More Web Proxy on the site http://driver.im/

article

Simultaneous Identification of Duplications, Losses, and Lateral Gene Transfers

Authors:

Zhi-Zhong Chen,

Lusheng WangAuthors Info & Claims

IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), Volume 9, Issue 5

Pages 1515 - 1528

https://doi.org/10.1109/TCBB.2012.79

Published: 01 September 2012 Publication History

Abstract

We give a fixed-parameter algorithm for the problem of enumerating all minimum-cost LCA-reconciliations involving gene duplications, gene losses, and lateral gene transfers (LGTs) for a given species tree S and a given gene tree G. Our algorithm can work for the weighted version of the problem, where the costs of a gene duplication, a gene loss, and an LGT are left to the user's discretion. The algorithm runs in O(m+3^{k/c} n) time, where m is the number of vertices in S, n is the number of vertices in G, c is the smaller between a gene duplication cost and an LGT cost, and k is the minimum cost of an LCA-reconciliation between S and G. The time complexity is indeed better if the cost of a gene loss is greater than 0. In particular, when the cost of a gene loss is at least 0.614c, the running time of the algorithm is O(m+2.78^{k/c}n).

References

[1]

L. Arvestad, J. Lagergren, and B. Sennblad, "The Gene Evolution Model and Computing Its Associated Probabilities," J. ACM, vol. 56, no. 2, pp. 1-44, 2009.

Digital Library

[2]

M. Bansal and O. Eulenstein, "The Multiple Gene Duplication Problem Revisited," Bioinformatics, vol. 24, pp. 132-138, 2008.

Digital Library

[3]

H. Birin, Z. Gal-Or, I. Elias, and T. Tuller, "Inferring Horizontal Transfers in the Presence of Rearrangements by the Minimum Evolution Criterion," Bioinformatics, vol. 24, no. 6, pp. 826-832, 2008.

Digital Library

[4]

A. Boc, H. Philippe, and V. Makarenkov, "Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity," Systematic Biology, vol. 59, no. 2, pp. 195-211, 2010.

[5]

R. Bock, "The Give-and-Take of DNA," Trends in Plant Science, vol. 15, no. 1, pp. 11-22, 2010.

[6]

K. Chen, D. Durand, and M. Farach-Colton, "NOTUNG: A Program for Dating Gene Duplications and Optimizing Gene Family Trees," J. Computational Biology, vol. 7, pp. 429-447, 2000.

[7]

J. Cotton and R. Page, "Rates and Patterns of Gene Duplication and Loss in the Human Genome," Proc. Biological Sciences, vol. 272, no. 1560, pp. 277-283, 2005.

[8]

M. Csürös and I. Miklós, "A Probabilistic Model for Gene Content Evolution with Duplication, Loss, and Horizontal Transfer," Proc. 10th Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 206-220, 2006.

Digital Library

[9]

J. Demuth, T. De Bie, J. Stajich, N. Cristianini, and M. Hahn, "The Evolution of Mammalian Gene Families," PLoS One, vol. 1, no. 1, p. e85, 2006.

[10]

W. Doolittle and E. Bapteste, "Pattern Pluralism and the Tree of Life Hypothesis," Proc. Nat'l Academy of Sciences USA, vol. 104, no. 7, pp. 2043-2049, 2007.

[11]

J. Doyon, C. Scornavacca, K. Gorbunov, G. Szöllösi, V. Ranwez, and V. Berry, "An Efficient Algorithm Algorithm for Gene/ Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers," Proc. Int'l Conf. Comparative Genomics, pp. 93- 108, 2011.

Digital Library

[12]

M. Goodman, J. Czelusniak, G. Moore, A. Romero-Herrera, and G. Matsuda, "Fitting the Gene Lineage into its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences," Systematic Biology, vol. 28, no. 2, pp. 132-163, 1979.

[13]

P. Górecki, "Reconciliation Problems for Duplication, Loss and Horizontal Gene Transfer," Proc. Eighth Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 316-325, 2004.

Digital Library

[14]

R. Guigó, I. Muchnik, and T. Smith, "Reconstruction of Ancient Molecular Phylogeny," Molecular Phylogenetics and Evolution, vol. 6, no. 2, pp. 189-213, 1996.

[15]

D. Gusfield, K. Balasubramanian, and D. Naor, "Parametric Optimization of Sequence Alignment," Algorithmica, vol. 12, pp. 312-326, 1994.

