A comparative population genomic approach for high-resolution inference of natural selection in fruit flies

用于果蝇自然选择高分辨率推断的比较群体基因组方法

• 批准号: 10229346
• 负责人: Bernard Youngsoo Kim
• 金额: $ 6.64万
• 依托单位: STANFORD UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-07-20 至 2022-07-19
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10229346
• 关键词: Address; Bar Codes; Base Pairing; Biological; Biological Models; Biological Process; Biology; Communities; Complement; DNA Resequencing; Data; Data Set; Demography; Drosophila genus; Drosophilidae; Elements; Event; Evolution; Family; Fellowship; Foundations; Future; Genes; Genetic Polymorphism; Genetic Variation; Genome; Genomic Segment; Genomic approach; Genomics; Goals; Hybrids; Individual; Lead; Leadership; Logistics; Maps; Measures; Methods; Modeling; Modernization; National Research Service Awards; Natural Selections; Organism; Pattern; Phenotype; Population; Population Genetics; Positioning Attribute; Postdoctoral Fellow; Process; Radiation; Research; Research Personnel; Research Proposals; Resolution; Resources; Sampling; Secure; Signal Transduction; Site; Subgroup; Testing; Time; Training; Variant; Work; base; comparative; comparative genomics; cost; density; design; empowered; experience; experimental study; fly; genomic data; genomic tools; improved; novel strategies; pesticide resistance; response; simulation; skills; tool

Project Summary/Abstract The number of sequenced organisms continues to grow exponentially, providing evolutionary biologists with an unprecedented resolution for mapping natural selection in the genome. Comparative genomic methods identify function by searching for genomic elements that are constrained by natural selection. Modern comparative datasets are saturated with substitutions accumulated over many millions of years of evolution, allowing functional elements to be identified at the resolution of a few base pairs. Since comparative methods rely on sequence conservation as evidence of natural selection, substitutions caused by fluctuations in the strength of selection or rare adaptive events can be mistaken for a lack of function. Population genomic data are robust to these issues and are the best way to measure constraint in principle, but suffer from low per-site densities, limiting the resolution at which function can be studied. Here, we propose a comparative population genomics approach for addressing these limitations by combining polymorphism data across multiple species. Specifically, we will create an unprecedented dataset of genome assemblies of and population polymorphism data of up to 100 individuals from each of 100 species from the model system of fruit flies (family Drosophilidae). In Aim 1, we will map selective constraint at the resolution of less than 3 base pairs and use these maps to test how constraint evolves across a clade. In Aim 2, we will develop new a test for adaptive evolution that jointly utilizes substitution and polymorphism data from multiple species and test whether the same genes are utilized by adaptation in drosophilids. Successful completion of the project will contribute significantly to the emerging field of comparative population genomics by providing an important publicly available genomic dataset for the scientific community, new ways to design and analyze large sequencing experiments, and test fundamental assumptions about the relationship between evolution in populations and evolution over macro-evolutionary time scales. The primary goal of this NRSA F32 fellowship is to prepare me with the scientific and professional foundation to become a leader in the new field of comparative population genomics as an independent researcher. My long-term scientific goal is to lead an independent research group that utilizes comparative genomics and population genetics tools to bridge micro and macroevolutionary processes. As a postdoctoral fellow in the Petrov Lab at Stanford, I will receive new scientific training in wet lab skills, designing sequencing experiments, and comparative genomics tools by generating and analyzing a genomic dataset that will be the first of its kind. I will receive substantial training in professional leadership and network building by leading the effort to build this large genomic resource for the scientific community.

