Data from: Multiple processes drive genetic structure of humpback whale (Megaptera novaeangliae) populations across spatial scales

Elucidating patterns of population structure for species with complex life histories, and disentangling the processes driving such patterns, remains a significant analytical challenge. Humpback whale (Megaptera novaeangliae) populations display complex genetic structures that have not been fully resolved at all spatial scales. We generated a data set of nuclear markers for 3,575 samples spanning the seven breeding stocks and substocks found in the South Atlantic and western and northern Indian Oceans. For the total sample, and males and females separately, we assessed genetic diversity, tested for genetic differentiation between putative populations and isolation by distance, estimated the number of genetic clusters without a priori population information, and estimated rates of gene flow using maximum likelihood and Bayesian approaches. At the ocean basin scale, structure is governed by geographic distance (IBD p<0.05) and female fidelity to breeding areas, in line with current understanding of the drivers of broad-scale population structure. Consistent with previous studies, the Arabian Sea breeding stock was highly genetically differentiated (FST 0.034-0.161; p<0.01 for all comparisons). However, the breeding stock boundary between west South Africa and east Africa was more porous than expected based on genetic differentiation, cluster, and gene flow analyses. Instances of male-fidelity to breeding areas and relatively high rates of dispersal for females were also observed between the three substocks in the western Indian Ocean. This mismatch between demographic units and current management boundaries may have ramifications for assessments of the status and continued protections of populations still in recovery from commercial whaling.

阐明具有复杂生活史的物种种群结构模式，并厘清驱动该模式形成的潜在过程，仍是一项极具挑战性的分析难题。座头鲸（Megaptera novaeangliae）的种群呈现出复杂的遗传结构，目前尚未在所有空间尺度上得到完全解析。我们针对南大西洋、西印度洋及北印度洋已发现的7个繁殖种群与亚种群的3575份样本，构建了核标记数据集。我们分别针对全部样本、雄性样本与雌性样本开展了如下分析：评估遗传多样性水平，检验推定种群间的遗传分化与距离隔离（IBD）效应，在无先验种群信息的前提下估算遗传聚类组数量，并采用最大似然法与贝叶斯法估算基因流速率。在大洋盆地尺度上，种群结构受地理距离（IBD，P<0.05）与雌性个体对繁殖地的忠实性调控，这与当前学界对大尺度种群结构驱动因素的认知相符。与既往研究结果一致，阿拉伯海繁殖种群的遗传分化程度极高，FST值介于0.034~0.161之间，所有对比组的P值均<0.01。然而，基于遗传分化、聚类及基因流分析结果，南非西部与东非之间的繁殖种群边界相较于预期更为松散。在西印度洋的3个亚种群之间，还观测到雄性个体对繁殖地存在忠实性，以及雌性个体扩散速率相对较高的现象。种群统计单元与现行管理边界之间的这种错配，可能会对仍处于商业捕鲸恢复阶段的种群的现状评估及持续保护工作产生影响。