Species often include multiple ecotypes that are adapted to different environments1. However, it is unclear how ecotypes arise and how their distinctive combinations of adaptive alleles are maintained despite hybridization with non-adapted populations2–4. Here, by resequencing 1,506 wild sunflowers from 3 species (Helianthus annuus, Helianthus petiolaris and Helianthus argophyllus), we identify 37 large (1–100 Mbp in size), non-recombining haplotype blocks that are associated with numerous ecologically relevant traits, as well as soil and climate characteristics. Limited recombination in these haplotype blocks keeps adaptive alleles together, and these regions differentiate sunflower ecotypes. For example, haplotype blocks control a 77-day difference in flowering between ecotypes of the silverleaf sunflower H. argophyllus (probably through deletion of a homologue of FLOWERING LOCUS T (FT)), and are associated with seed size, flowering time and soil fertility in dune-adapted sunflowers. These haplotypes are highly divergent, frequently associated with structural variants and often appear to represent introgressions from other—possibly now-extinct—congeners. These results highlight a pervasive role of structural variation in ecotypic adaptation. Resequencing analyses of three species of wild sunflower identify large non-recombining haplotype blocks that correlate with ecologically relevant traits, soil and climate characteristics, and that differentiate species ecotypes.

中文翻译：

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大量单倍型是向日葵生态分化的基础

物种通常包括适应不同环境的多种生态型1。然而，尚不清楚生态型是如何产生的，以及它们的适应性等位基因的独特组合如何在与非适应性种群杂交的情况下得以维持 2-4。在这里，通过对来自 3 个物种（向日葵、叶柄向日葵和向日葵）的 1,506 种野生向日葵进行重新测序，我们确定了 37 个大型（大小为 1-100 Mbp）、与许多生态相关性状相关的非重组单倍型块，以及作为土壤和气候特征。这些单倍型块中的有限重组将适应性等位基因保持在一起，并且这些区域区分向日葵生态型。例如，单倍型块控制了银叶向日葵 H 生态型之间 77 天的开花差异。argophyllus（可能通过删除 FLOWERING LOCUS T (FT) 的同源物），并且与适应沙丘的向日葵的种子大小、开花时间和土壤肥力有关。这些单倍型高度不同，经常与结构变异相关联，并且通常似乎代表来自其他（可能现已灭绝的）同类的基因渗入。这些结果突出了结构变异在生态适应中的普遍作用。对三种野生向日葵进行重测序分析，确定了与生态相关性状、土壤和气候特征相关并区分物种生态型的大型非重组单倍型块。经常与结构变异相关联，并且通常似乎代表来自其他（可能现已灭绝的）同类物的基因渗入。这些结果突出了结构变异在生态适应中的普遍作用。对三种野生向日葵进行重测序分析，确定了与生态相关性状、土壤和气候特征相关并区分物种生态型的大型非重组单倍型块。经常与结构变异相关联，并且通常似乎代表来自其他（可能现已灭绝的）同类物的基因渗入。这些结果突出了结构变异在生态适应中的普遍作用。对三种野生向日葵进行重测序分析，确定了与生态相关性状、土壤和气候特征相关并区分物种生态型的大型非重组单倍型块。