Genomics of natural populations

自然群体基因组学

• 批准号: 8126352
• 负责人: Alan Olav Bergland
• 金额: $ 4.63万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2011
• 资助国家: 美国
• 起止时间: 2011-03-29 至 2014-03-28
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8126352
• 关键词: Affect; Animal Model; Area; Bioinformatics; Climate; Communities; Computational Biology; DNA Resequencing; DNA Sequence; Data; Demography; Diapause; Disease; Drosophila genus; Drosophila melanogaster; Environment; Equilibrium; Event; Fellowship; Frequencies; Fruit; Gene Frequency; Generations; Genes; Genetic; Genetic Polymorphism; Genetic Variation; Genome; Genomics; Growth; Human; Individual; Libraries; Life; Linkage Disequilibrium; Measures; Methods; New England; Pattern; Physiological Adaptation; Population; Population Genetics; Population Sizes; Recording of previous events; Research; Sampling; Scheme; Seasonal Variations; Seasons; Starvation; Structure; Technology; Testing; Time; Training; Variant; cold temperature; fly; genome sequencing; genome-wide; heuristics; human migration; male; migration; novel; response; skills; statistics; success; theories

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. PUBLIC HEALTH RELEVANCE: Using the model organism, Drosophila melanogaster, this project seeks to simultaneously identify genetic polymorphisms underlying adaptation to novel environments and document the effects of recent demographic events on patterns of genetic variation. Heuristic and analytic methods developed under this proposal can be applied to genomic data in humans to aid in disentangling the effects of demography and selection on patterns of genetic variation surrounding disease causing polymorphisms.

描述（由申请人提供）：在过去的一万年中，黑腹果蝇随着人类迁徙而遍布世界各地。因此，这些苍蝇的种群已经暴露在新的环境中，并随后进化以适应这些当地条件。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，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了一套生理适应性，增强了对寒冷和饥饿的耐受性。虽然已经确定了一些基因是这些生理适应的基础，但这些适应的大部分基因仍然未知。其次，冬季条件导致种群规模在夏季呈指数增长后收缩。这些种群规模的循环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，我们建议同时确定对温带气候适应的多态性位点，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，我们将在温带新英格兰的复制果园中收集整个生长季节的黑胃菊的样本。我们建议使用高通量测序技术对这些果园收集的果蝇基因组进行重测序。通过对生长季节收集的果蝇进行基因组重测序，我们寻求实现两个目标。首先，我们将确定在整个生长季节中所有果园中等位基因频率以单调方式一致变化的位点。我们假设这些基因座是适应季节环境的平衡多态性的基础。其次，我们的目标是描述基因组范围内的遗传变异模式。我们预测，在整个生长季节，周期性的种群盛衰会引起杂合性、连锁不平衡和种群结构特征的变化。这项为期三年的博士后研究将培养申请人在群体遗传学领域的能力，并将为申请人提供在生物信息学、计算生物学和高通量图书馆建设方面的宝贵技能。