Data from: Genomic data detect corresponding signatures of population size change on an ecological time scale in two salamander species

Understanding the demography of species over recent history (e.g., < 100 years) is critical in studies of ecology and evolution, but records of population history are rarely available. Surveying genetic variation is a potential alternative to census-based estimates of population size, and can yield insight into the demography of a population. However, to assess the performance of genetic methods it is important to compare their estimates of population history to known demography. Here, we leveraged the exceptional resources from a wetland with 37 years of amphibian mark-recapture data to study the utility of genetically-based demographic inference on salamander species with documented population declines (Ambystoma talpoideum) and expansions (A. opacum); patterns that have been shown to be correlated with changes in wetland hydroperiod. We generated ddRAD data from two temporally sampled populations of A. opacum (1993, 2013) and A. talpoideum (1984, 2011) and used coalescent-based demographic inference to compare alternate evolutionary models. For both species, demographic model inference supported population size changes that corroborated mark-recapture data. Parameter estimation in A. talpoideum was robust to our variations in analytical approach, while estimates for A. opacum were highly inconsistent, tempering our confidence in detecting a demographic trend in this species. Overall, our robust results in A. talpoideum suggest that genome-based demographic inference has utility on an ecological scale, but researchers should also be cognizant that these methods may not work in all systems and evolutionary scenarios. Demographic inference may be an important tool for population monitoring and conservation management planning.了解近百年（例如不足100年）以来物种种群动态，在生态学与进化研究中具有核心价值，但种群历史的直接普查记录往往稀缺难求。通过检测遗传变异来估算种群规模，可作为基于普查的种群数量统计的潜在替代方案，为解析种群动态提供关键视角。然而，若要评估遗传分析方法的有效性，需将其产出的种群历史估算结果与已知的真实种群动态进行比对验证。本研究依托一处拥有37年两栖动物标记重捕（mark-recapture）数据的湿地的珍贵研究资源，针对两种已被观测到种群下降（斑点钝口螈*Ambystoma talpoideum*）与种群扩张（横带钝口螈*Ambystoma opacum*）的钝口螈属物种，探究基于基因组学的种群历史推断方法的实用效能；上述种群动态模式已被证实与湿地水文周期的变化密切相关。我们对两个时间序列采样的横带钝口螈种群（1993年、2013年）与斑点钝口螈种群（1984年、2011年）开展了双酶切限制性位点相关DNA测序（ddRAD），并采用基于溯祖理论的种群历史推断方法对比不同进化模型的拟合效果。针对两个物种的种群历史模型推断结果均支持了与标记重捕数据相符的种群规模变化模式。其中，斑点钝口螈的参数估算结果对分析流程的调整具备高度稳健性，而横带钝口螈的估算结果则存在显著不一致性，这削弱了我们对该物种种群动态检测结果的可信度。总体而言，我们在斑点钝口螈中获得的稳健研究结果表明，基于基因组的种群历史推断方法在生态学研究尺度下具备应用价值，但研究者也需意识到，此类方法并非适用于所有研究系统与进化情景。种群历史推断有望成为种群监测与保护管理规划中的重要工具。