Data from: Genome-wide SNPs identify limits to connectivity in the extreme freshwater disperser, spangled perch Leiopotherapon unicolor (Terapontidae)

The utility of restriction-site associated DNA sequencing (RADseq) to resolve fine-scale population structure was tested on an abundant and vagile fish species in a tropical river. Australia’s most widespread freshwater fish, the “extreme disperser” Leiopotherapon unicolor was sampled from six locations in an unregulated system, the Daly River in Australia’s Northern Territory. Despite an expectation of high connectivity based on life history knowledge of this species derived from arid zone habitats, L. unicolor was not a panmictic population in the tropical lower Daly. Using ~14,000 polymorphic RADseq loci, we found a pattern of upstream versus downstream population subdivision and evidence for differentiation among tributary populations. The magnitude of population structure was low with narrow confidence intervals (global FST = 0.014; 95% CI = 0.012, 0.016). Confidence intervals around pairwise FST estimates were all non-zero and consistent with the results of clustering analyses. This population structure was not explained by spatially heterogeneous selection acting on a subset of loci, or by sampling groups of closely related individuals (average within-site relatedness ≈ 0). One implication of the low but significant structure observed in the tropics is the possibility that L. unicolor may exhibit contrasting patterns of migratory biology in tropical versus arid zone habitats. We conclude that the RADseq revolution holds promise for delineating subtle patterns of population subdivision in species characterized by high within-population variation and low among-population differentiation.

本研究以热带河流中一种丰富且活动能力较强的鱼类为对象，检验了限制性酶切位点相关DNA测序（restriction-site associated DNA sequencing, RADseq）解析精细种群结构的应用效能。作为澳大利亚分布最广的淡水鱼类——‘极端扩散者’银身小鲈（Leiopotherapon unicolor），其样本采自澳大利亚北领地未受人工调控的戴利河（Daly River）流域的6个采样点。尽管基于该物种在干旱区生境的生活史研究结果，学界此前曾预期其种群间具有较高的连通性，但在热带区域的戴利河下游，银身小鲈并非随机交配种群。本研究利用约14000个多态性RADseq位点，发现该流域种群呈现上游-下游的遗传分化格局，同时也获得了支流种群间存在遗传分化的证据。种群结构的分化程度较低，且置信区间较窄：全局遗传分化系数（fixation index, FST）=0.014，95%置信区间（confidence interval, CI）为0.012~0.016。所有两两配对的FST估计值的置信区间均不为零，且与聚类分析的结果一致。该种群结构并非由作用于部分位点的空间异质性选择所导致，也并非因采样了亲缘关系较近的个体群所致——各采样点内的平均亲缘关系系数约为0。在热带区域观测到的这种分化程度较低但具有统计学意义的种群结构，其一项潜在启示是：银身小鲈在热带生境与干旱区生境中，可能表现出截然不同的迁移生物学模式。本研究最终得出结论：RADseq技术为解析那些种群内变异水平高、种群间分化程度低的物种的精细种群分化格局，提供了极具前景的研究手段。