项目总结/摘要 测序生物的数量继续呈指数级增长，为进化生物学家提供了一个新的视角。 前所未有的解决方案来绘制基因组中的自然选择。比较基因组学方法鉴定 通过寻找受自然选择约束的基因组元素来发挥作用。现代比较 数据集充满了数百万年进化积累的替代， 在几个碱基对的分辨率下识别功能元件。由于比较方法依赖于 作为自然选择证据的序列保守性， 选择或罕见的适应性事件可能被误认为缺乏功能。人口基因组数据是强大的， 这些问题原则上是测量约束的最佳方式，但是遭受低的每站点密度， 限制了函数研究的分辨率。在这里，我们提出了一个比较人口基因组学 通过结合多个物种的多态性数据来解决这些限制的方法。 具体来说，我们将创建一个前所未有的基因组组装和人口多态性数据集， 来自果蝇（科）模型系统的100个物种中的每一个的多达100个个体的数据 果蝇科）。在目标1中，我们将以小于3个碱基对的分辨率映射选择性约束，并使用 这些地图来测试约束如何在进化枝中进化。在目标2中，我们将开发新的自适应测试 进化联合利用多个物种的替代和多态性数据并测试是否 果蝇的适应也利用了相同的基因。该项目的成功完成将有助于 显著的新兴领域的比较人口基因组学提供了一个重要的公共 科学界可用的基因组数据集，设计和分析大型测序的新方法 实验，并测试有关种群进化与 宏观进化时间尺度上的进化。 这个NRSA F32奖学金的主要目标是准备我的科学和专业 基金会成为比较人口基因组学新领域的领导者， 研究员我的长期科学目标是领导一个独立的研究小组， 基因组学和群体遗传学工具可以连接微观和宏观进化过程。担任博士后 作为斯坦福大学彼得罗夫实验室的研究员，我将接受新的科学培训，包括湿实验室技能、设计测序、 实验和比较基因组学工具，通过生成和分析基因组数据集， 第一个这样的。我将接受专业领导和网络建设的大量培训， 努力为科学界建立这个庞大的基因组资源。

项目成果

Evolution and development of male-specific leg brushes in Drosophilidae.

• DOI: 10.1007/s00427-022-00694-3
• 发表时间: 2022-12
• 期刊: DEVELOPMENT GENES AND EVOLUTION
• 影响因子: 2.4
• 作者: Tanaka, Kohtaro;Barmina, Olga;Thompson, Ammon;Massey, Jonathan H.;Kim, Bernard Y.;Suvorov, Anton;Kopp, Artyom
• 通讯作者: Kopp, Artyom

Highly contiguous assemblies of 101 drosophilid genomes.

• DOI: 10.7554/elife.66405
• 发表时间: 2021-07-19
• 期刊: eLife
• 影响因子: 7.7
• 作者: Kim BY;Wang JR;Miller DE;Barmina O;Delaney E;Thompson A;Comeault AA;Peede D;D'Agostino ERR;Pelaez J;Aguilar JM;Haji D;Matsunaga T;Armstrong EE;Zych M;Ogawa Y;Stamenković-Radak M;Jelić M;Veselinović MS;Tanasković M;Erić P;Gao JJ;Katoh TK;Toda MJ;Watabe H;Watada M;Davis JS;Moyle LC;Manoli G;Bertolini E;Košťál V;Hawley RS;Takahashi A;Jones CD;Price DK;Whiteman N;Kopp A;Matute DR;Petrov DA
• 通讯作者: Petrov DA

MaLAdapt Reveals Novel Targets of Adaptive Introgression From Neanderthals and Denisovans in Worldwide Human Populations.

• DOI: 10.1093/molbev/msad001
• 发表时间: 2023-01-04
• 期刊: MOLECULAR BIOLOGY AND EVOLUTION
• 影响因子: 10.7
• 作者: Zhang, Xinjun;Kim, Bernard;Singh, Armaan;Sankararaman, Sriram;Durvasula, Arun;Lohmueller, Kirk E.
• 通讯作者: Lohmueller, Kirk E.

Predictability and parallelism in the contemporary evolution of hybrid genomes.

• DOI: 10.1371/journal.pgen.1009914
• 发表时间: 2022-01
• 期刊: PLoS genetics
• 影响因子: 4.5
• 作者: Langdon QK;Powell DL;Kim B;Banerjee SM;Payne C;Dodge TO;Moran B;Fascinetto-Zago P;Schumer M
• 通讯作者: Schumer M

Widespread introgression across a phylogeny of 155 Drosophila genomes.

• DOI: 10.1016/j.cub.2021.10.052
• 发表时间: 2022-01-10
• 期刊: Current biology : CB
• 作者: Suvorov A;Kim BY;Wang J;Armstrong EE;Peede D;D'Agostino ERR;Price DK;Waddell P;Lang M;Courtier-Orgogozo V;David JR;Petrov D;Matute DR;Schrider DR;Comeault AA
• 通讯作者: Comeault AA