Using full-genomic data to assess defense and trophic niche differentiation within wild fish populations

我的研究考察了全基因组多样性和种群内环境多样性之间的关系，特别是不同的基因类型在其生活史上是否利用了不同的微生境。人们对此知之甚少，但这是进化和生态学理论(如适应过程)的关键组成部分，对保护遗传学、栖息地碎片化、种群瓶颈和物种丧失非常重要。我提议的研究支持对四名毕业生和一名博士后候选人的培训，并以来自夏威夷外海两个经过充分研究的湖泊的三条刺鱼为模型，评估基因类型的生态位专门化程度。我们利用一组新开发的3000多个遗传标记，分布在整个基因组的已知位置，并测量每条鱼的一大系列特征，包括身体形状、防御盔甲、性别、饮食和寄生虫，以及湖中收集个体鱼的每个地点的物理和化学参数。这种全基因组数据与详细的形态和生态数据的整合以前从未对任何物种进行过，无论结果如何，都将在两个层面上代表着实质性的进步。任何与生物学或湖泊学数据相关的可预测的不同遗传标记都可以深入了解特定的基因功能，这可能与理解这一功能在包括人类在内的其他脊椎动物中的运作方式有关。其次，小种群的灭绝通常与遗传多样性的丧失、近亲繁殖以及多种病原体和寄生虫的负面影响有关。如果我们的结果显示了特定于基因型的生态位，这意味着广泛的碎片化和种群减少导致的遗传多样性的丧失将进一步限制种群对不断变化的地球的适应能力。

My research examines the relationship between genome-wide diversity and environmental diversity within populations, specifically, whether different genotypes exploit different microhabitats during their life histories. This is poorly understood yet is a critical component of evolutionary and ecological theory such as the process of adaptation and is very important for conservation genetics, habitat fragmentation, population bottlenecks and loss of species. My proposed research supports the training of four graduates and a post-doctoral candidate and uses threespine stickleback fish from two well-studied lakes on Haida Gwaii as a model to assess the extent of niche-specialization of genotypes. We take advantage of a newly developed array of over 3000 genetic markers distributed at known positions across the entire genome and measure a large series of traits for each fish including body shape, defense armour, sex, diet, and parasites, as well as physical and chemical parameters at each site in the lake where individual fish are collected. This integration of genome-wide data with detailed morphological and ecological data has not been previously done for any species and irrespective of the results, would represent a substantive advance at two levels. Any of the genetic markers that differ predictably in relation to biological or limnological data allow insight into specific gene function, which may then be relevant to understanding how this operates in other vertebrates, including humans. Secondly, the extinction of small populations is usually associated with loss of genetic diversity, inbreeding and negative impact of multiple pathogens and parasites. If our results demonstrate genotype-specific niches, this implies that loss of genetic diversity from widespread fragmentation and population reduction will further constrain the adaptability of populations in a changing planet.