Zhen Ying, Harrigan Ryan J, Ruegg Kristen C, Anderson Eric C, Ng Thomas C, Lao Sirena, Lohmueller Kirk E, Smith Thomas B
Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA.
Center for Tropical Research, Institute of Environment and Sustainability, University of California, Los Angeles, CA, USA.
Mol Ecol. 2017 Oct;26(19):4966-4977. doi: 10.1111/mec.14270. Epub 2017 Aug 21.
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 behavioural divergence across rainforest-savannah 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 modelling 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 F 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 genomewide 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.
小翠鸟是一种来自撒哈拉以南非洲的常见雨林雀形目鸟类，一直是长期进化研究的对象，以了解导致雨林物种形成的机制。先前的研究发现，在雨林 - 稀树草原过渡带（生态交错带）存在形态和行为上的差异，以及一种伴有基因流的差异模式，这表明分歧性自然选择促成了适应性分化，且生态交错带可能是雨林物种形成的重要区域。基因组学和环境建模的最新进展使得以更全面的方式研究遗传分化模式成为可能。为了评估自然选择在多大程度上可能驱动分化模式，我们在此研究了不同环境梯度和区域的种群间基因组分化模式。我们发现了令人信服的证据，即个体形成了与独特环境特征和栖息地类型相对应的离散遗传簇。不同栖息地种群间的成对F值显著高于栖息地内的成对F值，且这种分化大于仅由地理距离所预期的程度。此外，通过全基因组选择扫描，我们鉴定出140个在种群间表现出极端分化的单核苷酸多态性（SNP）。这些异常值在外显子和编码区域显著富集，表明它们具有功能重要性。SNP变异的环境关联分析表明，包括温度和海拔在内的几个环境变量在驱动基因组多样化模式方面发挥着重要作用。研究结果为环境梯度在种群分化中起重要作用提供了重要的新基因组证据。
