Data from: Population structure and phylogeography of the Gentoo Penguin (Pygoscelis papua) across the Scotia Arc

Climate change, fisheries pressure on penguin prey, and direct human disturbance of wildlife have all been implicated in causing large shifts in the abundance and distribution of penguins in the Southern Ocean. Without mark-recapture studies, understanding how colonies form and, by extension, how ranges shift is challenging. Genetic studies, particularly focused on newly established colonies, provide a snapshot of colonisation and can reveal the extent to which shifts in abundance and occupancy result from changes in demographic rates (e.g., reproduction and survival) or migration among suitable patches of habitat. Here we describe the population structure of a colonial seabird breeding across a large latitudinal range in the Southern Ocean. Using multilocus microsatellite genotype data from 510 Gentoo penguin (Pygoscelis papua) individuals from 14 colonies along the Scotia Arc and Antarctic Peninsula, together with mitochondrial DNA data, we find strong genetic differentiation between colonies north and south of the Polar Front, that coincides geographically with the taxonomic boundary separating the subspecies P. p. papua and P. p. ellsworthii. Using a discrete Bayesian phylogeographic approach, we show that southern Gentoos expanded from a possible glacial refuge in the centre of their current range, colonising regions to the north and south through rare, long-distance dispersal. Our findings show that this dispersal is important for new colony foundation and range expansion in a seabird species that ordinarily exhibits high levels of natal philopatry, but persistent oceanographic features serve as barriers to movement.

气候变化、渔业对企鹅猎物的捕捞压力，以及人类对野生生物的直接干扰，均被证实为引发南大洋企鹅种群数量与分布发生剧烈变迁的核心诱因。若缺乏标记重捕（mark-recapture）研究，解析企鹅种群集群的形成机制，并进一步推演其分布范围的演变过程，将极具挑战性。遗传学研究，尤其是针对新建立种群的相关研究，能够提供种群定殖的动态快照，并可揭示种群数量与栖息范围的变化，在多大程度上由种群统计参数（如繁殖率与存活率）的改变，或是适宜生境斑块间的迁徙活动所驱动。
本研究针对南大洋内跨大纬度范围繁殖的集群性海鸟，阐述其种群遗传结构。我们利用取自斯科舍弧（Scotia Arc）与南极半岛沿线14个种群的510只巴布亚企鹅（Gentoo penguin, *Pygoscelis papua*）个体的多位点微卫星（microsatellite）基因型数据，结合线粒体DNA（mitochondrial DNA）数据，发现极锋（Polar Front）南北两侧的种群间存在显著遗传分化，这一地理分界恰好与划分亚种P. p. papua和P. p. ellsworthii的分类学边界相吻合。
借助离散贝叶斯系统发育地理学（discrete Bayesian phylogeographic）分析方法，我们证实南部巴布亚企鹅从其当前分布范围中部的一处潜在冰期避难地发生种群扩张，并通过罕见的长距离扩散事件向南北两侧完成种群定殖。本研究结果表明，尽管该海鸟物种通常表现出极高的出生地恋巢性（natal philopatry），但此类扩散事件对于新种群的建立与分布范围扩张至关重要；而持续存在的海洋水文特征则构成了种群扩散的障碍。