Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes
Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes
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DOI：
10.1098/rstb.2011.0245
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发表时间：
2012-02-05
影响因子：
6.3
通讯作者：
Cresko, William A.
中科院分区：
文献类型：
--
作者：
Hohenlohe, Paul A.;Bassham, Susan;Cresko, William A.
群体基因组研究开始为进化中的动态基因组规模过程提供更全面的视角。基因组结构的模式，例如差异增加的基因组岛，可能对于适应性种群分化和物种形成很重要。我们使用下一代测序数据来检查三刺刺鱼海洋和淡水种群的局部和长距离连锁不平衡（LD）模式，这是研究进化和物种形成的有用模型。我们寻找 LD 和发散选择特征之间的关联，并评估重组率变化在生成 LD 模式中的作用。正如根据从祖先海洋到衍生的淡水刺鱼种群的单向基因流的传统生物地理学模型所预测的那样，我们在淡水中发现了广泛的局部和长距离LD。令人惊讶的是，海洋种群表现出类似的 LD 升高模式，特别是在先前与淡水适应有关的大型基因组区域之间。这些结果支持刺鱼辐射的另一种生物地理模型，这是一种具有明显双向基因流的混合种群，与海洋和淡水种群之间的强烈分歧选择相结合。正如理论预测的那样，这些过程可以在基因组分歧岛内和之间维持 LD。这些发现表明，海洋刺鱼种群的基因组结构可能为新殖民淡水栖息地中多基因座基因型的快速重组和进化提供一种机制，并可能有助于解释独立淡水种群中相似基因座的平行表型变异的遗传图谱。
Population genomic studies are beginning to provide a more comprehensive view of dynamic genome-scale processes in evolution. Patterns of genomic architecture, such as genomic islands of increased divergence, may be important for adaptive population differentiation and speciation. We used next-generation sequencing data to examine the patterns of local and long-distance linkage disequilibrium (LD) across oceanic and freshwater populations of threespine stickleback, a useful model for studies of evolution and speciation. We looked for associations between LD and signatures of divergent selection, and assessed the role of recombination rate variation in generating LD patterns. As predicted under the traditional biogeographic model of unidirectional gene flow from ancestral oceanic to derived freshwater stickleback populations, we found extensive local and long-distance LD in fresh water. Surprisingly, oceanic populations showed similar patterns of elevated LD, notably between large genomic regions previously implicated in adaptation to fresh water. These results support an alternative biogeographic model for the stickleback radiation, one of a metapopulation with appreciable bidirectional gene flow combined with strong divergent selection between oceanic and freshwater populations. As predicted by theory, these processes can maintain LD within and among genomic islands of divergence. These findings suggest that the genomic architecture in oceanic stickleback populations may provide a mechanism for the rapid re-assembly and evolution of multi-locus genotypes in newly colonized freshwater habitats, and may help explain genetic mapping of parallel phenotypic variation to similar loci across independent freshwater populations.