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Topological Signatures for Population Admixture

  • Laxmi ParidaEmail author
  • Filippo Utro
  • Deniz Yorukoglu
  • Anna Paola Carrieri
  • David Kuhn
  • Saugata Basu
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, 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.

Keywords

Leaf Node Homology Group Homology Class Population Admixture Admixture Mapping 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer International Publishing Switzerland 2015

Authors and Affiliations

  • Laxmi Parida
    • 1
    Email author
  • Filippo Utro
    • 1
  • Deniz Yorukoglu
    • 2
  • Anna Paola Carrieri
    • 3
  • David Kuhn
    • 4
  • Saugata Basu
    • 5
  1. 1.Computational GenomicsIBM T.J. Watson Research CenterYorktown HeightsUSA
  2. 2.Department of Computer ScienceMassachusetts Institute of TechnologyCambridgeUSA
  3. 3.Department of Computer ScienceUniversity of Milano-BicoccaMilanItaly
  4. 4.USDA-ARS Subtropical Horticultural Research StationMiamiUSA
  5. 5.Department of MathematicsPurdue UniversityWest LafayetteUSA

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