| 项目编号: | 1601586
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| 项目名称: | DISSERTATION RESEARCH: Assessing gene- and site-specific support for deep amphibian relationships across nuclear loci that interact with mitochondria and ribosomes |
| 作者: | David Weisrock
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| 承担单位: | University of Kentucky Research Foundation
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| 批准年: | 2016
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| 开始日期: | 2016-07-01
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| 结束日期: | 2018-06-30
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| 资助金额: | 18967
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| 资助来源: | US-NSF
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| 项目类别: | Standard Grant
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| 国家: | US
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| 语种: | 英语
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| 特色学科分类: | Biological Sciences - Environmental Biology
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| 英文关键词: | researcher
; gene
; phylogenetic
; research
; nuclear gene
; ribosome
; relative support
; deep evolutionary relationship
; project
; general framework
; ribosomal gene
; life
; particular nuclear-encoded gene
; evolutionary relationship
; genetic datum
; deep amphibian relationship
; nuclear locus
; complete mitochondrial genome
; topological support
; model-based phylogenetic reconstruction
; undergraduate researcher
; mitochondrial-encoded protein
; molecular phylogenetic
; phylogenetic signal
|
| 英文摘要: | 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. |
| 资源类型: | 项目
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| 标识符: | http://119.78.100.158/handle/2HF3EXSE/91915
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| Appears in Collections: | 全球变化的国际研究计划
科学计划与规划
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| Recommended Citation: | |
David Weisrock. DISSERTATION RESEARCH: Assessing gene- and site-specific support for deep amphibian relationships across nuclear loci that interact with mitochondria and ribosomes. 2016-01-01.
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