Data from: Outlier analyses to test for local adaptation to breeding grounds in a migratory arctic seabird

Investigating the extent (or the existence) of local adaptation is crucial to understanding how populations adapt. When experiments or fitness measurements are difficult or impossible to perform in natural populations, genomic techniques allow us to investigate local adaptation through the comparison of allele frequencies and outlier loci along environmental clines. The thick-billed murre (Uria lomvia) is a highly philopatric colonial arctic seabird that occupies a significant environmental gradient, shows marked phenotypic differences among colonies, and has large effective population sizes. To test whether thick-billed murres from five colonies along the eastern Canadian Arctic coast show genomic signatures of local adaptation to their breeding grounds, we analyzed geographic variation in genome-wide markers mapped to a newly assembled thick-billed murre reference genome. We used outlier analyses to detect loci putatively under selection, and clustering analyses to investigate patterns of differentiation based on 2220 genomewide single nucleotide polymorphisms (SNPs) and 137 outlier SNPs. We found no evidence of population structure among colonies using all loci but found population structure based on outliers only, where birds from the two northernmost colonies (Minarets and Prince Leopold) grouped with birds from the southernmost colony (Gannet), and birds from Coats and Akpatok were distinct from all other colonies. Although results from our analyses did not support local adaptation along the latitudinal cline of breeding colonies, outlier loci grouped birds from different colonies according to their non-breeding distributions, suggesting that outliers may be informative about adaptation and/or demographic connectivity associated with their migration patterns or nonbreeding grounds.

探究本地适应（local adaptation）的程度或其存在性，对于理解种群的适应机制至关重要。当在自然种群中开展实验或适合度测量存在困难或无法实现时，基因组学技术可通过比较环境梯度（environmental clines）上的等位基因频率（allele frequencies）与异常位点（outlier loci），开展本地适应的相关研究。
厚嘴海鸦（thick-billed murre, *Uria lomvia*）是一种具有强恋巢习性的北极集群海鸟，其分布范围覆盖显著的环境梯度，不同种群间存在显著表型差异，且拥有较大的有效种群规模（effective population sizes）。
为验证加拿大北极东海岸5个种群的厚嘴海鸦是否存在与其繁殖地本地适应相关的基因组特征（genomic signatures），我们针对基于新组装的厚嘴海鸦参考基因组（reference genome）注释的全基因组标记（genome-wide markers）开展地理变异分析。
我们通过异常位点分析（outlier analyses）检测潜在受选择位点，并基于2220个全基因组单核苷酸多态性（single nucleotide polymorphisms, SNPs）与137个异常SNP开展聚类分析（clustering analyses），以探究种群分化模式。
基于全部位点的分析未发现种群间存在显著的种群结构，但仅基于异常位点的分析则检测到种群结构：两个最北端种群（米纳雷茨岛与利奥波德王子岛）的个体与最南端种群（甘尼特岛）聚为一类，而科茨岛与阿卡帕托克岛的个体则与其余所有种群存在显著分化。
尽管本研究的分析结果并不支持繁殖地纬度梯度（latitudinal cline）下的本地适应假说，但异常位点的聚类结果可依据不同种群的非繁殖期分布进行分组，这提示异常位点或许能反映与迁徙模式或越冬地（nonbreeding grounds）相关的适应及种群连通性（demographic connectivity）信息。