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Statistical Consistency of Coalescent-Based Species Tree Methods Under Models of Missing Data

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Comparative Genomics (RECOMB-CG 2017)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10562))

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Abstract

The estimation of species trees from multiple genes is complicated by processes such as incomplete lineage sorting, duplication and loss, and horizontal gene transfer, that result in gene trees that differ from the species tree. Methods to estimate species trees in the presence of gene tree discord resulting from incomplete lineage sorting (ILS) have been developed and proved to be statistically consistent when gene tree discord is due only to ILS and every gene tree has the full set of species. Here we address statistical consistency of coalescent-based species tree estimation methods when gene trees are missing species, i.e., in the presence of missing data.

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Acknowledgements

MN was supported by NSF grants DBI-1461364, CCF-1535977 and AF:1513629 and by a fellowship from the CompGen initiative in the Coordinated Science Laboratory at UIUC. JC was supported by the Mathematics Department at UIUC.

A great deal of thanks is owed to our advisor, Dr. Tandy Warnow, who guided this manuscript from start to finish and pushed us to leave no stone unturned.

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Authors and Affiliations

  1. Department of Statistics, University of Illinois at Urbana-Champaign, 725 S. Wright St., Champaign, IL, 61820, USA

    Michael Nute

  2. Department of Mathematics, University of Illinois at Urbana-Champaign, 1409 W. Green St., Urbana, IL, 61801, USA

    Jed Chou

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  1. Michael Nute
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Correspondence to Michael Nute .

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Editors and Affiliations

  1. University of Campinas, Campinas, São Paulo, Brazil

    Joao Meidanis

  2. Rice University, Houston, Texas, USA

    Luay Nakhleh

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Nute, M., Chou, J. (2017). Statistical Consistency of Coalescent-Based Species Tree Methods Under Models of Missing Data. In: Meidanis, J., Nakhleh, L. (eds) Comparative Genomics. RECOMB-CG 2017. Lecture Notes in Computer Science(), vol 10562. Springer, Cham. https://doi.org/10.1007/978-3-319-67979-2_15

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  • DOI: https://doi.org/10.1007/978-3-319-67979-2_15

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  • Publisher Name: Springer, Cham

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  • Online ISBN: 978-3-319-67979-2

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