Genomic changes underlying repeated niche shifts in an adaptive radiation

In adaptive radiations, single lineages rapidly diversify by adapting to many new niches. Little is known yet about the genomic mechanisms involved, i.e. the source of genetic variation or genomic architecture facilitating or constraining adaptive radiation. Here, we investigate genomic changes associated with repeated invasion of many different freshwater niches by threespine stickleback in the Haida Gwaii archipelago, Canada, by re-sequencing single genomes from one marine and 28 freshwater populations. We find 89 likely targets of parallel selection in the genome that are enriched for old standing genetic variation. In contrast to theoretical expectations, their genomic architecture is highly dispersed with little clustering. Candidate genes and genotype-environment correlations match the three major environmental axes predation regime, light environment and ecosystem size. In a niche space with these three dimensions, we find that the more divergent a new niche from the ancestral marine habitat, the more loci show signatures of parallel selection. Our findings suggest that the genomic architecture of parallel adaptation in adaptive radiation depends on the steepness of ecological gradients and the dimensionality of the niche space.

在适应辐射（adaptive radiation）过程中，单一谱系通过适应众多全新生态位快速实现物种多样化。目前学界对其背后涉及的基因组机制仍知之甚少，即调控适应辐射的遗传变异来源与基因组结构，二者分别发挥促进或限制作用。本研究以加拿大海达瓜依群岛（Haida Gwaii archipelago）的三棘刺鱼（threespine stickleback）为研究类群，该类群已多次入侵诸多不同淡水生态位；我们通过对1个海洋种群与28个淡水种群的单基因组开展重测序（re-sequencing），探究其伴随重复生态位入侵的基因组变化。我们在基因组中鉴定出89个潜在的平行选择（parallel selection）靶标，这些靶标显著富集于古老的现存遗传变异（standing genetic variation）。与理论预期相悖的是，这些靶标的基因组结构呈现高度分散的特征，几乎无成簇聚集现象。候选基因与基因型-环境关联分析结果，与三大核心环境轴——捕食格局（predation regime）、光照环境（light environment）与生态系统规模（ecosystem size）——高度契合。在由这三大维度构成的生态位空间（niche space）中，我们发现：新生生态位与祖先海洋栖息地的差异程度越高，表现出平行选择信号的基因座数量就越多。本研究结果表明，适应辐射中平行适应（parallel adaptation）的基因组结构，取决于生态梯度（ecological gradients）的陡峭程度与生态位空间的维度。

搜集汇总

背景与挑战

背景概述

该数据集研究了三刺鱼在适应辐射过程中多次生态位转变的基因组基础，通过对海达瓜依群岛一个海洋和28个淡水种群进行基因组重测序，发现了89个富含古老遗传变异的平行选择目标位点。研究发现这些位点的基因组结构高度分散，并与捕食压力、光照环境和生态系统大小等环境因素相关，表明生态位差异越大平行选择位点越多。