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

论文研究：评估与线粒体和核糖体相互作用的核位点之间深层两栖动物关系的基​​因和位点特异性支持

• 批准号: 1601586
• 负责人: David Weisrock
• 金额: $ 1.9万
• 依托单位: University of Kentucky Research Foundation
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-07-01 至 2018-06-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1601586&HistoricalAwards=false
• 关键词: DISSERTATION; RESEARCH; Assessing; gene; site

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.

地球上的生命可以追溯到一个共同的祖先，生活在近40亿年前。然而今天，生命已经多样化成数以千万计的物种。重建这些进化关系是系统发生学的目标，其见解对生物学的几乎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生物学领域，现在可以轻松生成任何生物体的基因组规模数据。然而，仅仅收集更多的遗传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与其他基因不同的进化历史。该项目解决了哪些基因以及这些基因中的哪些DNA位置对于解决两栖动物的深层关系最有信息量的问题，相反，这可能会产生误导。两栖动物（青蛙、蝾螈和螈）是一个古老而多样的类群，代表了重建深层进化史的许多困难。三个两栖目之间的关系已经被证明是脊椎动物进化史上最难解决的部分之一。这项工作可以作为一个总体框架，解决棘手的问题，在生物遗传学和生物信息学，高通量测序分析和基于模型的系统发育重建-在这个后基因组时代的关键技能的研究生培训建设的重要途径。这项研究将整合来自阿巴拉契亚和肯塔基州农村传统上代表性不足的群体的本科研究人员。这项研究对研究两栖动物的进化生物学家有着广泛的兴趣，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育良好的两栖动物系统，其中先前对完整线粒体基因组，核核糖体RNA和300个pupiran中性核外显子的分析都强烈支持基础两栖动物分歧的冲突场景。该项目测试了线粒体和核糖体基因及其核编码的功能对应物由于线粒体和核基因组之间的补偿性共同进化而支持相同的树形拓扑结构的假设。利用基因组资源，研究人员将开发一种靶向捕获试剂盒，对225个核基因的多个外显子进行测序，这些基因在功能上与144个两栖动物分类群中的核糖体和核糖体相互作用，代表每个主要谱系。检查不同的序数间拓扑结构在每个位点的相对支持，并与这些核基因座的哪些部分物理上与rRNA或蛋白质编码的蛋白质相互作用的知识，该项目将测试是否特定的核编码基因产生冲突的拓扑结构，因为细胞器的结构和功能的限制。