1. The way that organisms diverge into reproductively isolated species is a major question in biology. The recent accumulation of genomic data provides promising opportunities to understand the genomic landscape of divergence, which describes the distribution of differences across genomes. Genomic areas of unusually high differentiation have been called genomic islands of divergence. Their formation has been attributed to a variety of mechanisms, but a prominent hypothesis is that they result from divergent selection over a small portion of the genome, with surrounding areas homogenized by gene flow. Such islands have often been interpreted as being associated with divergence with gene flow. However, other mechanisms related to genomic structure and population history can also contribute to the formation of genomic islands of divergence.
2. We currently lack a quantitative framework to examine the dynamics of genomic landscapes under the complex and nuanced conditions that are found in natural systems. Here, we develop an individual‐based simulation to explore the dynamics of diverging genomes under various scenarios of gene flow, selection and genotype–phenotype maps.
3. Our modelling results are consistent with empirical observations demonstrating the formation of genomic islands under genetic isolation. Importantly, we have quantified the range of conditions that produce genomic islands. We demonstrate that the initial level of genetic diversity, drift, time since divergence, linkage disequilibrium, strength of selection and gene flow are all important factors that can influence the formation of genomic islands. Because the accumulation of genomic differentiation over time tends to erode the signal of genomic islands, genomic islands are more likely to be observed in recently divergent taxa, although not all recently diverged taxa will necessarily exhibit islands of genomic divergence. Gene flow primarily slows the swamping of islands of divergence with time.
4. By using this framework, further studies may explore the relative influence of particular suites of events that contribute to the emergence of genomic islands under sympatric, parapatric and allopatric conditions. This approach represents a novel tool to explore quantitative expectations of the speciation process, and should prove useful in elucidating past and projecting future genomic evolution of any taxa.

中文翻译：

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到基因组分歧岛的多种人口遗传和人口统计学途径

1. 生物体分化成繁殖分离物种的方式是生物学中的一个主要问题。基因组数据的最新积累为理解发散的基因组格局提供了广阔的机会，发散的格局描述了基因组间差异的分布。具有异常高分化的基因组区域被称为差异基因组孤岛。它们的形成归因于多种机制，但是一个突出的假设是它们是由于在基因组的一小部分上的不同选择而导致的，其周围区域被基因流均质化了。通常将这些岛解释为与基因流的发散有关。但是，与基因组结构和种群历史有关的其他机制也可能有助于形成基因组差异岛。
2. 我们目前缺乏定量框架来研究自然系统中复杂而细微的条件下的基因组景观动态。在这里，我们开发了一个基于个体的模拟，以探索在基因流，选择和基因型-表型图谱的各种情况下不同基因组的动力学。
3. 我们的建模结果与证明遗传隔离下基因组岛形成的经验观察结果一致。重要的是，我们已经量化了产生基因岛的条件范围。我们证明遗传多样性的初始水平，漂移，发散后的时间，连锁不平衡，选择强度和基因流都是可以影响基因组岛形成的重要因素。由于随着时间的流逝基因组分化的积累趋向于侵蚀基因组岛的信号，因此在最近发散的分类单元中更可能观察到基因组岛，尽管并非所有最近发散的分类单元都必然会显示出基因组发散的岛。基因流动主要是随着时间的流逝而减缓分散岛屿的沼泽化。
4. 通过使用该框架，进一步的研究可以探索在同胞，同伴异居和异源条件下特定事件组的相对影响，这些事件对基因组岛的出现做出了贡献。这种方法代表了一种探索物种形成过程的定量期望的新颖工具，并且在阐明过去和预测未来任何类群的基因组进化中应被证明是有用的。