Genomics of rapid adaptation in the lab and in the wild

实验室和野外快速适应的基因组学

• 批准号: 10794860
• 负责人: Dmitri Petrov
• 金额: $ 24.98万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-06-01 至 2026-05-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10794860
• 关键词: Biology; Communicable Diseases; Data; Drosophila genus; Drug resistance; Evolution; Foundations; Genomics; Human; Humanities; Liquid substance; Malignant Neoplasms; Modality; Organism; Phylogenetic Analysis; Population; Research; Resolution; Seasons; Series; System; Time; Variant; Virus; Yeasts; cost; de novo mutation; genomic data; robotic system; theories

Project Summary Adaptation is the foundational concept in biology. My lab aims to build an empirically and theoretically rich theory of adaptation. We focus specifically on the inference of adaptation from genomic data and on the study of rapid evolution in real time. The latter include (i) experimental evolution in yeast (adaptation by de novo mutation in well-mixed clonal system), (ii) adaptation on seasonal and ecological time-scales in Drosophila (adaptation from standing variation in a obligately sexual organism), and (iii) inference of adaptation from well resolved population genomic and phylogenetic data. These projects utilize a diversity of systems, high throughput and well-powered experimental modalities, and sophisticated and varied analytic frameworks, but they all focus on the overarching need to understand the dynamics of rapid adaptation. The reduction in the cost of sequencing is making it possible and imperative to increase the resolution through the increase in the number of replicates and this in turn requires the application of liquid handling robotic systems as the one I am requesting here.

项目摘要 适应是生物学的基础概念。我的实验室旨在建立一种经验和理论上丰富的理论 适应。我们专门关注从基因组数据和快速研究的适应性推论 实时进化。后者包括（i）酵母中的实验进化（通过从头突变适应 混合良好的克隆系统），（ii）果蝇中季节性和生态时间尺度的适应 有义务的性生物的常规差异）和（iii）对良好人群的适应性推断 基因组和系统发育数据。这些项目利用多样的系统，高吞吐量且功能良好 实验方式以及复杂和多样化的分析框架，但它们都集中在总体上 需要了解快速适应的动力。测序成本的降低是使其 通过增加重复数量的增加，可以提高解决方案的可能性和必要 转弯需要将液体处理机器人系统应用于我在此处要求的机器人系统。

项目成果

Recent Evolutionary History of Tigers Highlights Contrasting Roles of Genetic Drift and Selection.

• DOI: 10.1093/molbev/msab032
• 发表时间: 2021-05-19
• 期刊: Molecular biology and evolution
• 影响因子: 10.7
• 作者: Armstrong EE;Khan A;Taylor RW;Gouy A;Greenbaum G;Thiéry A;Kang JT;Redondo SA;Prost S;Barsh G;Kaelin C;Phalke S;Chugani A;Gilbert M;Miquelle D;Zachariah A;Borthakur U;Reddy A;Louis E;Ryder OA;Jhala YV;Petrov D;Excoffier L;Hadly E;Ramakrishnan U
• 通讯作者: Ramakrishnan U

Genome report: chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris).

• DOI: 10.1093/g3journal/jkac277
• 发表时间: 2022-12-01
• 期刊: G3 (Bethesda, Md.)

Revisiting the malaria hypothesis: accounting for polygenicity and pleiotropy.

• DOI: 10.1016/j.pt.2021.12.007
• 发表时间: 2022-04
• 期刊: Trends in parasitology
• 影响因子: 9.6
• 作者: Ebel ER;Uricchio LH;Petrov DA;Egan ES
• 通讯作者: Egan ES

Evolution of haploid and diploid populations reveals common, strong, and variable pleiotropic effects in non-home environments.

• DOI: 10.7554/elife.92899
• 发表时间: 2023-10-20
• 期刊: eLife
• 影响因子: 7.7
• 作者: Chen V;Johnson MS;Hérissant L;Humphrey PT;Yuan DC;Li Y;Agarwala A;Hoelscher SB;Petrov DA;Desai MM;Sherlock G
• 通讯作者: Sherlock G

Detection of hard and soft selective sweeps from Drosophila melanogaster population genomic data.

• DOI: 10.1371/journal.pgen.1009373
• 发表时间: 2021-03
• 期刊: PLoS genetics
• 影响因子: 4.5
• 作者: Garud NR;Messer PW;Petrov DA
• 通讯作者: Petrov DA