Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome.
Footprints of local adaptation span hundreds of linked genes in the Atlantic silverside genome.
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DOI：
10.1002/evl3.189
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发表时间：
2020-10
影响因子：
5
通讯作者：
Therkildsen NO
中科院分区：
文献类型：
--
作者：
Wilder AP;Palumbi SR;Conover DO;Therkildsen NO
在持续的基因流动存在的地方适应的研究是自然选择在行动中的研究，揭示了功能遗传多样性最相关的当代压力。除了单个基因之外，全基因组结构本身也可以进化以实现适应。大西洋银鱼分布在北美东海岸沿着的一个陡峭的温度梯度上，在一系列性状上表现出非凡的局部适应性，并且能够从现有的遗传变异中快速适应，但我们对整个物种范围内的基因组变异模式知之甚少，这些模式使这种显着的适应性成为可能。在这里，我们使用低覆盖率，全转录组测序大西洋银鱼采样沿着的环境渐变，以显示显着的签名，分歧的选择跨越梯度的中性分化。在其分布的南部1371公里处取样的大西洋银鱼具有非常低的全基因组分化（190万个变异体的中位数F ST = 0.006），与历史连接性和最近移民的观察结果一致。然而，几乎14，000个单核苷酸多态性（SNP）对于替代等位基因几乎是固定的（FST> 0.95）。高度分化的SNPs聚类成四个紧密连锁不平衡（LD）块，跨越数百个基因和几个兆碱基。在这些LD块的变体是不成比例的非同义词和富集的基因与已知的适应银汉鱼，包括在脂质储存，代谢率和产卵行为的变化的多个功能。绝对差异和人口模型的升高水平表明，在基因流动下，选择维持了这些区块的差异。这些发现代表了整个基因组分化水平异质性的极端情况，并强调了基因流如何在连续种群中塑造基因组结构。局部适应等位基因可能是沿着环境梯度分布的种群的共同特征，并且可能是保护变异以使未来能够对环境变化做出反应的关键。
The study of local adaptation in the presence of ongoing gene flow is the study of natural selection in action, revealing the functional genetic diversity most relevant to contemporary pressures. In addition to individual genes, genome‐wide architecture can itself evolve to enable adaptation. Distributed across a steep thermal gradient along the east coast of North America, Atlantic silversides (Menidia menidia) exhibit an extraordinary degree of local adaptation in a suite of traits, and the capacity for rapid adaptation from standing genetic variation, but we know little about the patterns of genomic variation across the species range that enable this remarkable adaptability. Here, we use low‐coverage, whole‐transcriptome sequencing of Atlantic silversides sampled along an environmental cline to show marked signatures of divergent selection across a gradient of neutral differentiation. Atlantic silversides sampled across 1371 km of the southern section of its distribution have very low genome‐wide differentiation (median F ST = 0.006 across 1.9 million variants), consistent with historical connectivity and observations of recent migrants. Yet almost 14,000 single nucleotide polymorphisms (SNPs) are nearly fixed (F ST > 0.95) for alternate alleles. Highly differentiated SNPs cluster into four tight linkage disequilibrium (LD) blocks that span hundreds of genes and several megabases. Variants in these LD blocks are disproportionately nonsynonymous and concentrated in genes enriched for multiple functions related to known adaptations in silversides, including variation in lipid storage, metabolic rate, and spawning behavior. Elevated levels of absolute divergence and demographic modeling suggest selection maintaining divergence across these blocks under gene flow. These findings represent an extreme case of heterogeneity in levels of differentiation across the genome, and highlight how gene flow shapes genomic architecture in continuous populations. Locally adapted alleles may be common features of populations distributed along environmental gradients, and will likely be key to conserving variation to enable future responses to environmental change.
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影响因子：
4.1
作者：
Conover DO;Baumann H
通讯作者：
Baumann H
影响因子：
4.9
作者：
Fabian DK;Kapun M;Nolte V;Kofler R;Schmidt PS;Schlötterer C;Flatt T
通讯作者：
Flatt T
影响因子：
5
作者：
Delmore KE;Lugo Ramos JS;Van Doren BM;Lundberg M;Bensch S;Irwin DE;Liedvogel M
通讯作者：
Liedvogel M
影响因子：
3.3
作者：
Fang, Zhou;Pyhajarvi, Tanja;Ross-Ibarra, Jeffrey
通讯作者：
Ross-Ibarra, Jeffrey
影响因子：
1.2
作者：
Cingolani, Pablo;Platts, Adrian;Ruden, Douglas M.
通讯作者：
Ruden, Douglas M.