A genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical forest tree
A genome-wide scan shows evidence for local adaptation in a widespread keystone Neotropical forest tree
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DOI：
10.1038/s41437-019-0188-0
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发表时间：
2019-08-01
期刊：
影响因子：
3.8
通讯作者：
Grattapaglia, Dario
中科院分区：
文献类型：
--
作者：
Collevatti, Rosane G.;Novaes, Evandro;Grattapaglia, Dario
在新热带地区，自然选择在形成多样性模式中的作用仍然知之甚少。我们对新热带地区的一种树木Handroanthus impetiginosus （Bignoniaceae）进行了首次全基因组群体基因组学研究，通过序列捕获在13个种群的128个个体中取样了75,838个snp。我们利用等位基因频率和环境变量（27个基因中的32个位点）的贝叶斯相关性找到了局部适应的证据，并利用SweepFinder2（47个基因中的81个位点）对选择性扫描和遗传搭便车事件进行了分析。两种方法共鉴定出15个基因。通过对群体遗传结构的分析，我们还发现了14个具有选择信号的位点，这些位点由来自5个群体的个体组成。所有方法都精确定位了影响植物发育和初级代谢过程的高度多样化和结构保守的基因。空间插值预测了不同选择位点的预期等位基因频率随时间的变化，表明蜱虫可能在气候变化中跟踪其栖息地。然而，通过自然选择的局部适应也可能发生，允许物种因生态位进化而持续存在。实验结果表明，该种群存在高度的遗传分化，限制了对背景选择、平衡选择和净化选择等软选择力的进一步检测。在广泛的人群中，等位基因频率分布的微小差异和可检测到的适应性扫描的低数量的位点提倡一种涉及潜在的大量小的全基因组效应的多基因适应模型。
The role of natural selection in shaping patterns of diversity is still poorly understood in the Neotropics. We carried out the first genome-wide population genomics study in a Neotropical tree, Handroanthus impetiginosus (Bignoniaceae), sampling 75,838 SNPs by sequence capture in 128 individuals across 13 populations. We found evidences for local adaptation using Bayesian correlations of allele frequency and environmental variables (32 loci in 27 genes) complemented by an analysis of selective sweeps and genetic hitchhiking events using SweepFinder2 (81 loci in 47 genes). Fifteen genes were identified by both approaches. By accounting for population genetic structure, we also found 14 loci with selection signal in a STRUCTURE-defined lineage comprising individuals from five populations, using Outflank. All approaches pinpointed highly diverse and structurally conserved genes affecting plant development and primary metabolic processes. Spatial interpolation forecasted differences in the expected allele frequencies at loci under selection over time, suggesting that H. impetiginosus may track its habitat during climate changes. However, local adaptation through natural selection may also take place, allowing species persistence due to niche evolution. A high genetic differentiation was seen among the H. impetiginosus populations, which, together with the limited power of the experiment, constrains the improved detection of other types of soft selective forces, such as background, balanced, and purifying selection. Small differences in allele frequency distribution among widespread populations and the low number of loci with detectable adaptive sweeps advocate for a polygenic model of adaptation involving a potentially large number of small genome-wide effects.