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.

研究目标（Aim）：气候变暖正导致山地冰川大范围消融，但目前学界对冰川退缩如何影响物种演化过程与遗传多样性的认知仍较为有限。将遗传结构与其形成影响因素相结合开展研究，有助于深化对物种响应环境变化机制的认知。本研究采用基因组规模数据（genome-scale data）与种群动态建模（demographic modelling）方法，解析仅分布于高山溪流的稀有水生昆虫Lednia tumana的演化历史；同时采用多种常用数据过滤方法，量化其对种群结构分析结果的影响程度。
研究区域（Location）：美国蒙大拿州冰川国家公园落基山脉区域的高山溪流。
研究类群（Taxon）：Lednia tumana，隶属于短石蝇科（Nemouridae）襀翅目（Plecoptera）的石蝇物种。
研究方法（Methods）：本研究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（Single Nucleotide Polymorphism, SNP）数据，以分析11个Lednia tumana种群的当代遗传结构格局。基于鉴定得到的遗传聚类群，本研究采用溯祖框架（coalescent framework）下的模型选择与参数估计方法，解析其种群动态历史。在种群结构分析环节，我们通过数据过滤处理，分别探究单例位点、缺失数据及标记总数量对分析结果的影响。
研究结果（Results）：当代种群结构格局显示，Lednia tumana在3个与地理分布匹配的遗传聚类群内部，种群间呈现距离隔离模式（isolation-by-distance）。种群间的平均两两遗传分化系数（FST）为0.033。基于溯祖分析的种群动态建模结果显示，自更新世（Pleistocene）末期（约1.3-1.7万年前）以来，各遗传聚类群间存在伴随基因流（gene flow）的分化过程，这一结果可能反映了威斯康星冰期（Wisconsin glaciation）形成的冰盖自南向北的退缩过程。
主要结论（Main conclusions）：本研究在一种受气候变化威胁、分布范围狭窄的石蝇物种中，揭示了冰川退缩、物种演化历史与遗传多样性格局之间的关联。该研究发现包含了“伴随基因流的分化”这一山顶物种中罕见的演化历史结论。除Lednia tumana之外，本研究还证实了对分化程度较弱的物种开展种群结构分析的复杂性，明确了稀有等位基因与缺失数据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。