Haplotype tagging reveals parallel formation of hybrid races in two butterfly species.
Haplotype tagging reveals parallel formation of hybrid races in two butterfly species.
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DOI：
10.1073/pnas.2015005118
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发表时间：
2021-06-22
影响因子：
11.1
通讯作者：
Chan YF
中科院分区：
文献类型：
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作者：
Meier JI;Salazar PA;Kučka M;Davies RW;Dréau A;Aldás I;Box Power O;Nadeau NJ;Bridle JR;Rolian C;Barton NH;McMillan WO;Jiggins CD;Chan YF
遗传学的一个明确目标是将DNA序列的变异与种群之间，最终与物种之间的性状进化联系起来。基因组测序有效地捕捉到了这种变异，但通常是在数百万个微小的片段中，这些片段忽略了单体型或连锁信息。我们提出了“单倍标记”，一种简单，快速的连接阅读测序技术，允许高通量测序，而不牺牲单倍型信息。我们验证了这种负担得起的方法，在大群体的全基因组单倍型。我们使用单倍标记调查一个新的混合变体在平行的混合区的两个comimetic Heliconius蝴蝶物种在厄瓜多尔的崛起。我们的研究结果表明，惊人的平行分歧，在他们的基因组产生协调的单倍型频率在整个混合区的变化，从而引起每个物种的共拟态混合变形。遗传变异分离为连锁的变体或单倍型集。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，基因组数据经常忽略单体型信息。在这里，我们提出了“单倍标记”，一个简单的，低成本的连接读取测序技术，允许测序的数百个人，同时保留连锁信息。我们应用单倍型标记技术为600多只蝴蝶（Heliconius erato和H。melpomene），其在厄瓜多尔的海拔梯度上形成重叠的混合区。单倍标记鉴定控制不同的高地和低地翅色模式的基因座。不同的单倍型被发现在相同的主要位点，在这两个物种，而染色体重排显示没有平行性。值得注意的是，在这两个物种中，地理倾斜的主要翅型位点位移18公里，导致一个新的混合变体的混合区中心的崛起。我们建议，共享的警告信号（Müllerian拟态）可能会耦合在这两个物种中看到的渐变群的变化，并促进一个新的混合变体在这两个comimetic物种的平行共存。我们的研究结果表明，当与来自自然群体的大规模测序数据相结合时，有效的单倍型分型方法具有强大的功能。
A defining goal in genetics is linking variation in DNA sequence to trait evolution between populations and, ultimately, species. Genome sequencing efficiently captures such variation but typically in millions of tiny fragments that omit haplotype or linkage information. We present “haplotagging,” a simple, rapid linked-read sequencing technique that allows high-throughput sequencing without sacrificing haplotype information. We validated this affordable approach for whole-genome haplotyping in large populations. We used haplotagging to investigate the rise of a novel hybrid morph in parallel hybrid zones of two comimetic Heliconius butterfly species in Ecuador. Our results reveal that strikingly parallel divergences in their genomes produced coordinated shifts in haplotype frequencies across the hybrid zone, giving rise to comimetic hybrid morphs in each species. 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.