RIG: Genome Size and Karyotype Evolution in Esociform Fishes

这项研究的目的是确定影响所观察到的鮈形目鱼类基因组大小和核型变异的因素，鮈形目鱼类是包括广泛认可的白斑狗鱼在内的一个谱系。 经典的细胞遗传学研究表明，该类鱼类的基因组特征存在广泛的多样性。 这种变异性，加上对群体进化关系的新共识，使其成为染色体和基因组水平上进化的潜在机制和后果的新兴想法的理想试验场。 该项目将产生的知识、数据和材料将为更广泛地研究鱼类（物种最丰富的脊椎动物谱系）染色体和基因组进化的模式和速度提供基础。 该研究有两个具体目标：a）确定暗影属基因组扩展的特征； b) 制定esociforms及其近亲的分子细胞遗传学研究所需的方案和试剂。 从长远来看，这些协议可以应用于表现出基因组组织独特特征的其他谱系。 本影的三个物种中的两个物种的基因组包含的 DNA 数量大约是其他伞形属中观察到的 DNA 的两倍。 鉴于最近人们对有机体进化和基因组大小之间的假设关系重新产生了兴趣，确定促成基因组扩张的因素具有重要意义。 初步数据表明，一些转座元件（TE）群体的扩增是导致 Umbra 基因组扩张的主要力量。 当前的项目旨在使用几个互补的证据来检验该假设。 Southern 和斑点印迹实验将揭示不同基因组成分对基因组扩展的相对贡献。 PCR靶向克隆实验的深度测序和系统发育分析将用于表征代表性esociform基因组中TE群体的多样性和相对年龄。 最后，荧光原位杂交观察将有助于定义基因组大小变化和核型排列之间任何假定关系的特征。 esociforms 基因组变异的另一个有趣的方面是染色体稳定性的明显变化，这是该群体核型多样性的基础。 具体来说，经典的细胞遗传学研究和化石证据表明，Esox 属成员的核型在超过 6000 万年的时间里几乎保持不变；而在另一个极端，不同的胸形 Dallia pectoralis 种群表现出不同的核型。 总体而言，esociforms 中的二倍体染色体数量范围为 22 至 78 条。核型和核型稳定性的这种变异凸显了 esociforms 染色体进化研究的价值，以揭示塑造基因组变异的机制特征。 该项目启动了通过开发和应用染色体特异性DNA探针来确定esociforms染色体进化模式和速率的任务。 这项工作还将有助于确定细胞遗传学数据在鱼类系统发育学中的效用。该项目将研究在染色体和基因组规模上塑造遗传变异的过程。 该研究重点关注一组已知在染色体和基因组特征方面具有广泛且有趣的多样性的鱼类。 从这项工作中获得的见解将加深人们对产生一些遗传多样性的机制的理解，这些遗传多样性是生命的特征，也是生物进化的燃料。 这项研究将有助于促进初级研究者的专业发展，该研究者是科学界代表性不足的群体的一员，也是一名研究生，他们将获得一套科学工具的实践经验，这些工具目前在美国进化生物学家中尚未广泛使用。由于该研究者隶属于自然历史博物馆并参与其教育活动，该项目的结果将及时、方便地向公众提供。

The goal of this research is to determine factors that played a role in shaping the observed variation in genome size and karyotype among the fishes of the order Esociformes, a lineage that includes the widely recognized Northern Pike. Classical cytogenetic studies have demonstrated extensive diversity in the genomic characteristics of the species in this group of fishes. This variability, coupled with emerging consensus on the evolutionary relationships of the group makes it an ideal testing ground for emerging ideas on the underlying mechanisms and consequences of evolution at the chromosome and genome levels. The knowledge, data and materials that this project will generate will provide the foundation for broader investigations of the mode and tempo of chromosome and genome evolution in fishes, the most species-rich vertebrate lineage. The research has two specific goals: a) to determine the characteristics of the expansion of the genome in the esociform genus Umbra; and b) to produce protocols and reagents necessary for molecular cytogenetic studies of esociforms and their closest relatives. In the long term, these protocols may be applied to other lineages that exhibit unique features of genomic organization. The genome of two of the three species of Umbra comprise approximately two times as much DNA as those observed in other esociform genera. Determining the factors that contribute to this genome expansion is significant in light of the recently renewed interest in hypothesized relationships between organismal evolution and genome size. Preliminary data point to the amplification of some transposable element (TE) populations as a primary force leading to genome expansion in Umbra. The current project is designed to test that hypothesis using several complementary lines of evidence. Southern and dot blot experiments will reveal the relative contributions of different genomic components to genome expansion. Deep sequencing of PCR-targeted cloning experiments and phylogenetic analyses will be used to characterize the diversity and relative age of TE populations in representative esociform genomes. Finally, fluorescence in situ hybridization observations will help define features of any putative relationships between changes in genome size and karyotypic arrangement. Another interesting aspect of genomic variation among esociforms is the apparent change in chromosomal stability that underlies the diversity of karyotypes in the group. Specifically, classical cytogenetic studies and fossil evidence indicate that the karyotypes of members of the genus Esox have remained virtually unchanged for more than 60 million years; while at the other extreme, different populations of the esociform Dallia pectoralis show divergent karyotypes. Overall, diploid chromosome numbers among esociforms range from 22 to 78. This variability in karyotype and karyotypic stability highlights the value of the study of chromosome evolution in esociforms to uncover characteristics of the mechanisms that shape genome variation. This project initiates the task of determining the mode and rate of chromosomal evolution in esociforms through the development and application of chromosome specific DNA probes. This effort will also help determine the utility of cytogenetic data in fish phylogenetics.This project will examine processes that shape genetic variability at the scale of chromosomes and genomes. The research focuses on one group of fishes that is known to possess extensive and interesting diversity in their chromosomal and genomic characteristics. The insights gained from this work will lead to increased understanding of the mechanisms that are responsible for generating some of the genetic diversity that characterizes life and that constitutes the fuel for biological evolution. This research will help foster the professional development of a beginning investigator who is a member of a group underrepresented in science and a graduate student, who will gain hands-on experience with a set of scientific tools that currently are not in widespread use among evolutionary biologists in the U.S. Thanks to the investigator's affiliation with a natural history museum and his participation in its educational activities, the project's results will be made promptly and conveniently available to the general public.