Data from: Genomic associations with bill length and disease reveal drift and selection across island bird populations

Island species provide excellent models for investigating how selection and drift operate in wild populations, and for determining how these processes act to influence local adaptation and speciation. Here, we examine the role of selection and drift in shaping genomic and phenotypic variation across recently separated populations of Berthelot's pipit (Anthus berthelotii), a passerine bird endemic to three archipelagos in the Atlantic. We first characterised genetic diversity and population structuring, which supported previous inferences of a history of recent colonisations and bottlenecks. We then tested for regions of the genome associated with the ecologically important traits of bill length and malaria infection, both of which vary substantially across populations in this species. We identified a SNP associated with variation in bill length among individuals, islands and archipelagos; patterns of variation at this SNP suggest that both phenotypic and genotypic variation in bill length is largely shaped by founder effects. Malaria was associated with SNPs near/within genes involved in the immune response, but this relationship was not consistent among archipelagos, supporting the view that disease resistance is complex and rapidly evolving. Although we found little evidence for divergent selection at candidate loci for bill length and malaria resistance, genome scan analyses pointed to several genes related to immunity and metabolism as having important roles in divergence and adaptation. Our findings highlight the utility and challenges involved with combining association mapping and population genetic analysis in non-equilibrium populations, to disentangle the effects of drift and selection on shaping genotypes and phenotypes.岛屿物种为探究野生种群中选择与遗传漂变的作用机制，以及阐明这些过程如何影响局部适应与物种形成提供了极佳的研究模型。本研究聚焦于伯氏鹨（Anthus berthelotii）——一种仅分布于大西洋三个群岛的特有雀形目鸟类——近期分化的不同种群，解析选择与遗传漂变对其基因组与表型变异的塑造作用。我们首先对遗传多样性与种群结构进行了表征，结果支持此前关于该物种近期殖民与种群瓶颈历史的推论。随后，我们针对基因组中与生态重要性状——喙长与疟疾感染——相关的区域开展了检验，这两个性状在该物种的不同种群间均存在显著差异。我们鉴定到一个与个体、岛屿以及群岛间喙长变异相关的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）；该SNP的变异模式提示，喙长的表型与基因型变异主要由奠基者效应塑造。疟疾感染与免疫应答相关基因附近/内部的SNP存在关联，但这一关联在不同群岛间并不一致，这支持了疾病抗性复杂且快速演化的观点。尽管我们在喙长与疟疾抗性的候选位点上未发现明显的歧化选择信号，但基因组扫描分析指出，多个与免疫及代谢相关的基因在种群分化与适应过程中发挥了重要作用。本研究结果凸显了在非平衡种群中结合关联作图与群体遗传分析，以厘清遗传漂变与选择对基因型与表型塑造效应的应用价值与研究挑战。