Data from: Stepwise evolution of a butterfly supergene via duplication and inversion

Supergenes maintain adaptive clusters of alleles in the face of genetic
mixing. Although usually attributed to inversions, supergenes can be
complex, and reconstructing the precise processes that led to
recombination suppression and their timing is challenging. We investigated
the origin of the BC supergene, which controls variation in warning
colouration in the African Monarch butterfly, Danaus chrysippus. By
generating chromosome-scale assemblies for all three alleles, we
identified multiple structural differences. Most strikingly, we find that
a region of >1 million bp underwent several segmental duplications
at least 7.5 million years ago. The resulting duplicated fragments appear
to have triggered four inversions in surrounding parts of the chromosome,
resulting in stepwise growth of the region of suppressed recombination.
Phylogenies for the inversions are incongruent with the species tree, and
suggest that structural polymorphisms have persisted for at least 4.1
million years. In addition to the role of duplications in triggering
inversions, our results suggest a previously undescribed mechanism of
recombination suppression through independent losses of divergent
duplicated tracts. Overall, our findings add support for a stepwise model
of supergene evolution involving a variety of structural changes.

超基因（supergene）可在基因混合的背景下维持适应性等位基因簇。尽管超基因通常被归因于染色体倒位（inversions），但其结构往往较为复杂，且重建导致重组抑制的精确过程及其发生时间极具挑战性。本研究以非洲斑蝶（Danaus chrysippus）中控制警戒色变异的BC超基因为研究对象，探究其起源。通过为三种等位基因均构建染色体级别的基因组组装，我们鉴定出了多种结构变异。最显著的是，一段长度超过100万碱基对的区域在至少750万年前发生了多次片段重复事件。由此产生的重复片段似乎触发了染色体周边区域的四次倒位，使得重组抑制区域逐步扩张。针对这些倒位构建的系统发育树与物种树并不一致，表明该结构多态性已存续至少410万年。除片段重复触发倒位的作用外，我们的研究结果还揭示了一种此前未被报道的重组抑制机制：通过独立丢失趋异的重复序列区域。综上，本研究结果为涉及多种结构变化的超基因演化阶梯模型提供了新的支持证据。