Schilling Martin P, Mullen Sean P, Kronforst Marcus, Safran Rebecca J, Nosil Patrik, Feder Jeffrey L, Gompert Zachariah, Flaxman Samuel M
Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
Department of Biology, Boston University, Boston, MA 02215, USA.
Genes (Basel). 2018 May 24;9(6):274. doi: 10.3390/genes9060274.
During speciation-with-gene-flow, a transition from single-locus to multi-locus processes can occur, as strong coupling of multiple loci creates a barrier to gene flow. Testing predictions about such transitions with empirical data requires building upon past theoretical work and the continued development of quantitative approaches. We simulated genomes under several evolutionary scenarios of gene flow and divergent selection, extending previous work with the additions of neutral sites and coupling statistics. We used these simulations to investigate, in a preliminary way, if and how selected and neutral sites differ in the conditions they require for transitions during speciation. For the parameter combinations we explored, as the per-locus strength of selection grew and/or migration decreased, it became easier for selected sites to show divergence-and thus to rise in linkage disequilibrium (LD) with each other as a statistical consequence-farther in advance of the conditions under which neutral sites could diverge. Indeed, even very low rates of effective gene flow were sufficient to prevent differentiation at neutral sites. However, once strong enough, coupling among selected sites eventually reduced gene flow at neutral sites as well. To explore whether similar transitions might be detectable in empirical data, we used published genome resequencing data from three taxa of butterflies. We found that fixation index ( F S T ) outliers and allele-frequency outliers exhibited stronger patterns of within-deme LD than the genomic background, as expected. The statistical characteristics of within-deme LD-likely indicative of the strength of coupling of barrier loci-varied between chromosomes and taxonomic comparisons. Qualitatively, the patterns we observed in the empirical data and in our simulations suggest that selection drives rapid genome-wide transitions to multi-locus coupling, illustrating how divergence and gene flow interact along the speciation continuum.
在有基因流的物种形成过程中，可能会发生从单基因座过程到多基因座过程的转变，因为多个基因座的强耦合会形成基因流的障碍。用经验数据检验关于这种转变的预测需要基于过去的理论工作，并持续发展定量方法。我们在几种基因流和分歧选择的进化场景下模拟基因组，通过增加中性位点和耦合统计扩展了先前的工作。我们利用这些模拟初步研究了在物种形成过程中，选择位点和中性位点在转变所需条件上是否存在差异以及如何存在差异。对于我们探索的参数组合，随着每个基因座的选择强度增加和/或迁移减少，选择位点更容易出现分歧，从而作为一种统计结果，在中性位点能够分歧的条件之前更早地出现彼此之间的连锁不平衡（LD）增加。事实上，即使非常低的有效基因流速率也足以阻止中性位点的分化。然而，一旦选择位点之间的耦合足够强，最终也会减少中性位点的基因流。为了探索在经验数据中是否可能检测到类似的转变，我们使用了已发表的来自三种蝴蝶类群的基因组重测序数据。我们发现，正如预期的那样，固定指数（FST）异常值和等位基因频率异常值在种群内LD模式上比基因组背景更强。种群内LD的统计特征——可能指示屏障基因座耦合的强度——在染色体和分类比较之间有所不同。定性地说，我们在经验数据和模拟中观察到的模式表明，选择驱动全基因组快速向多基因座耦合转变，说明了分歧和基因流在物种形成连续统中是如何相互作用的。