[16]

D. Gusfield and P. Stelling, "Parametric and Inverse-Parametric Sequence Alignment with XPARAL," Methods in Enzymology, vol. 266, pp. 481-491, 1996.

[17]

M. Hahn, T. De Bie, J. Stajich, C. Nguyen, and N. Cristianini, "Estimating the Tempo and Mode of Gene Family Evolution from Comparative Genomic Data," Genome Research, vol. 15, no. 8, pp. 1153-1160, 2005.

[18]

A. Tofigh, M. Hallett, and J. Lagergren, "Simultaneous Identification of Duplications and Lateral Gene Transfers," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 8, no. 2, pp. 517-535, Mar./Apr. 2011.

Digital Library

[19]

M. Hallett and J. Lagergren, "New Algorithms for the Duplication-Loss Model," Proc. Fourth Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 138-146, 2000.

Digital Library

[20]

M. Hallett and J. Lagergren, "Efficient Algorithms for Lateral Gene Transfer Problems," Proc. Fifth Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB), pp. 149-156, 2001.

Digital Library

[21]

G. Jin, L. Nakhleh, S. Snir, and T. Tuller, "Maximum Likelihood of Phylogenetic Networks," Bioinformatics, vol. 22, no. 21, pp. 2604- 2611, 2006.

Digital Library

[22]

P. Keeling and J. Palmer, "Horizontal Gene Transfer in Eukaryotic Evolution," Nature Rev. Genetics, vol. 9, no. 8, pp. 605-618, 2008.

[23]

M. Lynch and J. Conery, "The Evolutionary Fate and Consequences of Duplicate Genes," Science, vol. 290, no. 5494, pp. 1151- 1155, 2000.

[24]

M. Lynch and J. Conery, "The Evolutionary Demography of Duplicate Genes," J. Structural and Functional Genomics, vol. 3, no. 1, pp. 35-44, 2003.

[25]

B. Ma, M. Li, and L. Zhang, "From Gene Trees to Species Trees," SIAM J. Computing, vol. 30, no. 3, pp. 729-752, 2000.

Digital Library

[26]

O. Matte-Tailliez, C. Brochier, P. Forterre, and H. Philippe, "Archaeal Phylogeny Based on Ribosomal Proteins," Molecular Biology and Evolution, vol. 19, no. 5, pp. 631-639, 2002.

[27]

D. Merkle and M. Middendorf, "Reconstruction of the Cophylogenetic History of Related Phylogenetic Trees with Divergence Timing Information," Theory in Biosciences, vol. 123, pp. 277-299, 2005.

[28]

D. Merkle, M. Middendorf, and N. Wieseke, "A Parameter-Adaptive Dynamic Programming Approach for Inferring Cophylogenies," BMC Bioinformatics, vol. 11(Suppl 1), p. S60, 2010.

[29]

L. Nakhleh, D. Ruths, and L. Wang, "RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer," Proc. 11th Int'l Computing and Combinatorics Conf. (COCOON '05), pp. 84-93, 2005.

Digital Library

[30]

R. Page and M. Charleston, "From Gene to Organismal Phylogeny: Reconciled Trees and the Gene Tree/Species Tree Problem," Molecular Phylogenetics and Evolution, vol. 7, no. 2, pp. 231-240, 1997.

[31]

L. Wang and J. Zhao, "Parametric Alignment of Ordered Trees," Bioinformatics, vol. 19, no. 17, pp. 2237-2245, 2003.

[32]

I. Wapinski, A. Pfeffer, N. Friedman, and A. Regev, "Natural History and Evolutionary Principles of Gene Duplication in Fungi," Nature, vol. 449, no. 7158, pp. 54-61, 2007.

[33]

L. Zhang, "On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies," J. Computational Biology, vol. 4, no. 2, pp. 177-187, 1997.

[34]

L. Zhang, Y. Ng, T. Wu, and Y. Zheng, "Network Model and Efficient Method for Detecting Relative Duplications or Horizontal Gene Transfers," Proc. IEEE First Int'l Conf. in Computational Advances in Bio and Medical Sciences (ISSABS), pp. 214-219, 2011.

