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Effect of Incomplete Lineage Sorting on Tree-Reconciliation-Based Inference of Gene Duplication

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Bioinformatics Research and Applications (ISBRA 2013)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7875))

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Abstract

Incomplete lineage sorting (ILS) gives rise to stochastic variation in the topology of a gene tree and hence introduces false duplication events when gene tree and species tree reconciliation method is used for inferring the duplication history of a gene family. We quantify the effect of ILS on inference of gene duplication by examining the expected number of false duplication events inferred from reconciling a random gene tree, which occurs with a probability predicted in coalescent theory, and the given species tree. We computationally analyze the relationships between the number of false duplication events inferred on a branch and its length in a species tree, and the relationships between the expected number of false duplication events in a species tree and its topological parameters. This study provides evidence that inference of gene duplication based on tree reconciliation was affected by ILS to a greater extent on an asymmetric species tree than on a symmetric one. Our findings also suggest that the bias caused by ILS in reconciliation-based inference of gene duplication might not be negligible. Hence, when gene duplication is inferred via tree reconciliation or any other method that takes gene tree topology into account, the ILS-induced bias should be examined cautiously.

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Authors and Affiliations

  1. Department of Mathematics, National University of Singapore, 10 Lower Kent Ridge, Singapore, 119076

    Yu Zheng & Louxin Zhang

Authors
  1. Yu Zheng
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  2. Louxin Zhang
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Editors and Affiliations

  1. Computer Science, Georgia State University, 34 Peachtree Street, Suite 1410, 30303, Atlanta, GA, USA

    Zhipeng Cai

  2. Computer Science, Iowa State University, 50011, Ames, IA, USA

    Oliver Eulenstein

  3. Bioinformatics and Genomics, University of North Carolina at Charlotte, 9201 University City Blvd, Suite 315, 28223, Charlotte, NC, USA

    Daniel Janies

  4. Physiology and Neurobiology, University of Connecticut, 75 North Eagleville Road, Unit 3156, 06269, Storrs, CT, USA

    Daniel Schwartz

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Zheng, Y., Zhang, L. (2013). Effect of Incomplete Lineage Sorting on Tree-Reconciliation-Based Inference of Gene Duplication. In: Cai, Z., Eulenstein, O., Janies, D., Schwartz, D. (eds) Bioinformatics Research and Applications. ISBRA 2013. Lecture Notes in Computer Science(), vol 7875. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38036-5_26

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  • DOI: https://doi.org/10.1007/978-3-642-38036-5_26

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-38035-8

  • Online ISBN: 978-3-642-38036-5

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