Adaptation in 6 dimensions

描述(申请人提供)：在过去的10,000年里，随着人类的迁徙，果蝇和黑腹果蝇在世界各地传播开来。因此，这些现已国际化的物种暴露在各种新颖的环境和栖息地中。对于生活在温带环境中的苍蝇来说，冬天的寒冷代表着一个新的环境，这些物种以几种不同的方式进化以应对寒冷的温度。D.黑腹鼠进化出一种滞育综合症，使人的寿命延长，代谢率降低，并提高了对应激的耐受性；虽然滞育提高了冬季的存活率，但能够滞育的个体在夏季处于健康劣势，因此这种适应即使在高纬度也保持在中等频率。另一方面，拟人猿似乎对冬季条件有更温和的适应性反应：该物种在凉爽的温度下表现良好，但似乎没有能力长期暴露在严寒的温带冬季。人们对金丝猴的其他越冬机制知之甚少，甚至对新的温带环境的任何进化反应也知之甚少。在这里，我们建议识别在温带气候适应中潜在的多态，将这些多态与功能联系起来，并检验关于这些多态进化起源的假说。为此，我们将收集这两个物种的大量个体样本(I)横跨北美东西海岸的纬度，(Ii)在宾夕法尼亚州费城附近的几个地点的生长季节，以及(Iii)沿北加州的一个垂直样带重复四年。首先，我们将通过高通量测序技术识别在时间和空间上以一致方式变化的多态，并通过焦磷酸测序验证等位基因频率的变化。其次，我们将使用数量遗传学和转录切割技术来确定这些多态的子集的功能后果。我们假设，我们识别的许多多态与已知在许多果蝇中以克隆式方式变化的表型有关。最后，我们将通过评估周围基因座的全球单倍型多样性来测试关于这些多态的进化起源的假设。我们假设，这些适应等位基因中的大多数将受到软扫描的影响，这是具有极大种群规模的物种的特征，或者是那些在祖先群体中具有大量遗传变异的物种，如黑腹黑腹夜蛾和拟黑腹夜蛾。

DESCRIPTION (provided by applicant): Over the last 10,000 years Drosophila melanogaster and D. simulans have spread through the world in the wake of human migration. As a consequence, these now cosmopolitan species have been exposed to a variety of novel environments and habitats. For flies living in temperate environments, winter cold represents a novel environment and these species have evolved in response to cold temperatures in several distinct ways. D. melanogaster has evolved a diapause syndrome that confers extreme lifespan extension, reduction in metabolic rate, and elevated stress tolerance; although diapause increases winter survival, individuals able to diapause suffer a fitness disadvantage during the summer and thus this adaptation remains at intermediate frequencies even at high latitudes. D. simulans, on the other hand, appears to have a more modest adaptive response to winter conditions: this species performs well at cool temperatures but does not appear have the capacity to survive prolonged exposure to the harsh temperate winter. Little is known about other overwintering mechanisms in D. simulans, or indeed any evolutionary response to novel temperate environments. Herein, we propose to identify polymorphisms underlying adaptation to temperate climates in D. melanogaster and D. simulans, link these polymorphisms to function and test hypotheses about the evolutionary origin of these polymorphisms. To do this, we will collect large samples of individuals from both of these species (i) across latitude on the East and West coasts of North America, (ii) through the growing season at several sites near Philadelphia, PA and (iii) along an altitudinal transect in Northern California for four replicate years. First, we will identify polymorphisms that vary in consistent fashion through time and space through high- throughput sequencing technologies and we will verify changes in allele frequency through pyrosequencing. Second, we will identify the functional consequences of a subset of these polymorphisms using quantitative genetic and transcriptomic techniques. We hypothesize that many of the polymorphisms we identify will be associated with phenotypes known to vary in a clinal fashion amongst many drosophilid flies. Finally, we will test hypotheses about the evolutionary origin of these polymorphisms by assessing worldwide haplotype diversity at surrounding loci. We hypothesize that most of these adaptive alleles will be subject to soft- sweeps which are characteristic of species with extremely large population sizes or those with large amounts of genetic variation in ancestral populations such as both D. melanogaster and D. simulans.