Adaptation in 6 dimensions

描述（申请人提供）：在过去的10,000年里，黑腹果蝇和D。随着人类的迁徙，模拟人已经遍布世界各地。因此，这些现在世界性的物种已经暴露在各种新的环境和栖息地。对于生活在温带环境中的苍蝇来说，冬季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.黑腹果蝇已经进化出滞育综合征，其赋予极端的寿命延长、代谢率降低和应激耐受性提高;虽然滞育增加了冬季存活率，但是能够滞育的个体在夏季遭受适应性劣势，因此这种适应即使在高纬度也保持在中间频率。D.另一方面，simulans似乎对冬季条件的适应性反应较为温和：该物种在凉爽的温度下表现良好，但似乎没有能力在长期暴露于严酷的温带冬季中生存。对其他越冬机制知之甚少。simulans，或者实际上是对新的温带环境的任何进化反应。 在此，我们建议确定多态性的基础上适应温带气候的D。melanogaster和D. simulans，将这些多态性与功能联系起来，并测试关于这些多态性进化起源的假设。要做到这一点，我们将收集大样本的个人从这两个物种（一）横跨纬度的东海岸和西海岸的北美，（二）通过生长季节在费城附近的几个网站，PA和（三）沿着海拔样带在北方加州的四个重复年。首先，我们将通过高通量测序技术鉴定在时间和空间上以一致方式变化的多态性，并且我们将通过焦磷酸测序验证等位基因频率的变化。其次，我们将确定这些多态性的一个子集的功能后果，使用定量遗传学和转录组学技术。我们假设，我们确定的许多多态性将与已知的表型在许多果蝇中以临床方式变化。最后，我们将通过评估周围基因座的全球单倍型多样性来检验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在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.