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    Impact of Rates of Gene Duplication and Domain Shuffling on Species Tree Inference with Gene Tree Parsimony

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    Author
    Shi, Tao
    Issue Date
    2013
    Keywords
    Gene duplication
    Gene tree
    Species tree
    Ecology & Evolutionary Biology
    Domain architecture
    Advisor
    Sanderson, Michael J.
    
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    Show full item record
    Publisher
    The University of Arizona.
    Rights
    Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author.
    Embargo
    Release after 02-Feb-2014
    Abstract
    Genome sequencing technologies are providing huge quantities of data for phylogenetic inference. However, most phylogenomic studies exclude gene families, because many have a complicated history of gene duplication/loss and structural change by domain shuffling, especially in deep phylogenies. Gene tree parsimony (GTP) methods, which seek the species tree that minimizes the cost of gene duplication, have been successfully applied to gene families with frequent duplication history. Their utility and performance in the context of gene families with complex histories of gene duplication and domain reshuffling remains unclear. In this study, we analyzed 4389 gene families from six angiosperm genomes encompassing a wide range of duplication rates, and a broad diversity of domain architecture. Overall species tree inference accuracy increased monotonically with the inclusion of more gene trees, and high accuracy was achieved with 50-100 gene trees. The rate of gene duplication strongly influences species tree inference accuracy, with the highest accuracy at either very low or very high rates of duplication and lowest accuracy centered around one duplication per branch in the unrooted species tree. This is the opposite of the relationship between substitution rates on tree construction accuracy, in which intermediate rates have highest accuracy. Accuracy is generally higher in gene families with high domain architecture diversity but has high variance in families with relatively low domain architecture diversity. The latter is probably due to the high variation of gene duplication number for those gene families. We close with some discussion of potential impacts of domain evolution on phylogenomic reconstruction protocols in general, including its effect on alignment.
    Type
    text
    Electronic Thesis
    Degree Name
    M.S.
    Degree Level
    masters
    Degree Program
    Graduate College
    Ecology & Evolutionary Biology
    Degree Grantor
    University of Arizona
    Collections
    Master's Theses

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