Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, A.O.22085, 46071, Valencia, Spain.
School of Environmental Sciences, University of Hull, HU6 7RX, Hull, United Kingdom.
Sci Rep. 2018 Oct 30;8(1):16051. doi: 10.1038/s41598-018-34188-y.
Environmental fluctuations are ubiquitous and thus essential for the study of adaptation. Despite this, genome evolution in response to environmental fluctuations -and more specifically to the degree of environmental predictability- is still unknown. Saline lakes in the Mediterranean region are remarkably diverse in their ecological conditions, which can lead to divergent local adaptation patterns in the inhabiting aquatic organisms. The facultatively sexual rotifer Brachionus plicatilis shows diverging local adaptation in its life-history traits in relation to estimated environmental predictability in its habitats. Here, we used an integrative approach -combining environmental, phenotypic and genomic data for the same populations- to understand the genomic basis of this diverging adaptation. Firstly, a novel draft genome for B. plicatilis was assembled. Then, genome-wide polymorphisms were studied using genotyping by sequencing on 270 clones from nine populations in eastern Spain. As a result, 4,543 high-quality SNPs were identified and genotyped. More than 90 SNPs were found to be putatively under selection with signatures of diversifying and balancing selection. Over 140 SNPs were correlated with environmental or phenotypic variables revealing signatures of local adaptation, including environmental predictability. Putative functions were associated to most of these SNPs, since they were located within annotated genes. Our results reveal associations between genomic variation and the degree of environmental predictability, providing genomic evidence of adaptation to local conditions in natural rotifer populations.
环境波动是普遍存在的，因此对于适应研究至关重要。尽管如此，环境波动（更具体地说是环境可预测性的程度）对基因组进化的影响仍然未知。地中海地区的盐湖在生态条件上差异很大，这可能导致栖息在其中的水生生物产生不同的局部适应模式。兼性有性轮虫褶皱臂尾轮虫在其生活史特征方面表现出不同的局部适应，这与栖息地环境的可预测性估计有关。在这里，我们采用了一种综合方法——结合了同一群体的环境、表型和基因组数据——来理解这种分歧适应的基因组基础。首先，我们组装了褶皱臂尾轮虫的一个新的草图基因组。然后，通过对来自西班牙东部的 9 个种群的 270 个克隆进行测序分型，研究了全基因组多态性。结果，鉴定并分型了 4543 个高质量的 SNP。超过 90 个 SNP 被认为是受选择的，具有多样化和平衡选择的特征。超过 140 个 SNP 与环境或表型变量相关，显示出局部适应的特征，包括环境可预测性。大多数这些 SNP 与推定功能相关，因为它们位于注释基因内。我们的研究结果揭示了基因组变异与环境可预测性程度之间的关联，为自然轮虫种群对局部条件的适应提供了基因组证据。
