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.

杂交允许在谱系之间共享适应，并可能触发新物种的进化^1,2。然而，令人信服的同倍体杂交物种形成的例子仍然很少见，因为要证明杂交在产生生殖隔离中至关重要是具有挑战性的³。在这里，我们将种群基因组分析与物种特异性状的数量性状位点图谱相结合，以检查 Heliconius 蝴蝶的杂交物种形成案例。我们表明 Heliconius elevatus 是一个与父母同源的杂交物种，并且作为一个独立进化的谱系持续存在了至少 180,000 年。尽管与一个亲本 Heliconius pardalinus 存在普遍且持续的基因流动，该亲本使它们 99% 的基因组同质化。剩余的 1% 从另一个亲本 Heliconius melpomene 渗入，并广泛分布在 H. elevatus 基因组中与 H. pardalinus 不同的岛屿上。这些岛屿包含多种处于破坏性选择的性状，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，这些性状使 H. elevatus 处于自己的适应性高峰，并允许与亲本共存。我们的结果表明，物种形成是由生态性状的渗入驱动的，并且具有多位点遗传结构的基因流物种形成是可能的。