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林栖雀形目鸟类，长期以来一直是演化研究的核心对象，旨在阐明驱动雨林物种形成的内在机制。既往研究显示，在雨林-稀树草原过渡带（生态交错带，ecotones）中存在显著的形态与行为分化，且观测到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，而生态交错带可能是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突破使得研究者能够以更为全面的视角探究遗传分化模式。为评估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及地理区域内的种群基因组分化特征展开了系统探究。研究结果表明，个体可形成与独特环境特征及栖息地类型相匹配的离散遗传簇。不同栖息地种群间的两两FST值显著高于同栖息地内种群间的FST值，且该分化程度远超仅由地理距离所预期的水平。此外，通过全基因组选择扫描，本研究共鉴定出140个在种群间呈现极端分化的单核苷酸多态性（SNP）位点。这些异常位点在外显子区与编码区中显著富集，提示其具备重要的功能意义。针对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驱动基因组分化模式的过程中发挥了关键作用。本研究结果为“环境梯度在种群分化中具有重要意义”这一科学论断提供了至关重要的全新基因组学证据。