Abstract：
The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would help understanding how adaptation happens over environmental clines. To bring new insights to this issue we set up a broad framework which aimed to compare the adaptive trajectories over environmental clines in two domesticated mammal species co-distributed in diversified landscapes. We sequenced the genomes of 160 sheep and 161 goats extensively managed along environmental gradients, including temperature, rainfall, seasonality and altitude, to identify genes and biological processes shaping local adaptation. Allele frequencies at putatively adaptive loci were rarely found to vary gradually along environmental gradients, but rather displayed a discontinuous shift at the extremities of environmental clines. Of the 430 candidate adaptive genes identified, only 6 were orthologous between sheep and goats and those responded differently to environmental pressures, suggesting different putative mechanisms involved in local adaptation in these two closely related species. Interestingly, the genomes of the 2 species were impacted differently by the environment, genes related to signatures of selection were most related to altitude, slope and rainfall seasonality for sheep, and summer temperature and spring rainfall for goats. The diversity of candidate adaptive pathways may result from a high number of biological functions involved in the adaptations to multiple eco-climatic gradients, and a differential role of climatic drivers on the two species, despite their co-distribution along the same environmental gradients. This study describes empirical examples of clinal variation in putatively adaptive alleles with different patterns in allele frequency distributions over continuous environmental gradients, thus showing the diversity of genetic responses in adaptive landscapes and opening new horizons for understanding genomics of adaptation in mammalian species and beyond.
摘要：
局部适应如何发生的问题仍然是进化生物学中的一个基本问题。在环境梯度的选择下，基因中等位基因频率的变化仍然主要是理论上的，其经验评估将有助于理解适应环境的发生方式。为了给这个问题带来新的见解，我们建立了一个广泛的框架，旨在比较在多种景观中共同分布的两种驯化哺乳动物物种在环境中的适应性轨迹。我们对沿环境梯度广泛管理的160只绵羊和161只山羊的基因组进行了测序，包括温度,降雨,季节性和海拔，确定基因和生物过程塑造局部适应。很少发现推定自适应基因座的等位基因频率沿环境梯度逐渐变化，而是在环境的极端表现出不连续的变化。在确定的430个候选适应性基因中，只有6只绵羊和山羊是直系同源的，它们对环境压力的反应不同，表明这两个密切相关的物种的局部适应涉及不同的推定机制。有趣的是,这两个物种的基因组受到环境的不同影响，与选择特征相关的基因与海拔最相关，绵羊的坡度和降雨季节性，山羊的夏季温度和春季降雨。候选适应性途径的多样性可能是由于适应多种生态气候梯度所涉及的大量生物学功能所致。以及气候驱动因素对这两个物种的不同作用，尽管它们沿着相同的环境梯度共同分布。这项研究描述了在连续环境梯度上具有不同等位基因频率分布模式的推定适应性等位基因的克隆变异的经验示例，从而显示了适应性景观中遗传反应的多样性，并为理解哺乳动物及其他物种的适应性基因组学开辟了新的视野。
