Data from: Comparative population genomics reveals key barriers to dispersal in Southern Ocean penguins

The mechanisms that determine patterns of species dispersal are important factors in the production and maintenance of biodiversity. Understanding these mechanisms helps to forecast the responses of species to environmental change. Here we used a comparative framework and genome-wide data obtained through RAD-seq to compare the patterns of connectivity among breeding colonies for five penguin species with shared ancestry, overlapping distributions, and differing ecological niches, allowing an examination of the intrinsic and extrinsic barriers governing dispersal patterns. Our findings show that at-sea range and oceanography underlie patterns of dispersal in these penguins. The pelagic niche of emperor (Aptenodytes forsteri), king (A. patagonicus), Adélie (Pygoscelis adeliae) and chinstrap (P. antarctica) penguins facilitates gene flow over thousands of kilometres. In contrast, the coastal niche of gentoo penguins (P. papua) limits dispersal, resulting in population divergences. Oceanographic fronts also act as dispersal barriers to some extent. We recommend that forecasts of extinction risk incorporate dispersal and that management units are defined by at-sea range and oceanography in species lacking genetic data. Usage Notes Adelie penguins - VCF of SNP datasetAdelie.vcfChinstrap penguins - VCF of SNP datasetChinstrap.vcfGentoo penguins - VCF of full SNP datasetincludes outlier lociGentoos_all-SNPs.vcfGentoo penguins - VCF of neutral SNP datasetoutlier loci removedGentoos_neutral-SNPs.vcfGentoo penguins - nexus file for BFD*Input file of SNPs for BFD* species delimitationGentoos_input_for_BFD.nexGentoo penguins - phylip file for RAxMLPhylip alignment of SNPs for phylogenetic inference in RAxMLGentoos_input_for_RAxML.phyGentoos_input_for_SNAPP_set1XML input file for SNAPP analysis of gentoo penguins - set 1Gentoos_input_for_SNAPP_set2XML input file for SNAPP analysis - set 2

决定物种扩散模式的机制是生物多样性产生与维持的重要因素。明晰此类机制，有助于预测物种对环境变化的响应。本研究采用比较分析框架，结合通过RAD测序（RAD-seq）获取的全基因组数据，对5个具有共有祖先、分布重叠且生态位存在差异的企鹅物种的繁殖群落间连通模式展开对比分析，以此探究调控扩散模式的内在与外在障碍。研究结果显示，上述企鹅的扩散模式由其海域活动范围与海洋学特征所决定。帝企鹅（Aptenodytes forsteri）、王企鹅（A. patagonicus）、阿德利企鹅（Pygoscelis adeliae）以及帽带企鹅（P. antarctica）的远洋生态位，可支持其实现数千公里跨度的基因流。与之相对，巴布亚企鹅（P. papua）的近岸生态位则限制了扩散行为，进而引发种群分化。海洋锋面在一定程度上亦可作为扩散障碍。我们建议，在开展灭绝风险预测时应纳入扩散因素，且对于缺乏遗传数据的物种，其管理单元应依据海域活动范围与海洋学特征进行划定。使用说明：阿德利企鹅——单核苷酸多态性（Single Nucleotide Polymorphism, SNP）数据集的变异调用格式（Variant Call Format, VCF）文件：Adelie.vcf；帽带企鹅——SNP数据集的VCF文件：Chinstrap.vcf；巴布亚企鹅——包含异常位点的完整SNP数据集的VCF文件：Gentoos_all-SNPs.vcf；巴布亚企鹅——剔除异常位点的中性SNP数据集的VCF文件：Gentoos_neutral-SNPs.vcf；巴布亚企鹅——用于BFD*物种界定分析的SNP输入文件（Nexus格式）：Gentoos_input_for_BFD.nex；巴布亚企鹅——用于RAxML系统发育推断的SNP序列比对文件（Phylip格式）：Gentoos_input_for_RAxML.phy；巴布亚企鹅——第一组巴布亚企鹅SNAPP分析的XML输入文件：Gentoos_input_for_SNAPP_set1；巴布亚企鹅——第二组巴布亚企鹅SNAPP分析的XML输入文件：Gentoos_input_for_SNAPP_set2