Dynamics of Contemporary Genomic Evolution in Replicate Threespine Stickleback Populations

复制三刺刺鱼种群的当代基因组进化动态

• 批准号: 10237282
• 负责人: Krishna R Veeramah
• 金额: $ 30.99万
• 依托单位: STATE UNIVERSITY NEW YORK STONY BROOK
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-09-15 至 2024-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10237282
• 关键词: Address; Adverse effects; Alaska; Alaskan; Alleles; Appearance; Bacteria; Complex; Copy Number Polymorphism; DNA sequencing; Data; Disease; Drug resistance; Environment; Event; Evolution; Fishes; Frequencies; Fresh Water; Gasterosteidae; Gene Frequency; Generations; Genes; Genetic Variation; Genome; Genomics; Goals; HIV; Human; Individual; Invaded; Life Cycle Stages; Measurable; Methods; Microbe; Modeling; Mutation; Natural Selections; Nucleotides; Organism; Oryctolagus cuniculus; Phenotype; Population; Process; Running; Sampling; Sea; Series; Site; Skin Pigmentation; Time; Variant; Yeasts; base; cohort; ectodysplasin; experience; fitness; gene function; genetic evolution; genome-wide; genomic signature; genomic variation; human pathogen; insight; pathogen; pressure; sample fixation; trait; whole genome

We traditionally envision adaptation of organisms to new environments as starting with appearance of a new favorable mutation and spreading to the population. While this view applies well to microbes, such as yeast or bacteria, it usually takes much longer for new mutations to arise and spread in large-bodied, less-abundant species, and when they do, they are more likely to be lost. Accordingly, natural selection acting on new mutations apparently was rare during the last 250,000 years of human evolution. An alternative view for adaptation that may apply well to humans is emerging; many mutations persist in populations for a long time as “standing genetic variation” (SGV) even though they have weak or even adverse effects on chances to survive and reproduce (i.e., natural selection). When an environment changes or people migrate, variants in the SGV may become highly advantageous, allowing the population to adapt quickly to its new surroundings. There is growing evidence that SGV is crucial for adaptation of many species over short time scales, and is crucial for most complex human traits (including those for disease) and drug resistance in human pathogens (e.g., HIV). However, while examples of adaptation based on SGV in humans are growing, surprisingly little is known, either theoretically or empirically, about the ​evolutionary dynamics​ of adaptation based on SGV. In the last five years, the Threespine Stickleback (TS, ​Gasterost​eus aculeatus) fish has emerged as the premier subject to study adaptation based on SGV. Sea-run stickleback contain abundant SGV and have repeatedly invaded fresh water. Much of their adaptation to fresh water occurs within a decade after they colonize it and depends on SGV. Indeed, SGV for the very same gene has apparently contributed to adaptation for skin pigmentation in both humans and TS on similar time scales (in generations). The overall goal of this project is to understand the evolutionary dynamics of adaptation based on SGV in TS. The first aim to reach this goal is to sequence the genomes of ~1,000 marine TS from five Alaskan sea-run populations to identify genes with SGV and estimate the relative abundance of freshwater-adaptive SGV variants in the ancestral environment. The second aim is to sequence TS samples from three nearby Alaskan lakes annually for 10 years, including immediately after these lakes were colonized by sea-run TS. This will enable direct observation of how SGV changes in relative abundance during the earliest stages of adaptation, when most evolution from a sea-run to freshwater traits occurs. The third aim is to sequence a group of TS born simultaneously (i.e., a cohort) at biweekly to monthly intervals through the two-year life cycle in two new lake populations, allowing identification of which original SGV variants confer advantages for specific events during the life-cycle of adapting freshwater TS. This study will provide unique insights into the dynamics of adaptation based on SGV, which will be vital to better understand how humans and their pathogens adapt to new environments over short time scales.

