Data from: What influences the worldwide genetic structure of sperm whales (Physeter macrocephalus)?

The interplay of natural selection and genetic drift, influenced by geographic isolation, mating systems, and population size, determines patterns of genetic diversity within species. The sperm whale provides an interesting example of a long-lived species with few geographic barriers to dispersal. Worldwide mtDNA diversity is relatively low, but highly structured among geographic regions and social groups, attributed to female philopatry. However, it is unclear if this female philopatry is due to geographic regions or social groups, or how this might vary on a worldwide scale. To answer these questions, we combined mtDNA information for 1,091 previously published samples with 542 newly obtained DNA profiles (394 bp mtDNA, sex, 13 microsatellites) including the previously un-sampled Indian Ocean, and social group information for 541 individuals. We found low mtDNA diversity (π=0.430%) reflecting an expansion event <80,000 years bp, but strong differentiation by ocean, among regions within some oceans, and among social groups. In comparison, microsatellite differentiation was low at all levels, presumably due to male-mediated gene flow. A hierarchical AMOVA showed that regions were important for explaining mtDNA variance in the Indian Ocean, but not Pacific, with social group sampling in the Atlantic too limited to include in analyses. Social groups were important in partitioning mtDNA and microsatellite variance within both oceans. Therefore, both geographic and social philopatry influence genetic structure in the sperm whale, but their relative importance differs by sex and ocean, reflecting breeding behavior, geographic features, and perhaps a more recent origin of sperm whales in the Pacific. By investigating the interplay of evolutionary forces operating at different temporal and geographic scales, we show that sperm whales are perhaps a unique example of a worldwide population expansion followed by rapid assortment due to female social organization.自然选择与遗传漂变的交互作用，受地理隔离、交配系统及种群规模的调控，决定了物种内部的遗传多样性格局。抹香鲸便是一个极具研究价值的实例：作为长寿物种，其扩散几乎不存在地理屏障。全球范围的线粒体DNA（mtDNA）多样性相对偏低，但在地理区域与社会群体间呈现高度结构化特征，这一现象被归因于雌性恋巢行为（female philopatry）。然而目前尚不明确，这种雌性恋巢行为究竟是由地理区域还是社会群体主导，也不清楚其在全球尺度上的变异模式。为解答上述问题，本研究将1091份已发表样本的线粒体DNA数据，与542份新获得的DNA分型数据（涵盖394碱基对（bp）的线粒体DNA序列、性别信息及13个微卫星（microsatellite）位点）相结合，其中新数据覆盖了此前未被采样的印度洋海域；同时整合了541个个体的社会群体信息。研究结果显示，线粒体DNA多样性偏低（核苷酸多样性π=0.430%），这反映出抹香鲸在距今8万年前曾经历种群扩张事件；同时，抹香鲸的遗传结构在大洋间、部分大洋内部的区域间以及社会群体间均呈现显著分化。相较而言，微卫星位点在所有层级上的分化程度均较低，这大概率是由雄性介导的基因流所致。分层分子方差分析（hierarchical AMOVA）结果表明，地理区域对印度洋种群的线粒体DNA遗传变异具有显著解释力，但在太平洋种群中并非如此；大西洋的社会群体采样量过少，无法纳入分析。而在两个大洋的种群内部，社会群体均对线粒体DNA与微卫星位点的遗传变异分区具有重要作用。因此，地理恋巢与社会恋巢均会对抹香鲸的遗传结构产生影响，但二者的相对重要性因性别与大洋而异，这一结果反映了其繁殖行为、地理特征，或许还与太平洋抹香鲸的起源时间更近有关。本研究通过探究在不同时间与地理尺度上发挥作用的进化力量间的交互作用，证实抹香鲸或许是一个独特的研究案例：其经历了全球范围的种群扩张，随后因雌性的社会组织结构而快速形成了遗传分化格局。