Genomic Architecture of Rapid Parallel Adaptation to Fresh Water in a Wild Fish.
Genomic Architecture of Rapid Parallel Adaptation to Fresh Water in a Wild Fish.
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野生鱼类快速平行适应淡水的基因组结构
DOI：
10.1093/molbev/msaa290
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发表时间：
2021-04-13
影响因子：
10.7
通讯作者：
Liu JX
中科院分区：
文献类型：
--
作者：
Zong SB;Li YL;Liu JX
对新环境的快速适应可能通过自然选择驱动基因组区域发生变化。然而，这些适应性变化背后的遗传结构仍知之甚少。我们利用群体基因组学方法，通过比较四个淡水定居群体及其祖先的溯河洄游群体，研究了刀鲚快速平行适应淡水的基因组结构。连锁不平衡网络分析和群体遗传学分析揭示了LG6和LG22上两个假定的大染色体倒位，这些倒位富含离群位点，并与淡水适应呈现平行关联。在群体间观察到这两个染色体倒位的频率急剧变化以及遗传分化加剧，这表明这两个倒位在溯河洄游和定居生态型之间会经历分歧选择。染色体倒位内基因的富集分析显示，参与代谢过程、免疫调节、生长、成熟、渗透调节等的基因显著富集，这可能是溯河洄游和淡水定居形态、生理和行为差异的基础。有益的现有遗传变异的存在、海洋和淡水栖息地之间的巨大最适转变以及大种群规模下选择的高效性，可能导致了观察到的快速平行适应性基因组变化。我们提出，在刀鲚面对环境异质性时的快速平行生态分化进化过程中，染色体倒位可能起到了重要作用。我们的研究为新栖息地中复杂性状快速适应的基因组基础提供了见解，并强调了结构基因组变异在生态适应分析中的重要性。
Abstract Rapid adaptation to novel environments may drive changes in genomic regions through natural selection. However, the genetic architecture underlying these adaptive changes is still poorly understood. Using population genomic approaches, we investigated the genomic architecture that underlies rapid parallel adaptation of Coilia nasus to fresh water by comparing four freshwater-resident populations with their ancestral anadromous population. Linkage disequilibrium network analysis and population genetic analyses revealed two putative large chromosome inversions on LG6 and LG22, which were enriched for outlier loci and exhibited parallel association with freshwater adaptation. Drastic frequency shifts and elevated genetic differentiation were observed for the two chromosome inversions among populations, suggesting that both inversions would undergo divergent selection between anadromous and resident ecotypes. Enrichment analysis of genes within chromosome inversions showed significant enrichment of genes involved in metabolic process, immunoregulation, growth, maturation, osmoregulation, and so forth, which probably underlay differences in morphology, physiology and behavior between the anadromous and freshwater-resident forms. The availability of beneficial standing genetic variation, large optimum shift between marine and freshwater habitats, and high efficiency of selection with large population size could lead to the observed rapid parallel adaptive genomic change. We propose that chromosomal inversions might have played an important role during the evolution of rapid parallel ecological divergence in the face of environmental heterogeneity in C. nasus. Our study provides insights into the genomic basis of rapid adaptation of complex traits in novel habitats and highlights the importance of structural genomic variants in analyses of ecological adaptation.
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影响因子：
5.4
作者：
Guo B;DeFaveri J;Sotelo G;Nair A;Merilä J
通讯作者：
Merilä J
影响因子：
7.7
作者：
Kemppainen P;Knight CG;Sarma DK;Hlaing T;Prakash A;Maung Maung YN;Somboon P;Mahanta J;Walton C
通讯作者：
Walton C
影响因子：
3.8
作者：
Berg PR;Star B;Pampoulie C;Bradbury IR;Bentzen P;Hutchings JA;Jentoft S;Jakobsen KS
通讯作者：
Jakobsen KS
影响因子：
64.8
作者：
Jones, Felicity C.;Grabherr, Manfred G.;Chan, Yingguang Frank;Russell, Pamela;Mauceli, Evan;Johnson, Jeremy;Swofford, Ross;Pirun, Mono;Zody, Michael C.;White, Simon;Birney, Ewan;Searle, Stephen;Schmutz, Jeremy;Grimwood, Jane;Dickson, Mark C.;Myers, Richard M.;Miller, Craig T.;Summers, Brian R.;Knecht, Anne K.;Brady, Shannon D.;Zhang, Haili;Pollen, Alex A.;Howes, Timothy;Amemiya, Chris;Lander, Eric S.;Di Palma, Federica;Lindblad-Toh, Kerstin;Kingsley, David M.
通讯作者：
Kingsley, David M.
DOI：
10.1073/pnas.0401720101
发表时间：
2004-07-20
影响因子：
11.1
作者：
Innan, H;Kim, Y
通讯作者：
Kim, Y