Data from: A genomic assessment of population structure and gene flow in an aquatic salamander identifies the roles of spatial scale, barriers, and river architecture

Population structure and gene flow of species in lotic environments can be constrained by river network architecture, species life history and heterogeneous local barriers. Identifying the factors that influence population structure and gene flow, especially in species limited to movement within a river network, is vital for understanding the evolutionary and demographic history of a species.
We explored population structure and gene flow for a fully aquatic salamander, the common mudpuppy (Necturus maculosus), in Kentucky (USA) using genomic data. We examined population structure using both parametric and nonparametric methods, and we tested for a history of lineage divergence among identified genetic clusters. We quantified the partitioning of genetic variation at different hierarchical levels, and we tested for signatures of isolation by distance. Additionally, we used coalescent-based model selection to identify a best-fit model of gene flow between our three sampled basins.
We found the greatest support for population structure between the Kentucky River basin and the combined Licking and Kinniconick basins, with further subdivision within both the Kentucky and Licking River basins. However, we found no evidence for a history of lineage divergence among these structured units. The movement of N. maculosus is constrained by the lotic network architecture, which likely drives the evolution of this hierarchical population structure, with increasing differentiation between sites nested in river basins, and even greater differentiation between basins. However, we also found evidence for population structure not explained by river architecture, with an isolated population embedded within the Kentucky River basin.
This study demonstrates the heterogeneity in population structure that can evolve in aquatic species occupying lotic systems and illustrates the potential for genomic data to disentangle these complex patterns.

流水生境（lotic environments）中物种的种群结构与基因流，常会受到河流网络结构、物种生活史以及异质性局部障碍的制约。明确影响种群结构与基因流的因素，尤其是那些活动受限仅能在河流网络内移动的物种，对于理解物种的演化与种群历史至关重要。

本研究以美国肯塔基州境内的完全水生蝾螈——斑泥螈（Necturus maculosus）为研究对象，利用基因组数据探究其种群结构与基因流模式。研究采用参数化与非参数化两种方法解析种群结构，对已识别的遗传簇之间是否存在谱系分化历史进行检验；量化不同层级下的遗传变异分区情况，并检验距离隔离（isolation by distance）的信号。此外，本研究借助基于溯祖理论（coalescent theory）的模型选择方法，在三个采样流域之间筛选出最优的基因流拟合模型。

研究结果显示，肯塔基河流域与莱金（Licking）流域、基尼科尼克（Kinniconick）流域的合并组之间存在显著的种群结构，且肯塔基河与莱金河流域内部均存在进一步的亚结构。但本研究未发现这些结构单元之间存在谱系分化历史的证据。斑泥螈的移动受到流水生境网络结构的制约，这或推动了该层级式种群结构的演化：嵌套于流域内的采样点之间遗传分化逐渐升高，而不同流域之间的遗传分化程度更高。不过，本研究也发现了无法用河流网络结构解释的种群结构现象——肯塔基河流域内存在一个隔离种群。

本研究证实了栖息于流水生境的水生物种可演化出异质性的种群结构，同时展示了基因组数据在解析这类复杂种群模式方面的应用潜力。