Abstract
Phylogenetic tree reconciliation is a powerful approach for inferring evolutionary events like gene duplication, horizontal gene transfer, and gene loss, which are fundamental to our understanding of molecular evolution. While Duplication-Loss (DL) reconciliation leads to a unique maximum-parsimony solution, Duplication-Transfer-Loss (DTL) reconciliation yields a multitude of optimal solutions, making it difficult the infer the true evolutionary history of the gene family.
Here, we present an effective, efficient, and scalable method for dealing with this fundamental problem in DTL reconciliation. Our approach works by sampling the space of optimal reconciliations uniformly at random and aggregating the results. We present an algorithm to efficiently sample the space of optimal reconciliations uniformly at random in O(mn 2) time, where m and n denote the number of genes and species, respectively. We use these samples to understand how different optimal reconciliations vary in their node mapping and event assignments, and to investigate the impact of varying event costs.
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References
Storm, C.E.V., Sonnhammer, E.L.L.: Automated ortholog inference from phylogenetic trees and calculation of orthology reliability. Bioinformatics 18(1), 92–99 (2002)
Koonin, E.V.: Orthologs, paralogs, and evolutionary genomics. Annual Review of Genetics 39(1), 309–338 (2005)
Wapinski, I., Pferrer, A., Friedman, N., Regev, A.: Natural history and evolutionary principles of gene duplication in fungi. Nature 449, 54–61 (2007)
van der Heijden, R., Snel, B., van Noort, V., Huynen, M.: Orthology prediction at scalable resolution by phylogenetic tree analysis. BMC Bioinformatics 8(1), 83 (2007)
Vilella, A.J., Severin, J., Ureta-Vidal, A., Heng, L., Durbin, R., Birney, E.: Ensemblcompara genetrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Research 19(2), 327–335 (2009)
Sennblad, B., Lagergren, J.: Probabilistic orthology analysis. Syst. Biol. 58(4), 411–424 (2009)
Chen, K., Durand, D., Farach-Colton, M.: Notung: dating gene duplications using gene family trees. In: RECOMB, pp. 96–106 (2000)
David, L.A., Alm, E.J.: Rapid evolutionary innovation during an archaean genetic expansion. Nature 469, 93–96 (2011)
Rasmussen, M.D., Kellis, M.: A bayesian approach for fast and accurate gene tree reconstruction. Molecular Biology and Evolution 28(1), 273–290 (2011)
Burleigh, J.G., Bansal, M.S., Eulenstein, O., Hartmann, S., Wehe, A., Vision, T.J.: Genome-scale phylogenetics: Inferring the plant tree of life from 18,896 gene trees. Syst. Biol. 60(2), 117–125 (2011)
Goodman, M., Czelusniak, J., Moore, G.W., Romero-Herrera, A.E., Matsuda, G.: Fitting the gene lineage into its species lineage. a parsimony strategy illustrated by cladograms constructed from globin sequences. Systematic Zoology 28, 132–163 (1979)
Page, R.D.M.: Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol. 43(1), 58–77 (1994)
Bonizzoni, P., Vedova, G.D., Dondi, R.: Reconciling a gene tree to a species tree under the duplication cost model. Theor. Comput. Sci. 347(1-2), 36–53 (2005)
Górecki, P., Tiuryn, J.: Dls-trees: A model of evolutionary scenarios. Theor. Comput. Sci. 359, 378–399 (2006)
Chauve, C., Doyon, J.P., El-Mabrouk, N.: Gene family evolution by duplication, speciation, and loss. J. Comput. Biol. 15(8), 1043–1062 (2008)
Gorbunov, K.Y., Liubetskii, V.A.: Reconstructing genes evolution along a species tree. Molekuliarnaia Biologiia 43(5), 946–958 (2009)
Doyon, J.-P., Scornavacca, C., Gorbunov, K.Y., Szöllősi, G.J., Ranwez, V., Berry, V.: An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers. In: Tannier, E. (ed.) RECOMB-CG 2010. LNCS, vol. 6398, pp. 93–108. Springer, Heidelberg (2010)
Tofigh, A., Hallett, M.T., Lagergren, J.: Simultaneous identification of duplications and lateral gene transfers. IEEE/ACM Trans. Comput. Biology Bioinform. 8(2), 517–535 (2011)
Tofigh, A.: Using Trees to Capture Reticulate Evolution: Lateral Gene Transfers and Cancer Progression. PhD thesis, KTH Royal Institute of Technology (2009)
Chen, Z.Z., Deng, F., Wang, L.: Simultaneous identification of duplications, losses, and lateral gene transfers. IEEE/ACM Trans. Comput. Biology Bioinform. 9(5), 1515–1528 (2012)
Bansal, M.S., Alm, E.J., Kellis, M.: Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics 28(12), 283–291 (2012)
Stolzer, M., Lai, H., Xu, M., Sathaye, D., Vernot, B., Durand, D.: Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees. Bioinformatics 28(18), 409–415 (2012)
Charleston, M.: Jungles: A new solution to the host-parasite phylogeny reconciliation problem. Mathematical Biosciences 149, 191–223 (1998)
Ronquist, F.: Parsimony analysis of coevolving species associations. In: Page, R.D.M. (ed.) Tangled Trees: Phylogeny, Cospeciation and Coevolution, pp. 22–64. The University of Chicago Press (2003)
Merkle, D., Middendorf, M., Wieseke, N.: A parameter-adaptive dynamic programming approach for inferring cophylogenies. BMC Bioinformatics 11(suppl. 1), S60 (2010)
Conow, C., Fielder, D., Ovadia, Y., Libeskind-Hadas, R.: Jane: a new tool for the cophylogeny reconstruction problem. Algorithm. Mol. Biol. 5(1), 16 (2010)
Ovadia, Y., Fielder, D., Conow, C., Libeskind-Hadas, R.: The cophylogeny reconstruction problem is np-complete. J. Comput. Biol. 18(1), 59–65 (2011)
Rutschmann, F.: Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times. Divers. Distrib. 12(1), 35–48 (2006)
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Bansal, M.S., Alm, E.J., Kellis, M. (2013). Reconciliation Revisited: Handling Multiple Optima When Reconciling with Duplication, Transfer, and Loss. In: Deng, M., Jiang, R., Sun, F., Zhang, X. (eds) Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science(), vol 7821. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-37195-0_1
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DOI: https://doi.org/10.1007/978-3-642-37195-0_1
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