Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer

Authors Mathieu Gascon, Nadia El-Mabrouk

Thumbnail PDF


  • Filesize: 0.97 MB
  • 20 pages

Document Identifiers

Author Details

Mathieu Gascon
  • Département d'informatique et de recherche opérationnelle (DIRO), Université de Montréal, Canada
Nadia El-Mabrouk
  • DIRO, Université de Montréal, Canada

Cite AsGet BibTex

Mathieu Gascon and Nadia El-Mabrouk. Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 5:1-5:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)


Gene transfer between the mitochondrial and nuclear genome of the same species, called endosymbiotic gene transfer (EGT), is a mechanism which has largely shaped gene contents in eukaryotes since a unique ancestral endosymbiotic event know to be at the origin of all mitochondria. The gene tree-species tree reconciliation model has been recently extended to account for EGTs: given a binary gene tree and a binary species tree, the EndoRex software outputs an optimal DLE-Reconciliation, that is an embedding of the gene tree into the species tree inducing a most parsimonious history of Duplications, Losses and EGT events. Here, we provide the first algorithmic study for DLE-Reconciliation in the case of a multifurcated (non-binary) gene tree. We present a general two-steps method: first, ignoring the mitochondrial-nuclear (or 0-1) labeling of leaves, output a binary resolution minimizing the DL-Reconciliation and, for each resolution, assign a known number of 0s and 1s to the leaves in a way minimizing EGT events. While Step 1 corresponds to the well studied non-binary DL-Reconciliation problem, the complexity of the formal label assignment problem related to Step 2 is unknown. Here, we show it is NP-complete even for a single polytomy (non-binary node). We then provide a heuristic which is exact for the unitary cost of operations, and a polynomial-time algorithm for solving a polytomy in the special case where genes are specific to a single genome (mitochondrial or nuclear) in all but one species.

Subject Classification

ACM Subject Classification
  • Applied computing → Molecular evolution
  • Reconciliation
  • Duplication
  • Endosymbiotic gene transfer
  • Multifurcated gene tree
  • Polytomy


  • Access Statistics
  • Total Accesses (updated on a weekly basis)
    PDF Downloads


  1. Y. Anselmetti, N. El-Mabrouk, M. Lafond, and A. Ouangraoua. Gene tree and species tree reconciliation with endosymbiotic gene transfer. Bioinformatics, 37(SI-1):i120-i132, 2021. Google Scholar
  2. W.C. Chang and O. Eulenstein. Reconciling gene trees with apparent polytomies. In D.Z. Chen and D. T. Lee, editors, Proceedings of the 12th Conference on Computing and Combinatorics (COCOON), volume 4112 of Lecture Notes in Computer Science, pages 235-244, 2006. Google Scholar
  3. C. Colijn and G. Plazzotta. A metric on phylogenetic tree shapes. Systematic Biology, 67(1):113-126, 2018. Google Scholar
  4. D. Durand, B.V. Haldórsson, and B. Vernot. A hybrid micro-macroevolutionary approach to gene tree reconstruction. Journal of Computational Biology, 13:320-335, 2006. Google Scholar
  5. N. El-Mabrouk and E. Noutahi. Bioinformatics and Phylogenetics: Seminal Contributions of Bernard Moret, chapter Gene Family Evolution - An Algorithmic Framework, pages 87-119. Springer International Publishing, t. warnow edition, 2019. Google Scholar
  6. M.W. Hahn. Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biology, 8(7):R141, 2007. Google Scholar
  7. S. Kannan, I. Rogozin, and E. Koonin. MitoCOGs: clusters of orthologous genes from mitochondria and implications for the evolution of eukaryotes. BMC Evolutionary Biology, 14(11):1-16, 2014. Google Scholar
  8. M. Lafond, N. El-Mabrouk, K.T. Huber, and V. Moulton. The complexity of comparing mutiply-labelled trees by extending phylogenetic-tree metrics. Theoretical Computer Science, 760:15-34, 2018. Google Scholar
  9. M. Lafond, E. Noutahi, and N. El-Mabrouk. Efficient Non-Binary Gene Tree Resolution with Weighted Reconciliation Cost. In Roberto Grossi and Moshe Lewenstein, editors, 27th Annual Symposium on Combinatorial Pattern Matching (CPM 2016), volume 54 of Leibniz International Proceedings in Informatics (LIPIcs), pages 14:1-14:12, Dagstuhl, Germany, 2016. Schloss Dagstuhl-Leibniz-Zentrum fuer Informatik. Google Scholar
  10. M. Lafond, K.M. Swenson, and N. El-Mabrouk. An optimal reconciliation algorithm for gene trees with polytomies. In LNCS, volume 7534 of WABI, pages 106-122, 2012. Google Scholar
  11. J. Sabir, R. Jansen, D. Arasappan, et al. The nuclear genome of Rhazya stricta and the evolution of alkaloid diversity in a medically relevant clade of Apocynaceae. Scientific Reports, 6(1):33782, 2007. Google Scholar
  12. Y. Zheng and L. Zhang. Reconciliation with nonbinary gene trees revisited. J. ACM, 64(4), August 2017. Google Scholar