Data from: Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow

Speciation, the evolution of reproductive isolation amongst populations, is continuous, complex, and involves multiple, interacting barriers. Until it is complete, the effects of this process vary along the genome and can lead to a heterogeneous genomic landscape with peaks and troughs of differentiation and divergence. When gene flow occurs during speciation, barriers restricting migration locally in the genome lead to patterns of heterogeneity. However, genomic heterogeneity can also be produced or modified by variation in factors such as background selection and selective sweeps, recombination- and mutation-rate variation, and heterogeneous gene density. Extracting the effects of gene flow, divergent selection and reproductive isolation from such modifying factors presents a major challenge to speciation genomics. We argue one of the principal aims of the field is to identify the barrier loci involved in limiting gene flow. We first summarise the expected signatures of selection at barrier loci, at the genomic regions linked to them and across the entire genome. We then discuss the modifying factors that complicate the interpretation of the observed genomic landscape. Finally, we end with a roadmap for future speciation research; a proposal for how to account for these modifying factors and to progress towards understanding the nature of barrier loci. Despite the difficulties of interpreting empirical data, we argue that the availability of promising technical and analytical methods will shed further light on the important roles that gene flow and divergent selection have in shaping the genomic landscape of speciation.

物种形成（Speciation）指种群间生殖隔离（reproductive isolation）的演化进程，该过程兼具连续性与复杂性，且涉及多种相互作用的生殖隔离障碍。在物种形成完全达成前，该过程的效应沿基因组并非均一分布，可形成带有分化与趋异峰谷特征的异质性基因组景观（genomic landscape）。当物种形成过程中发生基因流（gene flow）时，在基因组局部限制基因交流的生殖隔离障碍，会催生此类异质性分布模式。然而，基因组异质性也可由多种因素的变异产生或修饰，例如背景选择（background selection）、选择性清除（selective sweeps）、重组率（recombination rate）与突变率（mutation rate）的变异，以及基因密度（gene density）异质性。从这类修饰因素中剥离出基因流、趋异选择（divergent selection）与生殖隔离的效应，是物种形成基因组学（speciation genomics）领域面临的核心挑战之一。我们认为，该领域的核心目标之一是鉴定出参与限制基因流的障碍位点（barrier loci）。我们首先总结了障碍位点、与其连锁的基因组区域以及全基因组范围内预期存在的选择印记（signatures of selection）。随后，我们讨论了会使观测到的基因组景观解读变得复杂化的各类修饰因素。最后，我们为未来的物种形成研究绘制了研究路线图，提出了如何纳入上述修饰因素、逐步解析障碍位点本质的研究方案。尽管解读实证数据（empirical data）存在诸多困难，但我们认为，极具前景的技术与分析方法（analytical methods）的涌现，将进一步阐明基因流与趋异选择在塑造物种形成基因组景观中所发挥的关键作用。