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

导致今天深海鱼类多样性的进化途径仍然知之甚少。在其1亿年的历史中，贝壳类和金枪鱼已经成功地在近岸和深海栖息地之间多次过渡。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特殊的机会。该项目将提供迄今为止关于这种辐射的最详细的系统发育研究，为今后调查深海鱼类种群多样化的方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式组，也为系统发育实验设计的分子标记筛选设定了新的标准。在系统发育推论中，一个常见的问题涉及到在特定研究中使用的基因的选择。这个项目将经验地描述先验地为给定问题筛选标记的效用，并展示当不仔细检查基因座时不正确但得到有力支持的推论的可能性。这提供了一个客观的衡量标准，用于筛选适用于任何分类类群的系统发育问题的序列数据的实用性。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，并进一步向博物馆藏品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.