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.

岛屿物种是研究野生种群中选择与遗传漂变作用机制，以及阐明这两类过程如何影响局部适应与物种形成的极为理想的模型体系。本研究以分布于大西洋三个群岛的特有雀形目鸟类——伯氏鹨（Anthus berthelotii）为研究对象，探究选择与遗传漂变对其近期分化种群的基因组与表型变异的塑造作用。我们首先对该物种的遗传多样性与种群结构进行了系统表征，结果支持此前关于其近期拓殖与种群瓶颈的演化历史推断。随后，我们针对与该物种两类核心生态性状——喙长与疟疾感染——相关的基因组区域开展关联分析，这两类性状在该物种的不同种群间均存在显著分化。我们鉴定出一个与个体、岛屿及群岛间喙长变异相关的单核苷酸多态性（Single Nucleotide Polymorphism, SNP）位点；该位点的变异模式表明，喙长的表型与基因型变异在很大程度上由奠基者效应塑造。疟疾感染与免疫应答相关基因的侧翼或编码区内的SNP存在显著关联，但该关联模式在不同群岛间并不一致，这佐证了疾病抗性具有复杂性且演化迅速的观点。尽管我们在喙长与疟疾抗性的候选位点上未发现显著的歧化选择证据，但基因组扫描分析显示，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关键作用。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。