Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern, Switzerland.
Mol Ecol. 2011 Apr;20(7):1450-62. doi: 10.1111/j.1365-294X.2011.05015.x. Epub 2011 Feb 24.
Adaptation to adverse environmental conditions such as high altitude requires physiological and/or morphological changes. Genome scans provide a means to identify the genetic basis of such adaptations without previous knowledge about the particular genetic variants or traits under selection. In this study, we scanned 3027 amplified fragment length polymorphisms (AFLP) in four populations of the common vole Microtus arvalis for loci associated with local adaptation and high altitude. We investigated voles from two populations at high elevation (~2000 m a.s.l.) representing the upper limit of the altitudinal distribution of the species and two geographically close low-altitude populations (<600 m a.s.l.). Statistical analysis incorporated a new Bayesian F(ST) outlier approach specifically developed for AFLP markers, which considers the intensity of AFLP bands instead of mere presence/absence and allows to derive population-based estimates of allele frequencies and F(IS) values. Computer simulations showed that this approach increases the statistical power of the detection of AFLP markers under selection almost to the power of single nucleotide polymorphism (SNP) data without compromising specificity. Our enhanced genome scan resulted in 20 prime candidate markers for positive selection, which show mostly extremely high allele frequency differences between the low- and high-altitude populations. The comparison of global- and pairwise-enhanced genome scans demonstrated further that very strong selective signatures may also be associated with single populations suggesting the importance of local adaptation in alpine populations of common voles.
适应不利的环境条件，如高海拔，需要生理和/或形态上的变化。基因组扫描提供了一种方法，可以在没有关于特定遗传变异或受选择特征的先验知识的情况下，识别这种适应的遗传基础。在这项研究中，我们在四个普通田鼠（Microtus arvalis）种群中扫描了 3027 个扩增片段长度多态性（AFLP），以寻找与局部适应和高海拔相关的基因座。我们研究了来自两个高海拔（约 2000 米海拔）种群的田鼠，它们代表了该物种海拔分布上限，以及两个地理上接近的低海拔种群（<600 米海拔）。统计分析纳入了一种新的贝叶斯 F（ST）异常值方法，该方法专门为 AFLP 标记开发，它考虑了 AFLP 带的强度，而不仅仅是存在/不存在，并允许根据种群估计等位基因频率和 F（IS）值。计算机模拟表明，这种方法几乎可以将 AFLP 标记选择检测的统计能力提高到单核苷酸多态性（SNP）数据的能力，而不会影响特异性。我们增强的基因组扫描导致了 20 个候选的正选择标记，它们在低海拔和高海拔种群之间显示出大多数非常高的等位基因频率差异。全局和成对增强基因组扫描的比较进一步表明，非常强烈的选择特征也可能与单个种群相关，这表明在高山普通田鼠种群中，局部适应的重要性。
