Data from: The challenges of detecting subtle population structure and its importance for the conservation of emperor penguins

Understanding the boundaries of breeding populations is of great importance for conservation efforts and estimates of extinction risk for threatened species. However, determining these boundaries can be difficult when population structure is subtle. Emperor penguins are highly reliant on sea ice, and some populations may be in jeopardy as climate change alters sea-ice extent and quality. An understanding of emperor penguin population structure is therefore urgently needed. Two previous studies have differed in their conclusions, particularly whether the Ross Sea, a major stronghold for the species, is isolated or not. We assessed emperor penguin population structure using 4,596 genome-wide single nucleotide polymorphisms (SNPs), characterized in 110 individuals (10–16 per colony) from eight colonies around Antarctica. In contrast to a previous conclusion that emperor penguins are panmictic around the entire continent, we find that emperor penguins comprise at least four metapopulations, and that the Ross Sea is clearly a distinct metapopulation. Using larger sample sizes and a thorough assessment of the limitations of different analytical methods, we have shown that population structure within emperor penguins does exist and argue that its recognition is vital for the effective conservation of the species. We discuss the many difficulties that molecular ecologists and managers face in the detection and interpretation of subtle population structure using large SNP data sets, and argue that subtle structure should be taken into account when determining management strategies for threatened species, until accurate estimates of demographic connectivity among populations can be made.明晰繁殖种群的边界，对于濒危物种的保护工作以及灭绝风险评估具有重要意义。然而，当种群结构较为细微时，确定这些边界往往颇具难度。帝企鹅高度依赖海冰，随着气候变化导致海冰范围与质量发生改变，部分种群或面临生存危机。因此，亟需厘清帝企鹅的种群结构。此前两项相关研究结论存在分歧，尤其是针对该物种的核心栖息地罗斯海是否存在种群隔离这一问题。本研究针对南极周边8个繁殖种群的110只个体（每个种群取样10至16只），利用4596个全基因组范围的单核苷酸多态性（single nucleotide polymorphisms, SNPs）标记，对帝企鹅的种群结构进行了评估。与此前认为帝企鹅在整个南极大陆范围内均为泛交种群的结论不同，本研究发现帝企鹅至少可划分为4个集合种群（metapopulation），且罗斯海种群明显为独立的集合种群。本研究通过扩大样本量，并全面评估了不同分析方法的局限性，证实帝企鹅内部确实存在种群结构，并主张对该结构的识别对于该物种的有效保护至关重要。本研究还探讨了分子生态学家与管理者在利用大规模SNP数据集检测和解读细微种群结构时所面临的诸多难题，并主张在精准估算种群间的连通性之前，制定濒危物种管理策略时应将这类细微种群结构纳入考量范围。