Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria)
Explorative genome scan to detect candidate loci for adaptation along a gradient of altitude in the common frog (Rana temporaria)
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DOI：
10.1093/molbev/msj087
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发表时间：
2006-04-01
影响因子：
10.7
通讯作者：
Pompanon, F
中科院分区：
文献类型：
--
作者：
Bonin, A;Taberlet, P;Pompanon, F
在种群基因组学迅速发展的今天，适应的遗传基础可以直接在基因组水平上被揭开，而不需要任何关于选择优势基因或性状的先决条件。对于非模式物种，现在可以筛选随机分布在基因组中的许多标记，并区分中性遗传背景和显示非典型行为的离群值基因座(例如，种群之间的高度分化)。本研究以392个扩增片段长度多态标记为基础，通过基因组扫描研究了中国林蛙对海拔梯度的适应遗传框架。使用两种迄今从未应用于显性数据的离群值检测方法，当比较来自不同海拔的种群时，我们寻找遗传分化偏离中性预期的基因座。所有检测到的基因座都根据其最可能的异常行为原因进行了分类，并将其归类为假阳性、局部影响的异常值或与海拔相关的异常值。总共有8个好的候选基因座被确定为可能与海拔适应有关，因为它们是在几个独立的海拔间比较中挑选出来的。这一结果说明了全基因组调查沿着选择梯度揭示选择特征的潜力，其中环境变量和适应相关特征之间的关联可能是复杂的和/或神秘的。在这篇文章中，我们还强调了确认异常值基因座选择足迹的必要性。最后，我们对普通青蛙沿海拔斜坡适应的遗传基础提供了一些初步的见解。
Today, with the rapid development of population genomics, the genetic basis of adaptation can be unraveled directly at the genome level, without any prerequisites about the selectively advantageous genes or traits. For nonmodel species, it is now possible to screen many markers randomly scattered across the genome and to distinguish between the neutral genetic background and outlier loci displaying an atypical behavior (e.g., a higher differentiation between populations). This study investigated the genetic frame of adaptation to a gradient of altitude in the common frog (Rana temporaria) by means of a genome scan based on 392 amplified fragment length polymorphism markers. Using two outlier detection methods never applied to dominant data so far, we sought for loci with a genetic differentiation diverging from neutral expectations when comparing populations from different altitudes. All the detected loci were sorted out according to their most probable cause for outlier behavior and classified as false positives, outliers due to local effects, or outliers associated with altitude. Altogether, eight good candidate loci were identified as potentially involved in adaptation to altitude because they were picked out in several independent interaltitude comparisons. This result illustrated the potential of genome-wide surveys to reveal selection signatures along selection gradients, where the association between environmental variables and fitness-related traits may be complex and/or cryptic. In this article, we also underlined the need for confirmation of the selection footprints for the outlier loci. Finally, we provided some preliminary insights into the genetic basis of adaptation along an altitudinal cline in the common frog.