The effective size of a population (N_e), which determines its level of neutral variability, is a key evolutionary parameter. N_e can substantially depart from census sizes of present-day breeding populations (N_C) as a result of past demographic changes, variation in life-history traits and selection at linked sites. Using genome-wide data we estimated the long-term coalescent N_e for 17 pinniped species represented by 36 population samples (total n = 458 individuals). N_e estimates ranged from 8,936 to 91,178, were highly consistent within (sub)species and showed a strong positive correlation with N_C (\({R}_{\mathrm{adj}}^2\) = 0.59; P = 0.0002). N_e/N_C ratios were low (mean, 0.31; median, 0.13) and co-varied strongly with demographic history and, to a lesser degree, with species’ ecological and life-history variables such as breeding habitat. Residual variation in N_e/N_C, after controlling for past demographic fluctuations, contained information about recent population size changes during the Anthropocene. Specifically, species of conservation concern typically had positive residuals indicative of a smaller contemporary N_C than would be expected from their long-term N_e. This study highlights the value of comparative population genomic analyses for gauging the evolutionary processes governing genetic variation in natural populations, and provides a framework for identifying populations deserving closer conservation attention.

决定种群中性变异水平的有效种群数量（N _e）是关键的进化参数。由于过去的人口统计变化，生活史特征的变化以及在相关地点的选择，N _e可以大大偏离当今育种种群的普查规模（N _C）。使用全基因组数据，我们估算了由36个种群样本代表的17种针刺物种的长期合并N _e（总共n  = 458个个体）。N _e估计值在8,936至91,178之间，在（亚）物种内高度一致，并且与N呈强正相关。_C（\（{R} _ {\ mathrm {adj}} ^ 2 \）  = 0.59; P  = 0.0002）。N _e / N _C比很低（平均值为0.31；中位数为0.13），并且与人口历史以及在较小程度上与物种的生态和生活史变量（例如繁殖栖息地）密切相关。在控制了过去的人口波动之后，N _e / N _C的残留变化包含了人类世期间近期种群规模变化的信息。具体而言，需要关注的物种通常具有正残留，表明当代N _C比其长期预期的要小。ñ _Ë。这项研究突出了比较种群基因组分析对于衡量控制自然种群遗传变异的进化过程的价值，并提供了一个框架，可用于识别值得更密切关注的种群。