Digital Library

Cited By

Mondal AKordi MBansal M(2020)A Supervised Machine Learning Approach for Distinguishing Between Additive and Replacing Horizontal Gene TransfersProceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics10.1145/3388440.3412428(1-11)Online publication date: 21-Sep-2020
https://dl.acm.org/doi/10.1145/3388440.3412428
Kordi MKundu SBansal MShi XBuck MMa JVeltri P(2019)On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic ReconciliationProceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics10.1145/3307339.3342168(514-523)Online publication date: 4-Sep-2019
https://dl.acm.org/doi/10.1145/3307339.3342168
Haack JZupke ERamirez AWu YLibeskind-Hadas R(2019)Computing the Diameter of the Space of Maximum Parsimony Reconciliations in the Duplication-Transfer-Loss ModelIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2018.284973216:1(14-22)Online publication date: 1-Jan-2019
https://dl.acm.org/doi/10.1109/TCBB.2018.2849732
Show More Cited By

Recommendations

A Characterization of the Set of Species Trees that Produce Anomalous Ranked Gene Trees

Ranked gene trees, which consider both the gene tree topology and the sequence in which gene lineages separate, can potentially provide a new source of information for use in modeling genealogies and performing inference of species trees. Recently, we ...
Simultaneous Identification of Duplications and Lateral Gene Transfers

The incongruency between a gene tree and a corresponding species tree can be attributed to evolutionary events such as gene duplication and gene loss. This paper describes a combinatorial model where so-called DTL-scenarios are used to explain the ...
Mathematical Properties of the Deep Coalescence Cost

In the minimizing-deep-coalescences (MDC) approach for species tree inference, a tree that has the minimal deep coalescence cost for reconciling a collection of gene trees is taken as an estimate of the species tree topology. The MDC method possesses ...

Comments

Please enable JavaScript to view thecomments powered by Disqus.

Information & Contributors

Information

Published In

cover image IEEE/ACM Transactions on Computational Biology and Bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics Volume 9, Issue 5

September 2012

287 pages

ISSN:1545-5963

Issue’s Table of Contents

Publisher

IEEE Computer Society Press

Washington, DC, United States

Publication History

Published: 01 September 2012

Published in TCBB Volume 9, Issue 5

Author Tags

Qualifiers

Article

Contributors

Other Metrics

View Article Metrics

Bibliometrics & Citations

Bibliometrics

Article Metrics

6
Total Citations
View Citations
63
Total Downloads

Downloads (Last 12 months)2
Downloads (Last 6 weeks)1

Reflects downloads up to 13 Dec 2024

Other Metrics

View Author Metrics

Citations

Cited By

Mondal AKordi MBansal M(2020)A Supervised Machine Learning Approach for Distinguishing Between Additive and Replacing Horizontal Gene TransfersProceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics10.1145/3388440.3412428(1-11)Online publication date: 21-Sep-2020
https://dl.acm.org/doi/10.1145/3388440.3412428
Kordi MKundu SBansal MShi XBuck MMa JVeltri P(2019)On Inferring Additive and Replacing Horizontal Gene Transfers Through Phylogenetic ReconciliationProceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics10.1145/3307339.3342168(514-523)Online publication date: 4-Sep-2019
https://dl.acm.org/doi/10.1145/3307339.3342168
Haack JZupke ERamirez AWu YLibeskind-Hadas R(2019)Computing the Diameter of the Space of Maximum Parsimony Reconciliations in the Duplication-Transfer-Loss ModelIEEE/ACM Transactions on Computational Biology and Bioinformatics10.1109/TCBB.2018.284973216:1(14-22)Online publication date: 1-Jan-2019
https://dl.acm.org/doi/10.1109/TCBB.2018.2849732
Zheng YZhang L(2017)Reconciliation With Nonbinary Gene Trees RevisitedJournal of the ACM10.1145/308851264:4(1-28)Online publication date: 17-Aug-2017
https://dl.acm.org/doi/10.1145/3088512
Zheng YZhang L(2014)Reconciliation with Non-binary Gene Trees RevisitedProceedings of the 18th Annual International Conference on Research in Computational Molecular Biology - Volume 839410.1007/978-3-319-05269-4_33(418-432)Online publication date: 2-Apr-2014
https://dl.acm.org/doi/10.1007/978-3-319-05269-4_33
Bansal MAlm EKellis M(2013)Reconciliation revisitedProceedings of the 17th international conference on Research in Computational Molecular Biology10.1007/978-3-642-37195-0_1(1-13)Online publication date: 7-Apr-2013
https://dl.acm.org/doi/10.1007/978-3-642-37195-0_1

View Options

Login options

Check if you have access through your login credentials or your institution to get full access on this article.

Full Access

Get this Article

View options

PDF

View or Download as a PDF file.

eReader

View online with eReader.

Media

Figures

Other

Tables

View Issue’s Table of Contents