Genetic variation segregates as linked sets of variants or haplotypes. Haplotypes and linkage are central to genetics and underpin virtually all genetic and selection analysis. Yet, genomic data often omit haplotype information due to constraints in sequencing technologies. Here, we present “haplotagging,” a simple, low-cost linked-read sequencing technique that allows sequencing of hundreds of individuals while retaining linkage information. We apply haplotagging to construct megabase-size haplotypes for over 600 individual butterflies (Heliconius erato and H. melpomene), which form overlapping hybrid zones across an elevational gradient in Ecuador. Haplotagging identifies loci controlling distinctive high- and lowland wing color patterns. Divergent haplotypes are found at the same major loci in both species, while chromosome rearrangements show no parallelism. Remarkably, in both species, the geographic clines for the major wing-pattern loci are displaced by 18 km, leading to the rise of a novel hybrid morph in the center of the hybrid zone. We propose that shared warning signaling (Müllerian mimicry) may couple the cline shifts seen in both species and facilitate the parallel coemergence of a novel hybrid morph in both comimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations.

遗传变异分离为变体或单倍型的链接集。单倍型和连锁是遗传学的核心，几乎是所有遗传和选择分析的基础。然而，由于测序技术的限制，基因组数据通常会忽略单倍型信息。在这里，我们展示了“haplotagging”，这是一种简单、低成本的连锁读取测序技术，可以对数百个个体进行测序，同时保留连锁信息。我们应用 haplotagging 为超过 600 只蝴蝶（Heliconius erato和H. melpomene）构建百万碱基大小的单倍型)，在厄瓜多尔的海拔梯度上形成重叠的混合带。Haplotagging 识别控制独特的高地和低地翼颜色模式的位点。在两个物种的相同主要位点上都发现了不同的单倍型，而染色体重排没有显示出平行性。值得注意的是，在这两个物种中，主要翼型位点的地理系发生了 18 公里的位移，导致杂交区中心出现了一种新的杂交变种。我们建议共享警告信号（Müllerian 拟态）可能会结合两个物种中看到的克隆变化，并促进两个拟态物种中新的杂种形态的平行出现。我们的结果表明，当与来自自然种群的大规模测序数据相结合时，有效的单体型分析方法的威力。