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Journal of Mathematical Biology

, Volume 77, Issue 5, pp 1459–1491 | Cite as

Reconstructing gene trees from Fitch’s xenology relation

  • Manuela Geiß
  • John Anders
  • Peter F. Stadler
  • Nicolas Wieseke
  • Marc HellmuthEmail author
Article

Abstract

Two genes are xenologs in the sense of Fitch if they are separated by at least one horizontal gene transfer event. Horizonal gene transfer is asymmetric in the sense that the transferred copy is distinguished from the one that remains within the ancestral lineage. Hence xenology is more precisely thought of as a non-symmetric relation: y is xenologous to x if y has been horizontally transferred at least once since it diverged from the least common ancestor of x and y. We show that xenology relations are characterized by a small set of forbidden induced subgraphs on three vertices. Furthermore, each xenology relation can be derived from a unique least-resolved edge-labeled phylogenetic tree. We provide a linear-time algorithm for the recognition of xenology relations and for the construction of its least-resolved edge-labeled phylogenetic tree. The fact that being a xenology relation is a heritable graph property, finally has far-reaching consequences on approximation problems associated with xenology relations.

Keywords

Fitch xenology Phylogenetic tree Least-resolved tree Rooted triples Informative triple sets Di-cograph Heritable graph property Forbidden induced subgraphs Recognition algorithm Fixed parameter tractable 

Mathematics Subject Classification

05C05 05C85 68R05 68R10 

Notes

Acknowledgements

We thank Maribel Hernández Rosales and her team for stimulating discussions. This work was funded in part by the BMBF-funded project “Center for RNA-Bioinformatics” (031A538A, de.NBI-RBC) and a travel grant from DAAD PROALMEX (Proj. No. 278966).

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Manuela Geiß
    • 1
    • 2
  • John Anders
    • 1
    • 2
  • Peter F. Stadler
    • 1
    • 2
    • 3
    • 4
    • 5
    • 6
    • 7
    • 8
  • Nicolas Wieseke
    • 9
  • Marc Hellmuth
    • 10
    • 11
    Email author
  1. 1.Bioinformatics Group, Department of Computer ScienceLeipzig UniversityLeipzigGermany
  2. 2.Interdisciplinary Center of BioinformaticsLeipzig UniversityLeipzigGermany
  3. 3.German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and SolutionsLeipzig UniversityLeipzigGermany
  4. 4.Leipzig Research Center for Civilization DiseasesLeipzig UniversityLeipzigGermany
  5. 5.Department of DiagnosticsFraunhofer Institute for Cell Therapy and Immunology – IZILeipzigGermany
  6. 6.Max-Planck-Institute for Mathematics in the SciencesLeipzigGermany
  7. 7.Inst. f. Theoretical ChemistryUniversity of ViennaWienAustria
  8. 8.Santa Fe InstituteSanta FeUSA
  9. 9.Swarm Intelligence and Complex Systems Group, Department of Computer ScienceLeipzig UniversityLeipzigGermany
  10. 10.Institute of Mathematics and Computer ScienceUniversity of GreifswaldGreifswaldGermany
  11. 11.Center for BioinformaticsSaarland UniversitySaarbrückenGermany

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