Understanding the genetic and fitness consequences of anthropogenic bottlenecks is crucial for biodiversity conservation. However, studies of bottlenecked populations combining genomic approaches with fitness data are rare. Theory predicts that severe bottlenecks deplete genetic diversity, exacerbate inbreeding depression and decrease population viability. However, actual outcomes are complex and depend on how a species’ unique demography affects its genetic load. We used population genetic and veterinary pathology data, demographic modelling, whole-genome resequencing and forward genetic simulations to investigate the genomic and fitness consequences of a near-extinction event in the northern elephant seal. We found no evidence of inbreeding depression within the contemporary population for key fitness components, including body mass, blubber thickness and susceptibility to parasites and disease. However, we detected a genomic signature of a recent extreme bottleneck (effective population size = 6; 95% confidence interval = 5.0–7.5) that will have purged much of the genetic load, potentially leading to the lack of observed inbreeding depression in our study. Our results further suggest that deleterious genetic variation strongly impacted the post-bottleneck population dynamics of the northern elephant seal. Our study provides comprehensive empirical insights into the intricate dynamics underlying species-specific responses to anthropogenic bottlenecks.

了解人为瓶颈对遗传和适应性的影响对于生物多样性保护至关重要。然而，将基因组方法与适应度数据相结合的瓶颈群体研究却很少。理论预测，严重的瓶颈会耗尽遗传多样性，加剧近交衰退并降低种群生存能力。然而，实际结果很复杂，并且取决于物种独特的人口统计学如何影响其遗传负荷。我们利用种群遗传和兽医病理学数据、人口统计模型、全基因组重测序和正向遗传模拟来研究北象海豹濒临灭绝事件的基因组和适应性后果。我们没有发现任何证据表明当代人群的关键健康指标（包括体重、鲸脂厚度以及对寄生虫和疾病的易感性）存在近亲繁殖衰退。然而，我们检测到了最近极端瓶颈的基因组特征（有效种群规模 = 6；95% 置信区间 = 5.0–7.5），这将清除大部分遗传负荷，可能导致我们的研究中缺乏观察到的近交衰退。我们的结果进一步表明，有害的遗传变异强烈影响了北象海豹的瓶颈后种群动态。我们的研究为物种特异性对人为瓶颈的反应背后的复杂动态提供了全面的实证见解。