Using full-genomic data to assess individual niche in wild fish populations

使用全基因组数据评估野生鱼类种群中的个体生态位

• 批准号: RGPIN-2014-06243
• 负责人: Reimchen, Thomas
• 金额: $ 1.97万
• 依托单位: University of Victoria
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2018
• 资助国家: 加拿大
• 起止时间: 2018-01-01 至 2019-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=663166
• 关键词: Using; full; genomic; data; assess

My research addresses a basic component to ecological genomics by examining the extent to which morphological and genetic differences among individuals in wild populations differ in their use of niche space and if so, estimate the importance to ecological, evolutionary and conservation policy. Much of the past efforts to identify such associations have been limited because until recently, genome-wide markers for individuals have not been available and therefore observed differences in the individual niche have received little attention. I am studying this issue using a small freshwater fish, the threespine stickleback. The stickleback is one of the first fish species to be fully-sequenced and this has allowed development of thousands of genetic markers (SNPs) throughout the genome that can be rapidly identified and used to assess genetic variability in wild populations. My proposal supports the training of one MSc, one PhD and at least four undergraduate students and will entail multiple field and lab protocols involving morphometric, isotopic and genetic protocols as a rigorous test of the niche-width or adaptive variation hypotheses. As well, the proposal supports one Post-doctoral position for analyses of the newly available full genome sequences of 57 stickleback from 29 lake populations of stickleback on Haida Gwaii, coastal British Columbia. These stickleback span over short geographical distances much of the morphological and ecological diversity in the entire species and which largely represent independent and replicated colonization events from marine ancestors including lake-stream species pairs. Such integration of morphometrics, life histories and physiochemical traits with full genome data has not been attempted before and can be expected to yield novel insight into ecological and physiological components to genomic variability and possibly insight to the function of multiple genes in other vertebrates.

我的研究致力于生态基因组学的一个基本组成部分，通过检查野生种群中个体在利用生态位空间方面的形态和遗传差异的程度，如果是这样的话，估计其对生态、进化和保护政策的重要性。过去识别这种关联的大部分努力都是有限的，因为直到最近，还没有针对个体的全基因组标记，因此在个体生态位中观察到的差异几乎没有受到关注。我正在用一种叫三刺鱼的小淡水鱼来研究这个问题。刺鱼是第一批被完全测序的鱼类物种之一，这使得在整个基因组中开发出数千个遗传标记(SNPs)，可以快速识别并用于评估野生种群的遗传变异性。我的建议支持培养一名硕士、一名博士和至少四名本科生，并将需要多个现场和实验室方案，包括形态计量学、同位素和遗传方案，作为对生态位宽度或适应性变异假说的严格测试。此外，该提案还支持一个博士后职位，用于分析来自不列颠哥伦比亚省沿海城市海达格瓦伊的29个湖中刺鱼种群的57条刺鱼的最新全基因组序列。这些刺鱼跨越很短的地理距离，整个物种的形态和生态多样性很大程度上代表了海洋祖先，包括湖泊-溪流物种对的独立和复制的殖民事件。这种将形态计量学、生活史和物理化学特征与全基因组数据相结合的方法以前从未尝试过，有望对基因组变异的生态和生理成分产生新的见解，并可能深入了解其他脊椎动物中多个基因的功能。