionary history and patterns of genetic diversity for a range-restricted stonefly imperiled by climate change. This finding included a history of divergence with gene flow, an unexpected conclusion for a mountaintop species. Beyond L. tumana, this study demonstrates the complexity of assessing genetic structure for weakly differentiated species, shows the degree to which rare alleles and missing data may influence results, and highlights the usefulness of genome-scale data to extend population genetic inquiry in non-model species.

研究目的：气候变暖正在引发山地冰川大范围消融，然而当前学界对冰川退缩如何影响演化进程与遗传多样性的认知仍存在局限。将遗传结构与其塑造因素相关联，可深化对物种响应环境变化机制的理解。本研究借助基因组规模数据与种群历史模拟模型，解析了栖息于高山溪流的珍稀特有水生昆虫*Lednia tumana*的演化历史；同时采用多种广泛应用的数据过滤方法，量化了不同处理策略对种群结构分析结果的影响。

研究区域：美国蒙大拿州冰川国家公园落基山脉的高山溪流。

研究类群：卷石蝇科（Nemouridae）、襀翅目（Plecoptera）的石蝇*Lednia tumana*。

研究方法：通过限制性酶切位点相关DNA测序（restriction-site associated DNA sequencing, RAD-seq）获取单核苷酸多态性数据，以评估11个*L. tumana*种群的当代遗传结构模式。基于鉴定得到的遗传聚类群，在溯祖理论框架下通过模型选择与参数估计分析种群演化历史。在种群结构分析环节，我们通过对数据开展不同过滤处理，量化了单例突变（singletons）、数据缺失率以及标记总数对分析结果的影响。

研究结果：当代种群遗传结构模式显示，*L. tumana*在三个与地理分布匹配的遗传聚类群内，种群间呈现距离隔离模式。种群间平均成对遗传分化系数（F_ST）为0.033。基于溯祖理论的种群历史模拟模型支持，自更新世末期（约1.3万~1.7万年前）以来，各遗传聚类群间存在伴随基因流的分化事件，这大概率反映了威斯康星冰期堆积的冰盖自南向北退缩的过程。

主要结论：本研究明确了受气候变化威胁的狭域分布石蝇物种*Lednia tumana*的冰川退缩、演化历史与遗传多样性模式之间的关联，其中包含伴随基因流的分化历史——这对于山地特有物种而言是一项出乎意料的发现。除*L. tumana*之外，本研究还揭示了对弱分化物种开展遗传结构分析的复杂性，阐明了稀有等位基因与数据缺失对分析结果的影响程度，并凸显了基因组规模数据在拓展非模式物种（non-model species）种群遗传学研究维度中的应用价值。