Repeated Selection of Alternatively Adapted Haplotypes Creates Sweeping Genomic Remodeling in Stickleback
Repeated Selection of Alternatively Adapted Haplotypes Creates Sweeping Genomic Remodeling in Stickleback
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DOI：
10.1534/genetics.117.300610
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发表时间：
2018-07-01
期刊：
影响因子：
3.3
通讯作者：
Cresko, William A.
中科院分区：
文献类型：
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作者：
Bassham, Susan;Catchen, Julian;Cresko, William A.
当种群适应不同的栖息地时，异质性遗传分化可以在基因组中积累，同时仍然交换等位基因。多样化需要多长时间，基因组的多少受到影响？当分歧发生平行从常设遗传变异，有多少次是相同的单倍型参与？我们探索这些问题，使用限制性位点相关的DNA测序基因分型数据，并表明，大规模的基因组重新构图，燃料丰富的常设变异，可以出现在短短几十代复制自然种群的三棘鱼（Gasterosteus aculeatus）。在1964年阿拉斯加灾难性的地震之后，海洋棘鱼在地震隆起的岛屿上新形成的池塘中定居。我们发现，这些年轻池塘中的淡水鱼与它们的海洋祖先不同，它们的基因组片段与以前在更古老的湖泊种群中出现分歧的基因组片段相同。在这些核心分歧区域之外，基因组没有显示出跨越海洋-淡水分水岭的种群结构，这与在替代环境中对仍然通过显著基因流连接的棘鱼种群起作用的强局部选择一致。强化这一推论，大多数不同的单倍型，在池塘中的高频率是在海洋中检测到的，即使在很大的地理距离。在此模式物种以前的人口基因组学工作的基础上，我们的数据表明，在海洋和淡水栖息地的棘鱼种群之间的分歧选择和基因流的悠久历史，保持了多态性的替代适应的DNA序列，促进平行进化。
Heterogeneous genetic divergence can accumulate across the genome when populations adapt to different habitats while still exchanging alleles. How long does diversification take and how much of the genome is affected? When divergence occurs in parallel from standing genetic variation, how often are the same haplotypes involved? We explore these questions using restriction site-associated DNA sequencing genotyping data and show that broad-scale genomic repatterning, fueled by copious standing variation, can emerge in just dozens of generations in replicate natural populations of threespine stickleback fish (Gasterosteus aculeatus). After the catastrophic 1964 Alaskan earthquake, marine stickleback colonized newly created ponds on seismically uplifted islands. We find that freshwater fish in these young ponds differ from their marine ancestors across the same genomic segments previously shown to have diverged in much older lake populations. Outside of these core divergent regions the genome shows no population structure across the ocean-freshwater divide, consistent with strong local selection acting in alternative environments on stickleback populations still connected by significant gene flow. Reinforcing this inference, a majority of divergent haplotypes that are at high frequency in ponds are detectable in the sea, even across great geographic distances. Building upon previous population genomics work in this model species, our data suggest that a long history of divergent selection and gene flow among stickleback populations in oceanic and freshwater habitats has maintained polymorphisms of alternatively adapted DNA sequences that facilitate parallel evolution.