Hybridization allows adaptations to be shared among lineages and may trigger the evolution of new species^1,2. However, convincing examples of homoploid hybrid speciation remain rare because it is challenging to demonstrate that hybridization was crucial in generating reproductive isolation³. Here we combine population genomic analysis with quantitative trait locus mapping of species-specific traits to examine a case of hybrid speciation in Heliconius butterflies. We show that Heliconius elevatus is a hybrid species that is sympatric with both parents and has persisted as an independently evolving lineage for at least 180,000 years. This is despite pervasive and ongoing gene flow with one parent, Heliconius pardalinus, which homogenizes 99% of their genomes. The remaining 1% introgressed from the other parent, Heliconius melpomene, and is scattered widely across the H. elevatus genome in islands of divergence from H. pardalinus. These islands contain multiple traits that are under disruptive selection, including colour pattern, wing shape, host plant preference, sex pheromones and mate choice. Collectively, these traits place H. elevatus on its own adaptive peak and permit coexistence with both parents. Our results show that speciation was driven by introgression of ecological traits, and that speciation with gene flow is possible with a multilocus genetic architecture.

杂交允许谱系之间共享适应性，并可能引发新物种的进化^1,2。然而，同倍体杂交物种形成的令人信服的例子仍然很少，因为证明杂交对于产生生殖隔离至关重要³具有挑战性。在这里，我们将群体基因组分析与物种特定性状的数量性状基因座作图结合起来，以研究Heliconius蝴蝶的杂交物种形成案例。我们证明，Heliconius elevatus是一种与双亲同域的杂交物种，并且作为一个独立进化的谱系持续存在了至少 18 万年。尽管与一个亲本Heliconius pardalinus存在普遍且持续的基因流动，其 99% 的基因组均质化。剩下的 1% 是从另一个亲本Heliconius melpomene渗入的，并且广泛分散在H. elevatus基因组中与H. pardalinus不同的岛屿中。这些岛屿包含多种处于破坏性选择下的性状，包括颜色图案、翅膀形状、寄主植物偏好、性信息素和配偶选择。总的来说，这些特征使H. elevatus处于其自身的适应高峰，并允许与父母共存。我们的结果表明，物种形成是由生态性状的渗入驱动的，并且通过多位点遗传结构，基因流的物种形成是可能的。