Genomics of natural populations

描述(申请人提供)：在过去的一万年里，随着人类的迁徙，黑腹果蝇已经在世界各地传播开来。因此，这些苍蝇的种群暴露在新的环境中，并随后随着这些当地条件的变化而进化。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，种群以几种不同的方式进化以应对寒冷的温度。首先，生活在温带气候的苍蝇进化出了一套生理适应能力，提高了对寒冷和饥饿的耐受性。虽然已经确定了几个支持这些生理适应的基因，但大多数支持这些适应的基因仍然未知。其次，冬季条件导致人口规模在夏季指数增长期后收缩。种群大小的这些周期性变化将显著影响遗传变异的背景水平，但这些模式在整个基因组中还没有得到充分的记录。在这里，我们建议同时识别温带气候适应的多态基因座，并描述周期性种群繁荣-萧条对遗传变异背景水平的影响。为了做到这一点，我们将在整个生长季节从温带新英格兰的重复果园中收集黑腹果蝇的样本。我们建议使用高通量测序技术对从这些果园收集的苍蝇基因组进行重新排序。通过对整个生长季节收集的苍蝇基因组进行重新测序，我们寻求实现两个目标。首先，我们将确定等位基因频率在整个生长季节在所有果园中以单调方式一致变化的基因座。我们假设这些基因座构成了对季节环境适应的平衡多态。其次，我们的目标是描述全基因组范围内的遗传变异模式。我们预测，周期性种群盛衰将导致种群结构的杂合度、连锁不平衡和特征在整个生长季发生变化。这项为期三年的博士后奖学金将在人口遗传学领域对申请者进行培训，并将为他提供生物信息学、计算生物学和高通量图书馆建设方面的宝贵技能。

DESCRIPTION (provided by applicant): Over the last 10,000 years Drosophila melanogaster has spread through the world in the wake of human migration. As a consequence, populations of these flies have been exposed to novel environments and have subsequently evolved in response to these local conditions. For flies living in temperate environments, winter cold represents a novel environment and populations have evolved in response to cold temperatures in several distinct ways. First, flies living in temperate climates have evolved a suite of physiological adaptations that increase tolerance to cold and starvation. While several genes have been identified that underlie these physiological adaptations, the majority of the genes underlying these adaptations remain unknown. Second, winter conditions cause population size contractions following periods of exponential growth during the summer. These cyclic changes in population size will significantly affect background levels of genetic variation, yet these patterns have not been adequately documented throughout the genome. Herein, we propose to simultaneously identify polymorphic loci underlying adaptations to temperate climates and describe the consequences of cyclic populations boom-busts on background levels of genetic variation. To do this, we will collect samples of D. melanogaster through the growing season from replicate orchards in temperate New England. We propose to resequence the genomes of flies collected from these orchards using high-throughput sequencing technologies. By resequencing the genomes of flies collected through the growing season, we seek to accomplish two aims. First, we will identify loci which change in allele frequency in a monotonic fashion consistently among all orchards through the growing season. We hypothesize that these loci underlie balanced polymorphisms underlying adaptation to seasonal environments. Second, we aim to characterize patterns of genetic variation genome wide. We predict that cyclic population boom-busts will cause changes in heterozygosity, linkage disequilibrium and signatures of population structure through the growing season. This three year postdoctoral fellowship will train the applicant in the field of population genetics and will provide him with invaluable skills in bioinformatics, computational biology and high-throughput library construction.