DISSERTATION RESEARCH: Assessing gene- and site-specific support for deep amphibian relationships across nuclear loci that interact with mitochondria and ribosomes

地球上的生命可以追溯到一个生活在近40亿年前的共同祖先。然而今天，生命已经多样化成数千万种。重建这些进化关系是系统遗传学的目标，它的见解对生物学的几乎所有领域都至关重要。基因组学革命从根本上改变了历史上数据有限的分子系统发育领域，现在可以很容易地为任何生物体生成基因组规模的数据。然而，单纯地收集更多的基因数据本身并不足以解决生命之树上的困难分支，因为一些基因将支持不同的进化历史。这个项目解决的问题是，哪些基因以及这些基因中的哪些DNA位置对解决深层次的两栖动物关系最有帮助，反过来，哪些可能会产生误导。两栖动物（青蛙、蝾螈和无尾螈）是一个古老而多样的群体，它代表了重建深层系统发育的许多困难。三个两栖目之间的关系已被证明是脊椎动物系统发育中最难解决的部分之一。这项工作可以作为解决系统发育中棘手问题的一般框架，并为生物信息学、高通量测序分析和基于模型的系统发育重建的研究生培训建立重要途径-这是后基因组时代的关键技能。这项研究将整合来自阿巴拉契亚和肯塔基州农村地区传统上代表性不足的群体的本科生研究人员。该研究对两栖动物研究的进化生物学家具有广泛的意义，对两栖动物系统学的研究具有重要意义。它解决了我们如何分析基因组数据以准确重建深层进化关系的问题。研究人员将通过分析与线粒体和核糖体相互作用的核基因之间的拓扑支持的位点特异性模式，来测试关于线粒体和核基因组相互冲突的系统发育信号来源的假设。研究人员将使用一个发达的两栖动物系统，在这个系统中，先前对完整的线粒体基因组、核糖体RNA和300个假定的中性核外显子的分析都有力地支持了两栖动物基础分化的相互矛盾的假设。该项目验证了线粒体和核糖体基因及其核编码功能对应体由于线粒体和核基因组之间的代偿性共同进化而支持相同树拓扑结构的假设。利用基因组资源，研究人员将开发一种靶向捕获试剂盒，对代表每个主要谱系的144种两栖动物类群中与线粒体和核糖体相互作用的225个核基因的多个外显子进行测序。研究每个基因座中不同位点间序间拓扑的相对支持度，并了解这些核基因座的哪些部分与rRNA或线粒体编码蛋白物理相互作用，该项目将测试特定核编码基因是否由于细胞器结构和功能的限制而产生冲突的拓扑。

Life on Earth traces its origins back to a single common ancestor that lived nearly four billion years ago. Yet today, life has diversified into tens of millions of species. Reconstructing these evolutionary relationships is the aim of phylogenetics, and its insights are critical to nearly all areas of biology. The genomics revolution is radically altering the historically data-limited field of molecular phylogenetics and genome-scale data are now easily generated for any organism. Yet, simply collecting more genetic data, on its own, will not be sufficient to resolve difficult branches on the Tree of Life because some genes will support different evolutionary histories than others. This project addresses the questions of which genes and which DNA positions in those genes are most informative for resolving deep amphibian relationships, and conversely, which may be misleading. Amphibians (frogs, salamanders, and caecilians) are an ancient and diverse group typifying many of the difficulties of reconstructing deep phylogeny. The relationships among the three amphibian orders have proven one of the most difficult portions of the vertebrate phylogeny to resolve. This work may serve as a general framework for tackling thorny problems in phylogenetics and builds important avenues for graduate training in bioinformatics, high-throughput sequencing analysis, and model-based phylogenetic reconstruction - key skills in this post-genomic era. The research will integrate undergraduate researchers from traditionally under-represented groups across rural Appalachia and Kentucky. This research is of broad interest to evolutionary biologists working on amphibians, and stands to make important contributions to amphibian systematics. It addresses questions about how we analyze genomic data to accurately reconstruct deep evolutionary relationships. The researchers will test hypotheses about the source of conflicting phylogenetic signals from mitochondrial and nuclear genomes by analyzing site-specific patterns of topological support across nuclear genes that interact with the mitochondrion and ribosomes. The researchers will use a well-developed amphibian system in which previous analyses of complete mitochondrial genomes, nuclear ribosomal RNA, and 300 putatively neutral nuclear exons have each strongly supported conflicting scenarios for basal amphibian divergences. This project tests the hypothesis that mitochondrial and ribosomal genes and their nuclear-encoded functional counterparts support the same tree topologies due to compensatory co-evolution between mitochondrial and nuclear genomes. Leveraging genomic resources, the researchers will develop a targeted capture kit to sequence multiple exons of 225 nuclear genes that functionally interact with the mitochondrion and ribosomes in 144 amphibian taxa, representing each major lineage. Examining the relative support for different inter-ordinal topologies across sites in each locus, and with knowledge of which portions of these nuclear loci physically interact with rRNA or mitochondrial-encoded proteins, this project will test whether particular nuclear-encoded genes yield conflicting topologies because of constraints on organellar structure and function.