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.

探究局部适应的程度（或其存在性），对于理解种群适应的内在机制至关重要。当在自然种群中难以或无法开展实验或适合度测量时，基因组学技术可通过沿环境梯度（environmental clines）比较等位基因频率（allele frequencies）与异常位点（outlier loci），以此探究局部适应现象。厚嘴海鸦（thick-billed murre，Uria lomvia）是一种高度恋巢的北极集群海鸟，其分布范围覆盖显著的环境梯度，不同繁殖群落间存在显著表型差异，且具备较大的有效种群大小（effective population sizes）。为验证加拿大北极东海岸5个繁殖群落的厚嘴海鸦是否存在适应其繁殖地的基因组特征，我们对基于新组装的厚嘴海鸦参考基因组（reference genome）所注释的全基因组标记（genome-wide markers）开展了地理变异分析。本研究采用异常位点分析（outlier analyses）检测潜在受选择的位点，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位点进行聚类分析，以探究种群分化模式。基于全部位点的分析未发现繁殖群落间存在种群结构（population structure），但仅基于异常位点的分析则呈现出明显的种群结构：两个最北端的群落（米纳雷茨岛与利奥波德王子岛）的个体与最南端的群落（甘尼特岛）的个体聚为一支，而科茨岛与阿卡帕托克岛的个体则与其余所有群落的个体均存在显著分化。尽管本研究的分析结果并不支持繁殖群落沿纬度梯度发生局部适应，但异常位点却能依据不同群落个体的非繁殖分布进行聚类，这表明异常位点或可揭示与迁徙模式或非繁殖栖息地相关的适应特征及/或种群连通性。