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，并厘清驱动此类模式的核心过程，仍是一项极具挑战性的分析难题。座头鲸（Megaptera novaeangliae）种群展现出复杂的遗传结构，目前尚未在所有空间尺度上得到完整解析。本研究针对南大西洋、西印度洋及北印度洋范围内已发现的7个繁殖种群（breeding stock）与亚种群（substock）的3575份样本，构建了核标记（nuclear markers）数据集。针对全体样本以及雄性、雌性单独样本，我们依次评估了遗传多样性，检验了推定种群间的遗传分化与距离隔离（isolation by distance, IBD）效应，在无先验种群信息的前提下估算了遗传聚类数目，并借助最大似然法（maximum likelihood）与贝叶斯方法（Bayesian approaches）估算了基因流速率。在大洋盆地尺度上，种群结构由地理距离（IBD，p<0.05）与雌性对繁殖区域的归巢偏好共同塑造，这与当前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值为0.034~0.161；所有对比的p值均<0.01）。然而，基于遗传分化、聚类与基因流分析结果，南非西部与东非之间的繁殖种群边界较预期更为松散，种群间基因交流更为频繁。在西印度洋的3个亚种群之间，还观测到雄性对繁殖区域的归巢现象，以及雌性相对较高的扩散速率。这种种群统计单元与现行管理边界之间的错配，可能会影响对仍处于商业捕鲸恢复进程中的种群的现状评估与后续保护工作。