Natural CMT2 variation is associated with genome-wide methylation changes and temperature adaptation
Xia Shen, Simon Forsberg, Mats Pettersson, Zheya Sheng, Orjan Carlborg
备注：
Rewrite to improve clarity of presentation. Results unchanged. 43 p, 3 main fig, 1 main table, 15 suppl fig, 2 suppl tables. Particular updates - New title - More detailed abstract and introduction - Updated results section for clarity and focus - Updated discussion connecting work to unpublished work in other research groups - Corrected typos - Updated references and acknowledgements
A central problem when studying adaptation to a new environment is the interplay between genetic variation and phenotypic plasticity. Arabidopsis thaliana has colonized a wide range of habitats across the world and it is therefore an attractive model for studying the genetic mechanisms underlying environmental adaptation 4,5. Here, we used publicly available data from two collections of A. thaliana accessions, covering the native range of the species, to identify loci associated with differences in climates at the sampling sites. To address the confounding between geographic location, climate and population structure, a new genome-wide association analysis method was developed that facilitates detection of potentially adaptive loci where the alternative alleles display different tolerable climate ranges. Sixteen novel such loci, many of which contained candidate genes with amino acid changes, were found including a strong association between Chromomethylase 2 (CMT2) and variability in seasonal temperatures. The reference allele dominated in areas with less seasonal variability in temperature, and the alternative allele, which disrupts genome-wide CHH-methylation, existed in both stable and variable regions. Our results link natural variation in CMT2, and differential genome-wide CHH methylation, to the distribution of A. thaliana accessions across habitats with different seasonal temperature variability. They also suggest a role for genetic regulation of epigenetic modifications in natural adaptation, potentially through differential allelic plasticity, and illustrate the importance of re-analyses of existing data using new analytical methods to obtain a more complete understanding of the mechanisms contributing to adaptation.
Genome wide signals of pervasive positive selection in human evolution
积极选择在人类进化中的作用仍然存在争议。一方面，对正选择的扫描已经确定了数百个候选基因座，并且全基因组的多态性模式显示出与频繁的正选择一致的特征。另一方面，最近的研究认为，许多候选基因座是假阳性的，大多数明显的全基因组适应特征实际上是由于中性多样性的减少，这种中性多样性是由连锁的经常性有害突变（称为背景选择）造成的。在这里，我们分析了来自1,000个基因组项目（Abecasis et al. 2012）的人类多态性数据，并在校正背景选择的影响后检测到普遍的正选择特征。我们发现，中性多态性的水平较低附近的氨基酸取代，观察到的最强的减少，特别是附近的功能性后果氨基酸取代。此外，氨基酸取代与不应该由背景选择产生的最近适应的特征相关，例如存在异常长且频繁的单倍型和位点频谱中的特定扭曲。我们使用正向模拟表明，所观察到的签名需要在附近的氨基酸变化的强适应性取代的高速率。我们进一步证明，如ENCODE（Gerstein et al. 2012）所预测的，所观察到的阳性选择的特征与调控序列的存在的相关性比与氨基酸取代的位置的相关性更强。我们的研究结果表明，适应在人类进化中是频繁的，并为King和Wilson的假设提供了支持（King和Wilson 1975），即适应性差异主要是由监管变化驱动的。
Detecting interspecific and geographic differentiation patterns in two interfertile oak species (Quercus petraea (Matt.) Liebl. and Q. robur L.) using small sets of microsatellite markers
