The Evolution of Two Genomes: Sequence and Functional Divergence

这项研究旨在确定发生在所有动物细胞中的两个独立基因组中遗传变异的重要性：核基因组和线粒体基因组。这些基因组共同作用形成一种代谢途径中的酶，即氧化磷酸化代谢途径。氧化磷酸化途径使动物呼吸氧气时产生的绝大多数ATP能量。为了研究该途径中遗传变异的重要性，研究目标包括：（1）确定氧化磷酸化途径中所有基因的测序变异，（2）量化这些基因的RNA表达差异，以及（3）确定蛋白质多态性和基因表达的功能和生化后果。为了了解自然发生的遗传差异，本研究使用了两个基因组的盐沼小鱼，F。heteroclitus，分布沿着陡峭的热梯度，其中南部种群比北方种群高12°C。这种温度的梯度变化与酶动力学和酶表达的适应性变化有关。这种方法整合了温度对蛋白质变体、核苷酸多态性和RNA表达中的定量变异的生理效应，并通过定义由自然选择进化的变化来定义生物学上重要的差异（即，进化适应）。结合核苷酸变异的发现，RNA表达的定量变异，以及这种变异的功能后果将增强我们对两个基因组的进化以及基因组内部和之间的约束和冲突如何影响进化过程的理解。通过分析一个完整的代谢途径，我们将获得一个广泛的了解适应性进化如何影响许多相互作用的基因之间的变化，以实现适应性生理变化。因此，这些数据提供了一个独特的视角，如何全球变暖可能会影响动物的生理和进化。更广泛的影响：这项研究将加强本科生和研究生的培训和教育，在科学研究中使用DNA测序，生物化学和生理学。为了提高代表性不足的群体的参与，少数民族本科生将通过我们与科学计划，是面向少数民族在迈阿密大学的互动招募。此外，社会和科学界将受益于不断变化的热环境与许多完整线粒体基因组核苷酸变异之间关系的经验数据。这些数据将在实验室中获得，将为Fundulus研究社区，从事线粒体功能研究的生理学家和建模单倍体基因组进化的研究人员提供丰富的数据库。

This research intends to determine the importance of genetic variation in the two separate genomes that occur in all animal cells: the nuclear and mitochondrial genomes. These genomes work together to form the enzymes in one metabolic pathway, the Oxidative Phosphorylation metabolic pathway. The Oxidative Phosphorylation pathway makes the vast majority of ATP energy produced in animals breathing oxygen. To investigate the importance of genetic variation in this pathway, the research goals include 1) determining the sequencing variation among all the genes in the oxidative phosphorylation pathway, (2) quantifying the differences in RNA expression for these genes, and (3) determining the functional and biochemical consequences of both protein polymorphisms and gene expression. To understand the naturally occurring genetic differences, this research uses evolutionary analyses of the two genomes among populations of the salt marsh minnow, F. heteroclitus, that are distributed along a steep thermal cline where southern populations are 12°C warmer than northern populations. This clinal variation in temperature is associated with adaptive changes in enzyme kinetics and enzyme expression. This approach integrates the physiological effects of temperature on protein variants, nucleotide polymorphisms and quantitative variation in RNA expression, and defines biologically important differences by defining changes that have evolved by natural selection (i.e., are evolutionary adaptations). Combining the discovery of nucleotide variation, quantitative variation in RNA expression, and the functional consequences of this variation will enhance our understanding of the evolution of two genomes and how constraints and conflict within and between genomes affect evolutionary processes. By analyzing a complete metabolic pathway, we will gain a broad understanding of how adaptive evolution affects changes among many interacting genes to achieve adaptive physiological changes. Thus, these data provide a unique perspective of how global warming may affect the physiology and evolution of animals.Broader Impacts:This research will enhance undergraduate and graduate student training and education in scientific research using DNA sequencing, biochemistry and physiology. To enhance the participation of under-represented groups, minority undergraduates will be recruited through our interactions with science programs that are geared for minorities at the University of Miami. Additionally, society and the science community will benefit from the empirical data on the relationship between changing thermal environments and nucleotide variation across many whole mitochondrial genomes. These data, which will be publically available, will provide a rich database for the Fundulus research community, physiologists working on mitochondrial function, and researchers modeling haploid genome evolution.