Genomics of natural populations

描述（由申请人提供）：在过去的10,000年里，随着人类的迁徙，黑腹果蝇在世界各地传播开来。因此，这些苍蝇的种群已经暴露在新的环境中，并随后根据这些当地条件进行了进化。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，种群以几种不同的方式进化以应对寒冷的温度。首先，生活在温带气候中的苍蝇已经进化出一套生理适应，增加了对寒冷和饥饿的耐受性。虽然已经确定了几个基因，这些生理适应的基础，这些适应的基因仍然是未知的。第二，冬季条件导致种群规模在夏季指数增长期后收缩。种群规模的这些周期性变化将显著影响遗传变异的背景水平，但这些模式尚未在整个基因组中得到充分的记录。 在此，我们建议同时确定多态位点的适应温带气候和描述的后果，周期性种群繁荣萧条的背景水平的遗传变异。为此，我们将收集D.在生长季节从温带新英格兰的复制果园中的黑腹果蝇。我们建议使用高通量测序技术对从这些果园收集的苍蝇的基因组进行重新测序。通过对整个生长季节收集的果蝇基因组进行重新测序，我们试图实现两个目标。首先，我们将确定基因座的等位基因频率的变化在一个单调的方式始终在所有果园通过生长季节。我们推测，这些位点的基础平衡多态性的适应季节性环境。第二，我们的目标是表征基因组范围内的遗传变异模式。我们预测，周期性的种群繁荣-萧条将导致整个生长季节的杂合性，连锁不平衡和种群结构的变化。 这个为期三年的博士后奖学金将在群体遗传学领域培训申请人，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.