Abstract
Gene duplications are a dominant force in creating genetic novelty, and studying their evolutionary history is benefiting various research areas. The gene duplication model, which was introduced more than 40 years ago, is widely used to infer duplication histories by resolving the discordance between the evolutionary history of a gene family and the species tree through which this family has evolved. Today, for many gene families lower bounds on the number of gene duplications that have occurred along each edge of the species tree, called duplication scenarios, can be derived, for example from genome duplications. Recently, the gene duplication model has been augmented to include duplication scenarios and to address the question of whether such a scenario is feasible for a given gene family. Non-feasibility of a duplication scenario for a gene family can provide a strong indication that this family might not be well-resolved, and identifying well-resolved gene families is a challenging task in evolutionary biology. However, genome duplications are often followed by episodes of gene losses, and lost genes can explain non-feasible duplication scenarios. Here, we address this major shortcoming of the augmented duplication model, by proposing a gene duplication model that incorporates duplication-loss scenarios. We describe efficient algorithms that decide whether a duplication-loss scenario is feasible for a gene family; and if so, compute a gene tree for the family that infers the minimum duplication-loss events satisfying the scenario.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsNotes
- 1.
When it is clear from the context, the superscript G is omitted for clarity in \(\gamma \), \(\sigma \), \(\delta \) and \(\beta \).
- 2.
We assume that the maximum is \(-\infty \) if the set of s-feasible trees is empty.
References
Akerborg, O., Sennblad, B., Arvestad, L., Lagergren, J.: Simultaneous bayesian gene tree reconstruction and reconciliation analysis. Proc. Natl. Acad. Sci. U.S.A. 106(14), 5714–5719 (2009)
Altenhoff, A.M., Dessimoz, C.: Inferring orthology and paralogy. In: Anisimova, M. (ed.) Evolutionary Genomics, pp. 259–279. Humana Press, Totowa (2012)
Arvestad, L., Berglund, A.C., Lagergren, J., Sennblad, B.: Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 19(suppl1), 7–15 (2003)
Bininda-Emonds, O.R. (ed.): Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life. Computational Biology, vol. 4. Springer, Dordrecht (2004). https://doi.org/10.1007/978-1-4020-2330-9
Blanc, G., Wolfe, K.H.: Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16(7), 1667–1678 (2004)
Bonizzoni, P., Della Vedova, G., Dondi, R.: Reconciling a gene tree to a species tree under the duplication cost model. Theor. Comput. Sci. 347, 36–53 (2005)
Bordewich, M., Semple, C.: On the computational complexity of the rooted subtree prune and regraft distance. Ann. Comb. 8, 409–423 (2004)
Chauve, C., El-Mabrouk, N., Guéguen, L., Semeria, M., Tannier, E.: Duplication, rearrangement and reconciliation: a follow-up 13 years later. In: Chauve, C., El-Mabrouk, N., Tannier, E. (eds.) Models and Algorithms for Genome Evolution. Computational Biology, vol. 19, pp. 47–62. Springer, London (2013). https://doi.org/10.1007/978-1-4471-5298-9_4
Chen, K., Durand, D., Farach-Colton, M.: NOTUNG: a program for dating gene duplications and optimizing gene family trees. J. Comput. Biol. 7(3–4), 429–447 (2000)
Dujon, B., et al.: Genome evolution in yeasts. Nature 430, 35–44 (2004)
Eulenstein, O.: Vorhersage von Genduplikationen und deren Entwicklung in der Evolution. Ph.D. thesis, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany (1998)
Eulenstein, O., Huzurbazar, S., Liberles, D.: Reconciling phylogenetic trees. In: Dittmar, L. (ed.) Evolution After Gene Duplication. Wiley, New York (2010)
Goodman, M., Czelusniak, J., Moore, G., Romero-Herrera, A., Matsuda, G.: Fitting the gene lineage into its species lineage. A parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28(2), 132–163 (1979)
Górecki, P., Eulenstein, O., Tiuryn, J.: Unrooted tree reconciliation: a unified approach. IEEE/ACM TCBB 10(2), 522–536 (2013)
Górecki, P., Tiuryn, J.: DLS-trees: a model of evolutionary scenarios. Theor. Comput. Sci. 359(1–3), 378–399 (2006)
Huson, D.H., Scornavacca, C.: A survey of combinatorial methods for phylogenetic networks. Genome Biol. Evol. 3, 23–35 (2011)
Ihara, K., et al.: Evolution of the archaeal rhodopsins: evolution rate changes by gene duplication and functional differentiation. J. Mol. Biol. 285(1), 163–174 (1999)
Kamneva, O.K., Knight, S.J., Liberles, D.A., Ward, N.L.: Analysis of genome content evolution in PVC bacterial super-phylum: assessment of candidate genes associated with cellular organization and lifestyle. Genome Biol. Evol. 4(12), 1375–1390 (2012)
Kamneva, O.K., Ward, N.L.: Reconciliation approaches to determining HGT, duplications, and losses in gene trees. In: Michael Goodfellow, I.S., Chun, J. (eds.) New Approaches to Prokaryotic Systematics, Methods in Microbiology, Chap. 9, vol. 41, pp. 183–199. Academic Press, Cambridge (2014)
Koonin, E.V.: Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet. 39, 309–338 (2005)
Maddison, W.P.: Gene trees in species trees. Syst. Biol. 46(3), 523–536 (1997)
Markin, A., Vadali, V.S.K.T., Eulenstein, O.: Solving the gene duplication feasibility problem in linear time. In: Wang, L., Zhu, D. (eds.) COCOON 2018. LNCS, vol. 10976, pp. 378–390. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-94776-1_32
Ohno, S.: Evolution by Gene Duplication. Springer, Heidelberg (1970). https://doi.org/10.1007/978-3-642-86659-3
Page, R.: From gene to organismal phylogeny: reconciled trees and the gene tree/species tree problem. Mol. Phylogenet. Evol. 7(2), 231–240 (1997)
Renny-Byfield, S., Wendel, J.F.: Doubling down on genomes: polyploidy and crop plants. Am. J. Bot. 101(10), 1711–1725 (2014)
Thornton, K., Long, M.: Rapid divergence of gene duplicates on the Drosophila melanogaster X chromosome. Mol. Biol. Evol. 19(6), 918–925 (2002)
Zhang, L.: From gene trees to species trees II: species tree inference by minimizing deep coalescence events. IEEE/ACM TCBB 8, 1685–1691 (2011)
Zhang, L.: On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. J. Comput. Biol. 4(2), 177–187 (1997)
Acknowledgments
The support was provided by the National Science Center grant 2017/27/B/ST6/02720 and the National Science Foundation under Grant No. 1617626.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2019 Springer Nature Switzerland AG
About this paper
Cite this paper
Górecki, P., Markin, A., Eulenstein, O. (2019). Feasibility Algorithms for the Duplication-Loss Cost. In: Du, DZ., Duan, Z., Tian, C. (eds) Computing and Combinatorics. COCOON 2019. Lecture Notes in Computer Science(), vol 11653. Springer, Cham. https://doi.org/10.1007/978-3-030-26176-4_17
Download citation
DOI: https://doi.org/10.1007/978-3-030-26176-4_17
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-26175-7
Online ISBN: 978-3-030-26176-4
eBook Packages: Computer ScienceComputer Science (R0)