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. And yet, genomic data often lack 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 colour 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 centre of the hybrid zone. We propose that shared warning signalling (Müllerian mimicry) may couple the cline shifts seen in both species, and facilitate the parallel co-emergence of a novel hybrid morph in both co-mimetic species. Our results show the power of efficient haplotyping methods when combined with large-scale sequencing data from natural populations.

中文翻译：

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单倍型标签揭示了两个蝴蝶物种中杂种的平行形成

遗传变异作为变异或单倍型的链接集分离。单倍型和连锁是遗传学的核心，实际上是所有遗传和选择分析的基础。然而，由于测序技术的限制，基因组数据通常缺少单倍型信息。在这里，我们介绍“单元标记”，这是一种简单的低成本链接阅读测序技术，可以对数百个人进行测序，同时保留链接信息。我们应用单元标记为600多只蝴蝶（Heliconius erato和H. melpomene）构建兆碱基大小的单倍型），在厄瓜多尔的海拔梯度上形成重叠的混合带。单倍标签识别可控制独特的高地和低地机翼颜色图案的基因座。在两个物种的相同主要基因座中发现了不同的单倍型，而染色体重排未显示平行性。值得注意的是，在这两个物种中，主要机翼模式基因座的地理直线都偏移了18 km，导致杂种区中心出现了新的杂种形态。我们建议共享的警告信号（缪勒式模仿）可能会耦合在两个物种中看到的直线移动，并促进两个共模拟物种中新型杂种形态的平行共现。我们的结果表明，与来自自然种群的大规模测序数据相结合时，有效的单体型方法具有强大的功能。