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.明晰近百年尺度内物种的种群动态，是生态学与进化研究的核心议题之一，但种群历史的直接记录往往极为匮乏。对遗传变异进行检测，可作为基于普查的种群规模估算的可行替代方案，亦能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效能，需将其得到的种群历史估算结果与已知的种群动态数据进行比对。 本研究依托一处拥有37年两栖动物标记重捕数据的湿地的长期监测资源，探究基于遗传学的种群动态推断方法在两种钝口螈属（*Ambystoma*）物种中的应用效能：分别为已记录种群数量下降的点斑钝口螈（*Ambystoma talpoideum*）与种群数量扩张的云斑钝口螈（*A. opacum*），且这两类种群动态模式已被证实与湿地淹水周期的变化密切相关。我们对两个物种的两组时间序列采样种群分别进行了双酶切限制性位点相关DNA测序（double digest restriction-site associated DNA sequencing, ddRAD）：云斑钝口螈的采样时间为1993年与2013年，点斑钝口螈的采样时间为1984年与2011年；随后采用基于溯祖理论的种群动态推断方法，对多种备选进化模型进行比较分析。 两种物种的种群动态模型推断结果均显示其种群规模发生了变化，且与标记重捕数据的结果相互印证。点斑钝口螈的参数估算结果对不同分析方法的变异具有较强鲁棒性，而云斑钝口螈的参数估算结果则极不稳定，这削弱了我们对该物种种群动态趋势检测结果的信心。 总体而言，我们在点斑钝口螈中得到的稳健结果表明，基于基因组的种群动态推断方法在生态学尺度上具备应用价值，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场景。种群动态推断或可成为种群监测与保护管理规划的重要工具。