Department of Biology, Indiana University, Bloomington, IN 47405, USA.
Philos Trans R Soc Lond B Biol Sci. 2012 Feb 5;367(1587):364-73. doi: 10.1098/rstb.2011.0199.
Genome scans have become a common approach to identify genomic signatures of natural selection and reproductive isolation, as well as the genomic bases of ecologically relevant phenotypes, based on patterns of polymorphism and differentiation among populations or species. Here, we review the results of studies taking genome scan approaches in plants, consider the patterns of genomic differentiation documented and their possible causes, discuss the results in light of recent models of genomic differentiation during divergent adaptation and speciation, and consider assumptions and caveats in their interpretation. We find that genomic regions of high divergence generally appear quite small in comparisons of both closely and more distantly related populations, and for the most part, these differentiated regions are spread throughout the genome rather than strongly clustered. Thus, the genome scan approach appears well-suited for identifying genomic regions or even candidate genes that underlie adaptive divergence and/or reproductive barriers. We consider other methodologies that may be used in conjunction with genome scan approaches, and suggest further developments that would be valuable. These include broader use of sequence-based markers of known genomic location, greater attention to sampling strategies to make use of parallel environmental or phenotypic transitions, more integration with approaches such as quantitative trait loci mapping and measures of gene flow across the genome, and additional theoretical and simulation work on processes related to divergent adaptation and speciation.
基因组扫描已成为一种常见的方法，用于识别自然选择和生殖隔离的基因组特征，以及与生态相关表型的基因组基础，其依据是种群或物种之间的多态性和分化模式。在这里，我们回顾了在植物中采用基因组扫描方法的研究结果，考虑了所记录的基因组分化模式及其可能的原因，根据在趋异适应和物种形成过程中基因组分化的最近模型讨论了这些结果，并考虑了其解释中的假设和注意事项。我们发现，在比较密切和更远缘的种群时，高度分化的基因组区域通常看起来相当小，而且在大多数情况下，这些分化区域分布在整个基因组中，而不是强烈聚集。因此，基因组扫描方法似乎非常适合识别基因组区域甚至候选基因，这些区域或基因是适应性分歧和/或生殖隔离的基础。我们考虑了可能与基因组扫描方法结合使用的其他方法，并提出了进一步的发展，这将是有价值的。这些包括更广泛地使用已知基因组位置的基于序列的标记，更多地关注采样策略，以利用平行的环境或表型转变，更多地与数量性状位点映射和基因组范围内基因流动的测量等方法相结合，以及与趋异适应和物种形成相关的过程的额外理论和模拟工作。
