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Couplet Supertree Based Species Tree Estimation

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Bioinformatics Research and Applications (ISBRA 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9096))

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Abstract

Inference of a species tree from multi-locus gene trees having topological incongruence due to incomplete lineage sorting (ILS), is currently performed by either consensus (supertree), parsimony analysis (minimizing deep coalescence), or statistical methods. However, statistical approaches involve huge computational complexity. Accuracy of approximation heuristics used in either consensus or parsimony analysis, also varies considerably. We propose COSPEDSpec, a novel two stage species tree estimation method, combining both consensus and parsimony approaches. First stage uses our earlier proposed couplet supertree technique COSPEDTree [2][3], whereas the second stage proposes a greedy heuristic to refine a non-binary (unresolved) supertree into a binary species tree. During each iteration, it reduces the number of extra lineages between the current species tree and the input gene trees, thus modeling ILS as the cause of gene tree / species tree incongruence. COSPEDSpec incurs time and space complexity lower or equal to the reference methods. For large scale datasets having hundreds of taxa and thousands of gene trees, COSPEDSpec produces species trees with lower branch dissimilarities and much less computation.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, Indian Institute of Technology, Kharagpur, WB, 721302, India

    Sourya Bhattacharyya & Jayanta Mukhopadhyay

Authors
  1. Sourya Bhattacharyya
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  2. Jayanta Mukhopadhyay
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Corresponding author

Correspondence to Sourya Bhattacharyya .

Editor information

Editors and Affiliations

  1. Georgia State University, Atlanta, USA

    Robert Harrison

  2. Old Dominion University, Norfolk, USA

    Yaohang Li

  3. University of Connecticut, Storrs, Connecticut, USA

    Ion Măndoiu

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Bhattacharyya, S., Mukhopadhyay, J. (2015). Couplet Supertree Based Species Tree Estimation. In: Harrison, R., Li, Y., Măndoiu, I. (eds) Bioinformatics Research and Applications. ISBRA 2015. Lecture Notes in Computer Science(), vol 9096. Springer, Cham. https://doi.org/10.1007/978-3-319-19048-8_5

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  • DOI: https://doi.org/10.1007/978-3-319-19048-8_5

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-19047-1

  • Online ISBN: 978-3-319-19048-8

  • eBook Packages: Computer ScienceComputer Science (R0)

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