我们传统上认为，生物体对新环境的适应始于新环境的出现。 有利的突变和传播到人口。虽然这种观点很好地适用于微生物，如酵母或 细菌，通常需要更长的时间才能产生新的突变，并在大型，不太丰富的细菌中传播。 物种，当它们这样做时，它们更有可能消失。因此，自然选择作用于新的 在人类进化的最后25万年里，突变显然是罕见的。另一种观点是， 可能适用于人类的适应正在出现;许多突变在人群中持续了很长时间， “常设遗传变异”（SGV），即使它们对生存机会有微弱甚至不利的影响 并再现（即，自然选择）。当环境发生变化或人们迁移时，SGV中的变体 可能变得非常有利，使种群能够迅速适应新的环境。有 越来越多的证据表明，SGV对许多物种在短时间内的适应至关重要， 大多数复杂的人类特征（包括疾病特征）和人类病原体的耐药性（例如，HIV）。 然而，尽管基于SGV的人类适应的例子越来越多，但令人惊讶的是，人们对SGV的了解却很少， 无论是理论上还是经验上，关于基于SGV的适应的进化动力学。在过去五 多年来，Threespine Stickleback（TS，Gasterost eus aculeatus）鱼已经成为首要的主题， 研究了基于SGV的适应性。海润刺鱼含有丰富的SGV， 淡水它们对淡水的大部分适应发生在它们殖民后的十年内， 在SGV。事实上，同样基因的SGV显然有助于适应皮肤色素沉着， 人类和TS在相似的时间尺度上（以代为单位）。本项目的总体目标是了解 TS中基于SGV的适应演化动力学。实现这一目标的第一个目标是测序 来自五个阿拉斯加海跑种群的约1,000个海洋TS的基因组，以识别SGV基因， 估计祖先环境中淡水适应性SGV变体的相对丰度。的 第二个目标是连续10年每年对阿拉斯加附近三个湖泊的TS样本进行测序，包括 就在这些湖泊被海上的TS殖民之后。这将有助于直接观察SGV如何 在适应的最早阶段，当大多数进化从海运行到 淡水特征发生。第三个目的是对同时出生的一组TS进行测序（即，一个队列）在 在两个新的湖泊种群的两年生命周期中，每两周至每月进行一次， 其中原始SGV变体在适应的生命周期中为特定事件提供优势 淡水TS这项研究将提供独特的见解适应动态的基础上SGV， 对于更好地了解人类及其病原体如何在短时间内适应新环境至关重要 鳞片

项目成果

Evolution of static allometry and constraint on evolutionary allometry in a fossil stickleback.

• DOI: 10.1111/jeb.13984
• 发表时间: 2022-03
• 期刊: Journal of evolutionary biology
• 影响因子: 2.1

Threespine Stickleback: A Model System For Evolutionary Genomics.

• DOI: 10.1146/annurev-genom-111720-081402
• 发表时间: 2021-08-31
• 期刊: Annual review of genomics and human genetics
• 影响因子: 8.7
• 作者: Reid K;Bell MA;Veeramah KR
• 通讯作者: Veeramah KR

Evolution of stickleback spines through independent cis-regulatory changes at HOXDB.

• DOI: 10.1038/s41559-022-01855-3
• 发表时间: 2022-10
• 期刊: Nature ecology & evolution
• 影响因子: 16.8

Cross-continental experimental infections reveal distinct defence mechanisms in populations of the three-spined stickleback Gasterosteus aculeatus.

• DOI: 10.1098/rspb.2021.1758
• 发表时间: 2021-09-29
• 期刊: Proceedings. Biological sciences
• 作者: Piecyk A;Hahn MA;Roth O;Dheilly NM;Heins DC;Bell MA;Kalbe M
• 通讯作者: Kalbe M

Inferring the evolution of reproductive isolation in a lineage of fossil threespine stickleback, Gasterosteus doryssus.

推断化石三刺鱼（Gasterosteus doryssus）谱系中生殖隔离的进化。

• DOI: 10.1098/rspb.2024.0337
• 发表时间: 2024
• 期刊: Proceedings. Biological sciences
• 作者: Siddiqui,Raheyma;Swank,Samantha;Ozark,Allison;Joaquin,Franklin;Travis,MatthewP;McMahan,CalebD;Bell,MichaelA;Stuart,YoelE
• 通讯作者: Stuart,YoelE