Data from: Inversions contribute disproportionately to parallel genomic divergence in dune sunflowers

AbstractThe probability of parallel genetic evolution is a function of the strength of selection and constraints imposed by genetic architecture. Inversions capture locally adapted alleles and suppress recombination between them, which limits the range of adaptive responses. Also, the combined phenotypic effect of alleles within inversions is likely to be greater than that of individual alleles, which should further increase the contributions of inversions to parallel evolution. We tested the hypothesis that inversions contribute disproportionately to parallel genetic evolution in independent dune ecotypes of Helianthus petiolaris. We analyzed habitat data and identified variables underlying parallel habitat shifts. Genotype-environment association analyses of these variables indicated parallel responses of inversions to shared selective pressures. We also confirmed larger seed size across the dunes and performed quantitative trait locus (QTL) mapping with multiple crosses. QTL shared between locations fell into inversions more than expected by chance. We used whole-genome sequencing data to identify selective sweeps in the dune ecotypes and found that the majority of shared swept regions were found within inversions. Phylogenetic analyses of shared regions indicate that within inversions the same allele typically was found in the dune habitat at both sites. These results confirm predictions that inversions drive parallel divergence in the dune ecotypes. MethodsThis dataset includes: Habitat data collected from areas where wild H. petiolaris sunflowers grow Seed size data collected from H. petiolaris growing in the wild and under common garden conditions Unfiltered vcfs used for QTL mapping seed size and looking for genotype environement associations Genomic locations of previously identified haploblocks (inversions) within H. petiolaris Inversion genotypes for the QTL mapping populations Please see the README file and associated publication for more complete descriptions of each dataset.摘要 平行遗传演化的概率是选择强度与遗传结构所施加约束的函数。倒位（inversions）可捕获局部适应性等位基因，并抑制等位基因间的重组，这会限制适应性响应的范围。此外，倒位内等位基因的综合表型效应往往大于单个等位基因的效应，这将进一步提升倒位对平行演化的贡献。我们针对柄花向日葵（Helianthus petiolaris）的独立沙丘生态型，检验了“倒位对平行遗传演化存在不成比例的贡献”这一假说。我们分析了生境数据，识别出驱动平行生境转变的关键变量。针对这些变量开展的基因型-环境关联分析（genotype-environment association analyses）显示，倒位对共同选择压力呈现平行响应。我们还证实了各沙丘种群均存在更大的种子尺寸，并通过多个杂交组合开展了数量性状位点（QTL, quantitative trait locus）定位。不同采样地点共享的QTL更多地位于倒位内，这一比例高于随机预期的结果。我们利用全基因组测序数据，识别了沙丘生态型中的选择性清除（selective sweeps）区域，发现多数共享的清除区域均位于倒位内部。对共享区域的系统发育分析表明，在两个采样点的沙丘生境中，倒位内通常存在相同的等位基因。上述结果验证了“倒位推动沙丘生态型发生平行分化”的预测。 方法 本数据集涵盖以下内容： 1. 野生柄花向日葵生长区域的生境数据； 2. 野生及同质栽培条件下柄花向日葵的种子尺寸数据； 3. 用于种子尺寸QTL定位及基因型-环境关联分析的未过滤变异识别格式（VCF, Variant Call Format）文件； 4. 柄花向日葵基因组内已鉴定的单倍型块（haploblocks，倒位）的基因组位置信息； 5. 用于QTL定位群体的倒位基因型数据。 如需了解各数据集的完整说明，请参阅README文件及相关已发表论文。