Adaptation in 6 dimensions

描述（由申请人提供）：在过去的一万年中，黑腹果蝇和拟象果蝇随着人类迁徙而遍布世界各地。因此，这些现在世界各地的物种已经暴露在各种新的环境和栖息地中。对于生活在温带环境中的苍蝇来说，冬天的寒冷代表了一种新的环境，这些物种以几种不同的方式进化以应对寒冷的温度。D. melanogaster已经进化出一种滞育综合征，这种综合征赋予了它们极端的寿命延长、代谢率降低和应激耐受性提高；虽然滞育增加了冬季的存活率，但能够滞育的个体在夏季会遭受适应性劣势，因此这种适应即使在高纬度地区也保持在中等频率。另一方面，拟马虎似乎对冬季条件有更温和的适应反应：这个物种在凉爽的温度下表现良好，但似乎没有能力长时间暴露在严酷的温带冬季。我们对拟陆龟的其他越冬机制知之甚少，或者对新的温带环境的任何进化反应。在此，我们提出确定黑腹扁扁鼠和拟马虎适应温带气候的多态性，将这些多态性与功能联系起来，并验证这些多态性进化起源的假设。为了做到这一点，我们将收集这两个物种的大量个体样本(i)在北美东西海岸的纬度上，（ii）在宾夕法尼亚州费城附近的几个地点的生长季节，（iii）在北加州沿海拔样带的四个重复年。首先，我们将通过高通量测序技术确定在时间和空间上以一致的方式变化的多态性，我们将通过焦磷酸测序验证等位基因频率的变化。其次，我们将使用定量遗传和转录组学技术确定这些多态性子集的功能后果。我们假设，我们确定的许多多态性将与已知在许多果蝇中以临床方式变化的表型相关。最后，我们将通过评估周围基因座的单倍型多样性来验证这些多态性进化起源的假设。我们假设，这些适应性等位基因中的大多数将受到软扫描，这是具有极大种群规模的物种或祖先种群中具有大量遗传变异的物种的特征，如D. melanogaster和D. simulans。

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.