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 conformed to 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）内物种种群动态，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难以获取。对遗传变异进行检测，可作为基于普查的种群数量估算的替代方案，同时能够为种群动态研究提供重要洞见。然而，为了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（mark-recapture）数据的湿地的珍贵研究资源，针对两种已被记录存在种群下降的蝾螈物种——斑点钝口螈（Ambystoma talpoideum）和种群扩张的云斑钝口螈（A. opacum），探究基于遗传学的种群动态推断方法的实用性；上述种群变化模式已被证实与湿地淹水周期的改变密切相关。我们分别对两个时间采样的云斑钝口螈种群（1993年、2013年）和斑点钝口螈种群（1984年、2011年）生成了双酶切限制性位点相关DNA测序（ddRAD）数据，并采用基于溯祖理论的种群动态推断方法，对不同的进化模型进行比较。针对两个物种的种群动态模型推断结果，均支持与标记重捕法数据相符的种群数量变化模式。斑点钝口螈的参数估算结果对我们采用的不同分析方法均具有稳健性，而云斑钝口螈的估算结果则存在显著不一致性，这降低了我们对该物种种群动态趋势检测结果的可信度。总体而言，我们在斑点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尺度上具备实用性，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中的重要工具。