DISSERTATION RESEARCH: The evolutionary history of beryciforms and the contribution of signal and noise to phylogenetic inference in multi-locus datasets

进化途径最终导致了今天深海鱼类的多样性，但人们对其了解甚少。在其1亿年的历史中，水蛭形和复鳞形鱼类多次成功地在近岸和深海栖息地之间过渡。因此，它们为研究与这些极端栖息地之间的过渡相关的进化动力学提供了一个绝佳的机会。该项目将提供迄今为止对这种辐射最详细的系统发育研究，为今后调查深海鱼类群体多样化的模式和速度提供必要的基础设施。我们利用这些鱼类作为进一步发展系统发育理论的模型群，也为系统发育实验设计的分子标记筛选提供了新的标准。系统发育推断中的一个常见问题涉及在给定研究中使用的基因的选择。本项目将从经验上描述筛选标记对给定问题先验的效用，并展示当位点没有仔细审查时，不正确但有力支持的推断的可能性。这提出了一个客观的度量，从中筛选序列数据的效用为系统发育问题，适用于任何分类组。该项目还为本科生提供系统发育、生物信息学和博物馆技术方面的培训，并进一步为博物馆收藏和公共数据库提供标本和数据。

The evolutionary pathways that culminated in the present day diversity of deep sea fishes remain poorly understood. Beryciform and stephanoberyciform fishes have successfully transitioned between near shore and deep-sea habitats multiple times over their 100 million year history. Thus, they provide an exceptional opportunity for investigating the evolutionary dynamics associated with transitions between these extreme habitats. This project will provide the most detailed phylogenetic study of this radiation to date, providing the necessary infrastructure for future investigations into the mode and tempo of diversification across deep-sea fish groups. Our utilization of these fishes as a model group for further developing phylogenetic theory also sets a new standard for the screening of molecular markers for phylogenetic experimental design. A common question in phylogenetic inference concerns the selection of genes to employ in a given study. This project will empirically depict the utility of screening markers for a given question a priori, and demonstrate the potential for incorrect, yet strongly supported, inferences when loci are not carefully scrutinized. This presents an objective metric from which to screen the utility of sequence data for a phylogenetic problem that is applicable to any taxonomic group. This project also provides training in phylogenetics, bioinformatics, and museum techniques to undergraduate students and further contributes specimens and data to museum collections and public databases.