Data from: Shared selective pressure and local genomic landscape lead to repeatable patterns of genomic divergence in sunflowers

<b>Abstract</b><br/>The repeated evolution of traits in organisms facing similar environmental conditions is considered to be fundamental evidence for the role of natural selection in moulding phenotypes. Yet, aside from case studies of parallel evolution and its genetic basis, the repeatability of evolution at the level of the whole genome remains poorly characterized. Here, through the use of transcriptome sequencing, we examined genomic divergence for three pairs of sister species of sunflowers. Two of the pairs (Helianthus petiolaris – H. debilis and H. annuus – H. argophyllus) have diverged along a similar latitudinal gradient and presumably experienced similar selective pressure. In contrast, a third species pair (H. exilis – H. bolanderi) diverged along a longitudinal gradient. Analyses of divergence, as measured in terms of FST, indicated little repeatability across the three pairs of species for individual genetic markers (SNPs), modest repeatability at the level of individual genes and the highest repeatability when large regions of the genome were compared. As expected, higher repeatability was observed for the two species pairs that have diverged along a similar latitudinal gradient, with genes involved in flowering time among the most divergent genes. Genes showing extreme low or high differentiation were more similar than genes showing medium levels of divergence, implying that both purifying and divergent selection contributed to repeatable patterns of divergence. The location of a gene along the chromosome also predicted divergence levels, presumably because of shared heterogeneity in both recombination and mutation rates. In conclusion, repeated genome evolution appeared to result from both similar selective pressures and shared local genomic landscapes.

<b>摘要</b><br/>当生物体面临相似环境条件时，其性状的重复演化被视为自然选择塑造表型（phenotype）的关键证据。然而，除平行演化及其遗传基础的个案研究外，全基因组层面的演化可重复性仍未得到充分表征。本研究通过转录组测序（transcriptome sequencing）技术，对3对向日葵姊妹物种的基因组分化展开分析。其中2对物种（Helianthus petiolaris – H. debilis 与 H. annuus – H. argophyllus）沿相似的纬度梯度发生分化，推测曾经历相似的选择压力。与之形成对照的是，第3对物种（H. exilis – H. bolanderi）沿经度梯度发生分化。以FST（Fixation Index，固定指数）作为分化衡量指标的分析结果显示，3对物种在单个遗传标记（单核苷酸多态性，Single Nucleotide Polymorphism, SNPs）层面的可重复性极低，在单个基因层面的可重复性较为适中，而在比较基因组大片段区域时可重复性达到最高。正如预期，沿相似纬度梯度分化的2对物种展现出更高的演化可重复性，其中与开花时间相关的基因属于分化程度最高的基因之列。分化程度极低或极高的基因，其分化模式的相似性要高于分化程度中等的基因，这表明纯化选择（purifying selection）与歧化选择（divergent selection）共同促成了可重复的分化模式。基因在染色体上的位置同样可以预测其分化水平，推测这是因为重组率与突变率均存在共通的异质性。综上，基因组的重复演化似乎是相似选择压力与共通的局部基因组景观共同作用的结果。