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Topological Signatures for Population Admixture

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Book cover Research in Computational Molecular Biology (RECOMB 2015)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9029))

Abstract

As populations with multilinear transmission (i.e., mixing of genetic material from two parents, say) evolve over generations, the genetic transmission lines constitute complicated networks. In contrast, unilinear transmission leads to simpler network structures (trees). The genetic exchange in multilinear transmission is further influenced by migration, incubation, mixing and so on. The task we address in the paper is to tease apart subtle admixtures from the usual interrelationships of related populations. We present a combinatorial approach based on persistence in topology to detect admixture in populations. We show, based on controlled simulations, that topological characteristics have the potential for detecting subtle admixture in related populations. We then apply the technique successfully to a set of avocado germplasm data indicating that the approach has the potential for novel characterizations of relatedness in populations. We believe that this approach also has the potential for not only detecting but also discriminating ancient from recent admixture.

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Author information

Authors and Affiliations

  1. Computational Genomics, IBM T.J. Watson Research Center, Yorktown Heights, NY, USA

    Laxmi Parida & Filippo Utro

  2. Department of Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA

    Deniz Yorukoglu

  3. Department of Computer Science, University of Milano-Bicocca, Milan, Italy

    Anna Paola Carrieri

  4. USDA-ARS Subtropical Horticultural Research Station, Miami, FL, USA

    David Kuhn

  5. Department of Mathematics, Purdue University, West Lafayette, IN, USA

    Saugata Basu

Authors
  1. Laxmi Parida
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  2. Filippo Utro
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  3. Deniz Yorukoglu
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  4. Anna Paola Carrieri
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  5. David Kuhn
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  6. Saugata Basu
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Corresponding author

Correspondence to Laxmi Parida .

Editor information

Editors and Affiliations

  1. National Center of Biotechnology Information, Bethesda, Maryland, USA

    Teresa M. Przytycka

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© 2015 Springer International Publishing Switzerland

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Parida, L., Utro, F., Yorukoglu, D., Carrieri, A.P., Kuhn, D., Basu, S. (2015). Topological Signatures for Population Admixture. In: Przytycka, T. (eds) Research in Computational Molecular Biology. RECOMB 2015. Lecture Notes in Computer Science(), vol 9029. Springer, Cham. https://doi.org/10.1007/978-3-319-16706-0_27

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  • DOI: https://doi.org/10.1007/978-3-319-16706-0_27

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-16705-3

  • Online ISBN: 978-3-319-16706-0

  • eBook Packages: Computer ScienceComputer Science (R0)

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