Detecting drivers of population divergence across phylogeographic breaks is a major challenge in marine population genetics, partly due to uncertainties in molecular dating. Although the calibration of demographic transition (CDT) method is the most promising rate calibration technique for population-level events, there is a risk of making the false assumption that post-glacial population expansions coincided with global temperature rise. Further generalization of the technique is required to evaluate population histories of marine species whose abundance may be independent of changes in temperature. We explored the population history of a dwarf eelpout Petroschmidtia teraoi on Japanese continental slopes in the Sea of Japan and Sea of Okhotsk as a model organism for phylogeographic study. For rate calibration, we estimated historical stock sizes from a species distribution model and incorporated this data into the CDT method as a proxy for demographic transition (we term this combined method extended CDT, or eCDT). Our species distribution model showed that the range of P. teraoi is mainly determined by water depth and locality (i.e., latitude and longitude). Reconstructed historical stock sizes revealed contrasting demographic trends in the northern and western Sea of Japan on either side of the Noto peninsula, located at the midpoint of the Japanese mainland. We also found a sharp genetic break in the same location, and inferred contrasting demographic histories of local populations from the molecular data. The striking differences in the demographic histories of local populations even on apparently continuous continental slopes are most likely due to differences in available habitat area. eCDT appeared to work well as a rate calibration method for our temperature-independent study species, and our species distribution model revealed that local populations could have diverged due to discontinuities in available habitat. Finally, we assessed the strengths and weakness of the novel calibration method by analyzing simulated sequences.

在海洋种群遗传学中​​，检测跨地理断裂的种群差异的驱动因素是一项重大挑战，部分原因是分子测年的不确定性。尽管人口统计跃迁（CDT）方法的校准是针对人口水平事件的最有前途的速率校准技术，但仍有可能做出错误的假设，即冰川后的人口膨胀与全球温度上升同时发生。需要对该技术作进一步的概括，以评估其丰度可能与温度变化无关的海洋物种的种群历史。我们探索了矮生矮脚石Petro的种群历史在日本海和鄂霍次克海的日本大陆斜坡上作为系统地理学研究的模式生物。为了进行速率校准，我们根据物种分布模型估算了历史种群大小，并将此数据合并到CDT方法中，作为人口统计转变的代理（我们称此组合方法为扩展CDT或eCDT）。我们的物种分布模型表明，P。teraoi的范围主要取决于水的深度和位置（即纬度和经度）。重建的历史种群规模揭示了位于日本大陆中点的能登半岛两侧的日本北部和西部海域的人口统计学趋势相反。我们还发现在同一位置发生了急剧的遗传断裂，并从分子数据推断出了当地人口的人口统计学对比历史。即使是在明显连续的大陆斜坡上，当地人口的人口历史也存在显着差异，这很可能是由于可用栖息地面积的差异所致。对于不受温度影响的研究物种，eCDT似乎可以作为一种速率校准方法，并且我们的物种分布模型表明，由于可用栖息地的不连续性，当地种群可能有所不同。