Strong Phylogeographic Structure in a Sedentary Seabird, the Stewart Island Shag (Leucocarbo chalconotus)

New Zealand's endemic Stewart Island Shag (Leucocarbo chalconotus) comprises two regional groups (Otago and Foveaux Strait) that show consistent differentiation in relative frequencies of pied versus dark-bronze morphotypes, the extent of facial carunculation, body size and breeding time. We used modern and ancient DNA (mitochondrial DNA control region one), and morphometric approaches to investigate the phylogeography and taxonomy of L. chalconotus and its closely related sister species, the endemic Chatham Island Shag (L. onslowi). Our analysis shows Leucocarbo shags in southern New Zealand comprise two well-supported clades, each containing both pied and dark-bronze morphs. However, the combined monophyly of these populations is not supported, with the L. chalconotus Otago lineage sister to L. onslowi. Morphometric analysis indicates that Leucocarbo shags from Otago are larger on average than those from Foveaux Strait. Principal co-ordinate analysis of morphometric data showed substantial morphological differentiation between the Otago and Foveaux Strait clades, and L. onslowi. The phylogeographic partitioning detected within L. chalconotus is marked, and such strong structure is rare for phalacrocoracid species. Our phylogenetic results, together with consistent differences in relative proportions of plumage morphs and facial carunculation, and concordant differentiation in body size and breeding time, suggest several alternative evolutionary hypotheses that require further investigation to determine the level of taxonomic distinctiveness that best represents the L. chalconotus Otago and Foveaux Strait clades.新西兰特有斯图尔特岛鸬鹚（Leucocarbo chalconotus）包含两个区域类群——奥塔哥类群与福沃海峡（Foveaux Strait）类群，二者在斑羽型与深青铜色羽型的相对频率、面部肉垂发育程度、体型大小以及繁殖时间上均存在稳定分化。本研究借助现代与古代DNA（线粒体DNA第一控制区（mitochondrial DNA control region one））以及形态计量学方法，对L. chalconotus及其近缘姊妹物种——查塔姆岛鸬鹚（L. onslowi）的系统地理学与分类学展开了探究。分析结果显示，新西兰南部的Leucocarbo属鸬鹚包含两个高支持度演化支，每个演化支中均同时存在斑羽型与深青铜色羽型个体。但这些类群的联合单系性并未得到支持，奥塔哥类群的L. chalconotus与L. onslowi构成姊妹支系。形态计量学分析表明，奥塔哥地区的Leucocarbo属鸬鹚平均体型大于福沃海峡类群。对形态计量学数据的主坐标分析（principal co-ordinate analysis）显示，奥塔哥与福沃海峡演化支，以及L. onslowi之间存在显著的形态分化。L. chalconotus内部检测到的系统地理分区特征十分显著，而这种强种群结构在鸬鹚科物种中较为罕见。本研究的系统发育结果，结合羽色形态型相对比例、面部肉垂的稳定差异，以及体型与繁殖时间的一致性分化，提出了多种可供后续探究的演化假说，需进一步研究以确定能够最佳体现L. chalconotus奥塔哥与福沃海峡演化支分类学独特性的分类等级。