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: 2015
• 资助国家: 加拿大
• 起止时间: 2015-01-01 至 2016-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=588894
• 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.

我的研究解决了生态基因组学的一个基本组成部分，通过研究野生种群中个体之间的形态和遗传差异在多大程度上不同，在他们使用的生态位空间，如果是这样，估计生态，进化和保护政策的重要性。过去的许多努力，以确定这种协会一直是有限的，因为直到最近，全基因组标记的个人还没有，因此观察到的差异，在个人生态位很少受到关注。 我正在研究这个问题，使用一种小型淡水鱼，三棘鱼。棘鱼是第一个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（SNP），这些标记可以快速识别并用于评估野生种群的遗传变异性。我的建议支持一个硕士，一个博士和至少四个本科生的培训，并将需要多个领域和实验室协议，涉及形态，同位素和遗传协议作为生态位宽度或适应性变异假设的严格测试。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海达湖29个棘鱼种群的57条棘鱼的新获得的全基因组序列。这些刺鱼跨越很短的地理距离，在整个物种的形态和生态多样性，这在很大程度上代表了独立的和复制的殖民活动，从海洋祖先，包括湖流物种对。这种整合的形态计量学，生活史和生理化学特征与全基因组数据还没有尝试过，可以预期产生新的洞察力的生态和生理成分的基因组变异性和可能的洞察力的功能，在其他脊椎动物的多个基因。