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An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree

Author Yao-ban Chan

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Yao-ban Chan
  • Melbourne Integrative Genomics / School of Mathematics and Statistics, The University of Melbourne, Australia

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Yao-ban Chan. An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 3:1-3:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
https://doi.org/10.4230/LIPIcs.WABI.2024.3

Abstract

The phylogenies of species and the genes they contain are similar but distinct, due to evolutionary events that affect genes but do not create new species. These events include gene duplication and loss, but also paralog exchange (non-allelic homologous recombination), where duplicate copies of a gene recombine. To account for paralog exchange, the evolutionary history of the genes must be represented in the form of a phylogenetic network. We reconstruct the interlinked evolution of the genes and species with reconciliations, which map the gene network into the species tree by explicitly accounting for these events. In previous work, we proposed the problem of reconciling a gene network and a species tree, but did not find an efficient solution for a general gene network. In this paper, we develop such a solution, and prove that it solves the most parsimonious reconciliation problem. Our algorithm is exponential only in the level of the gene network (with a base of 2), and we demonstrate that it is a practical solution through simulations. This allows, for the first time, a fine-grained study of the paralogy/orthology relationship between genes along their sequences.

Subject Classification

ACM Subject Classification
  • Applied computing → Computational biology
Keywords
  • Reconciliation
  • recombination
  • paralog exchange
  • phylogenetic network
  • gene duplication
  • gene loss

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References

  1. Magnus Bordewich, Celine Scornavacca, Nihan Tokac, and Mathias Weller. On the fixed parameter tractability of agreement-based phylogenetic distances. Journal of Mathematical Biology, 74:239-257, 2017. Google Scholar
  2. Débora YC Brandt, Christian D Huber, Charleston WK Chiang, and Diego Ortega-Del Vecchyo. The promise of inferring the past using the ancestral recombination graph. Genome Biology and Evolution, 16(2):evae005, 2024. Google Scholar
  3. Gabriel Cardona, Francesc Rossello, and Gabriel Valiente. Comparison of tree-child phylogenetic networks. IEEE/ACM Transactions on Computional Biology and Bioinformatics, 6(4):552-569, 2009. Google Scholar
  4. Yao-ban Chan, Vincent Ranwez, and Céline Scornavacca. Inferring incomplete lineage sorting, duplications, transfers and losses with reconciliations. Journal of Theoretical Biology, 432:1-13, 2017. Google Scholar
  5. Yao-ban Chan and Charles Robin. Reconciliation of a gene network and species tree. Journal of Theoretical Biology, 472:54-66, 2019. Google Scholar
  6. Antoine Claessens, William L Hamilton, Mihir Kekre, Thomas D Otto, Adnan Faizullabhoy, Julian C Rayner, and Dominic Kwiatkowski. Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of Var genes during mitosis. PLoS Genetics, 10(12):e1004812, 2014. Google Scholar
  7. Riccardo Dondi, Manuel Lafond, and Celine Scornavacca. Reconciling multiple genes trees via segmental duplications and losses. Algorithms for Molecular Biology, 14:1-19, 2019. Google Scholar
  8. Jean-Philippe Doyon, Celine Scornavacca, K Yu Gorbunov, Gergely J Szöllősi, Vincent Ranwez, and Vincent Berry. An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers. In RECOMB International Workshop on Comparative Genomics, pages 93-108. Springer, 2010. Google Scholar
  9. Benjamin Drinkwater, Angela Qiao, and Michael A Charleston. WiSPA: A new approach for dealing with widespread parasitism. arXiv preprint arXiv:1603.09415, 2016. Google Scholar
  10. Morris Goodman, John Czelusniak, G William Moore, Alejo E Romero-Herrera, and Genji Matsuda. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Systematic Biology, 28(2):132-163, 1979. Google Scholar
  11. Robert C Griffiths and Paul Marjoram. Ancestral inference from samples of DNA sequences with recombination. Journal of Computational Biology, 3(4):479-502, 1996. Google Scholar
  12. Damir Hasić and Eric Tannier. Gene tree reconciliation including transfers with replacement is NP-hard and FPT. Journal of Combinatorial Optimisation, 38(2):502-544, 2019. Google Scholar
  13. Damir Hasić and Eric Tannier. Gene tree species tree reconciliation with gene conversion. Journal of Mathematical Biology, 78(6):1981-2014, 2019. Google Scholar
  14. Melissa J Hubisz, Amy L Williams, and Adam Siepel. Mapping gene flow between ancient hominins through demography-aware inference of the ancestral recombination graph. PLoS Genetics, 16(8):e1008895, 2020. Google Scholar
  15. Daniel H Huson, Regula Rupp, and Celine Scornavacca. Phylogenetic networks: concepts, algorithms and applications. Cambridge University Press, 2010. Google Scholar
  16. Alexander L Lewanski, Michael C Grundler, and Gideon S Bradburd. The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics. PLoS Genetics, 20(1):e1011110, 2024. Google Scholar
  17. Qiuyi Li, Celine Scornavacca, Nicolas Galtier, and Yao-ban Chan. The multilocus multispecies coalescent: a flexible new model of gene family evolution. Systematic Biology, 2020. Google Scholar
  18. Ran Libeskind-Hadas, Yi-Chieh Wu, Mukul S Bansal, and Manolis Kellis. Pareto-optimal phylogenetic tree reconciliation. Bioinformatics, 30(12):i87-i95, 2014. Google Scholar
  19. Hugo Menet, Vincent Daubin, and Eric Tannier. Phylogenetic reconciliation. PLoS Computational Biology, 18(11):e1010621, 2022. Google Scholar
  20. Matthew D Rasmussen and Manolis Kellis. Unified modeling of gene duplication, loss, and coalescence using a locus tree. Genome Research, 22(4):755-765, 2012. Google Scholar
  21. Celine Scornavacca, Joan Carles Pons Mayol, and Gabriel Cardona. Fast algorithm for the reconciliation of gene trees and LGT networks. Journal of Theoretical Biology, 418:129-137, 2017. Google Scholar
  22. Thu-Hien To and Celine Scornavacca. Efficient algorithms for reconciling gene trees and species networks via duplication and loss events. BMC Genom., 16(10):S6, 2015. Google Scholar
  23. Yi-Chieh Wu, Matthew D Rasmussen, Mukul S Bansal, and Manolis Kellis. Most parsimonious reconciliation in the presence of gene duplication, loss, and deep coalescence using labeled coalescent trees. Genome Research, 24(3):475-486, 2014. Google Scholar
  24. Yufeng Wu. Coalescent-based species tree inference from gene tree topologies under incomplete lineage sorting by maximum likelihood. Evolution, 66(3):763-775, 2012. Google Scholar
  25. Louxin Zhang. On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. Journal of Computational Biology, 4(2):177-187, 1997. Google Scholar
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