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生活在近40亿年前的一个共同祖先。然而，今天，生命已经多样化，形成了数千万个物种。重建这些进化关系是系统发育学的目标，它的洞察力几乎对生物学的所有领域都至关重要。基因组学革命正在从根本上改变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，仅仅收集更多的基因数据本身并不足以解决生命树上的困难分支，因为一些基因将支持与其他基因不同的进化史。这个项目解决的问题是，哪些基因和这些基因中的哪些DNA位置对于解决深层次的两栖动物关系最有信息，反之，哪些可能具有误导性。两栖动物(青蛙、火蜥蜴和盲肠动物)是一个古老而多样的类群，代表了重建深层系统发育的许多困难。事实证明，三个两栖动物目之间的关系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--后基因组时代的关键技能--的研究生培训建立重要途径。这项研究将包括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。这项研究对研究两栖动物的进化生物学家具有广泛的兴趣，并将对两栖动物系统学做出重要贡献。它解决了关于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特定的拓扑支持模式，来测试关于线粒体和核基因组中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展良好的两栖动物系统，在该系统中，之前对完整线粒体基因组、核核糖体RNA和300个假定为中性的核外显子的分析都有力地支持了两栖动物基础分歧的相互冲突的情景。该项目测试了这样的假设，即由于线粒体和核基因组之间的补偿性共同进化，线粒体和核糖体基因及其核编码的功能对应物支持相同的树状拓扑结构。利用基因组资源，研究人员将开发一种有针对性的捕获试剂盒，对225个核基因的多个外显子进行测序，这些外显子在功能上与144个两栖动物分类群的线粒体和核糖体相互作用，代表每个主要谱系。该项目研究了每个基因座上不同位置的不同序间拓扑的相对支持率，以及这些核基因的哪些部分与rRNA或线粒体编码蛋白物理上相互作用的知识，该项目将测试特定的核编码基因是否由于细胞器结构和功能的限制而产生相互冲突的拓扑。

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.