Data from: Genomic divergence across ecological gradients in the Central African rainforest songbird (Andropadus virens)

The little greenbul, a common rainforest passerine from sub-Saharan Africa, has been the subject of long-term evolutionary studies to understand the mechanisms leading to rainforest speciation. Previous research found morphological and behavioral divergence across rainforest-savanna transition zones (ecotones), and a pattern of divergence with gene flow suggesting divergent natural selection has contributed to adaptive divergence and ecotones could be important areas for rainforests speciation. Recent advances in genomics and environmental modeling make it possible to examine patterns of genetic divergence in a more comprehensive fashion. To assess the extent to which natural selection may drive patterns of differentiation, here we investigate patterns of genomic differentiation among populations across environmental gradients and regions. We find compelling evidence that individuals form discrete genetic clusters corresponding to distinctive environmental characteristics and habitat types. Pairwise FST between populations in different habitats is significantly higher than within habitats, and this differentiation is greater than what is expected from geographic distance alone. Moreover, we identified 140 SNPs that showed extreme differentiation among populations through a genome-wide selection scan. These outliers were significantly enriched in exonic and coding regions, suggesting their functional importance. Environmental association analysis of SNP variation indicates that several environmental variables, including temperature and elevation, play important roles in driving the pattern of genomic diversification. Results lend important new genomic evidence for environmental gradients being important in population differentiation.

小绿鹎（little greenbul）是一种分布于撒哈拉以南非洲的常见雨林雀形目（passerine）鸟类，长期以来一直是解析雨林物种形成机制的进化生物学研究核心对象。既往研究发现，在雨林-稀树草原过渡带（生态交错带，ecotone）中存在显著的形态与行为分化，且存在伴随基因流的分化模式，这提示趋异自然选择推动了适应性分化，而生态交错带或为雨林物种形成的关键区域。近年来基因组学与环境建模技术的长足进步，使得我们能够更为全面地刻画种群的遗传分化格局。为量化自然选择对种群分化模式的驱动程度，本研究针对不同环境梯度与地理区域的种群间基因组分化模式展开了系统分析。研究结果提供了强有力的证据：个体可形成与独特环境特征及生境类型一一对应的离散遗传聚类群。不同生境种群间的两两群体分化指数（FST）显著高于同生境种群内部，且该分化程度远超仅由地理距离所能解释的预期水平。此外，通过全基因组选择扫描（genome-wide selection scan），我们共鉴定出140个在种群间呈现极端分化的单核苷酸多态性位点（SNPs, Single Nucleotide Polymorphism）。这些分化异常位点显著富集于外显子区（exonic region）及编码区（coding region），提示其具备重要的生物学功能。对SNP变异开展的环境关联分析显示，温度、海拔等多项环境变量在推动基因组分化格局形成的过程中发挥了关键作用。本研究结果为“环境梯度对种群分化具有重要影响”这一科学论断提供了全新的重要基因组学证据。