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Open Access

Distances Between Phylogenetic Trees: A Survey

School of Information Science and Engineering, Central South University, Changsha 410083, China
Department of Computer Science and Engineering, Texas A&M University, College Station, Texas 77843-3112, USA
Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong, China
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Abstract

Phylogenetic trees have been widely used in the study of evolutionary biology for representing the tree-like evolution of a collection of species. However, different data sets and different methods often lead to the construction of different phylogenetic trees for the same set of species. Therefore, comparing these trees to determine similarities or, equivalently, dissimilarities, becomes the fundamental issue. Typically, Tree Bisection and Reconnection (TBR) and Subtree Prune and Regraft (SPR) distances have been proposed to facilitate the comparison between different phylogenetic trees. In this paper, we give a survey on the aspects of computational complexity, fixed-parameter algorithms, and approximation algorithms for computing the TBR and SPR distances of phylogenetic trees.

Keywords

phylogenetic treetree bisection and reconnectionsubtree prune and regraftfixed-parameter algorithmapproximation algorithm

References

[1]
A. W. F.Edwardsand L. L.Cavalli-Sforza, The reconstruction of evolution, Annals of Human Genetics, vol. 27, pp. 105-106, 1963.
Google Scholar
[2]
W.Fitch, Toward defining the course of evolution: Minimum change for a specified tree topology, Systematic Biology, vol. 20, no. 4, pp. 406-416, 1971.
Crossref Google Scholar
[3]
D.Sankoff, Minimal mutation trees of sequences, SIAM Journal on Applied Mathematics, vol. 28, no. 1, pp. 35-42, 1975.
Crossref Google Scholar
[4]
W. J.Le Quesne, The uniquely evolved character concept and its cladistic application, Systematic Biology, vol. 23, no. 4, pp. 513-517, 1974.
Crossref Google Scholar
[5]
W. M.Fitchand E.Margoliash, Construction of phylogenetic trees, Science, vol. 155, no. 3760, pp. 279-284, 1967.
Crossref Google Scholar
[6]
N.Saitouand M.Nei, The neighbor-joining method: A new method for reconstructing phylogenetic trees, Molecular Biology and Evolution, vol. 4, no. 4, pp. 406-425, 1987.
Google Scholar
[7]
J.Felsenstein, Evolutionary trees for DNA sequences: A maximum likelihood approach, Journal of Molecular Evolution, vol. 17, no. 6, pp. 368-376, 1981.
Crossref Google Scholar
[8]
D.Barryand J. A.Hartigan, Statistical analysis of hominoid molecular evolution, Statistical Science, vol. 2, no. 2, pp. 191-210, 1987.
Crossref Google Scholar
[9]
D.Robinsonand L.Foulds, Comparison of phylogenetic trees, Mathematical Biosciences, vol. 53, nos. 1-2, pp. 131-147, 1981.
Crossref Google Scholar
[10]
D.Robinson, Comparison of labeled trees with valency three, Journal of Combinatorial Theory, Series B, vol. 11, no. 2, pp. 105-119, 1971.
Crossref Google Scholar
[11]
K.Culikand D.Wood, A note on some tree similarity measures, Information Processing Letters, vol. 15, no. 1, pp. 39-42, 1982.
Crossref Google Scholar
[12]
W.Day, Properties of the nearest neighbor interchange metric for trees of small size, Journal of Theoretical Biology, vol. 101, no. 2, pp. 275-288, 1983.
Crossref Google Scholar
[13]
R.Boland, E.Brown, and E.Day, Approximating minimum-length-sequence metrics: A cautionary note, Mathematical Social Sciences, vol. 4, no. 3, pp. 261-270, 1983.
Crossref Google Scholar
[14]
J.Jarvis, J.Luedeman, and D.Shier, Counterexamples in measuring the distance between binary trees, Mathematical Social Sciences, vol. 4, no. 3, pp. 271-274, 1983.
Crossref Google Scholar
[15]
J.Jarvis, J.Luedeman, and D.Shier, Comments on computing the similarity of binary trees, Journal of Theoretical Biology, vol. 100, no. 3, pp. 427-433, 1983.
Crossref Google Scholar
[16]
M.Krivanke, Computing the nearest neighbor interchange metric for unlabeled binary trees is NP-complete, Journal of Classification, vol. 3, no. 1, pp. 55-60, 1986.
Crossref Google Scholar
[17]
V.Kingand T.Warnow, On measuring the nni distance between two evolutionary trees, presented at the DIMACS Mini Workshop on Combinatorial Structures in Molecular Biology, South Plainfield, USA, 1994.
[18]
M.Li, J.Tromp, and L.Zhang, Some notes on the nearest neighbor interchange distance, in Proc. 2nd Annual International Computing and Combinatorics Conference (COCOON), Hong Kong, China, 1996, pp. 343-351.
Crossref
[19]
M.Li, J.Tromp, and L.Zhang, On the nearest neighbor interchange distance between evolutionary trees, Journal on Theoretical Biology, vol. 182, no. 4, pp. 463-467, 1996.
Crossref Google Scholar
[20]
J.Hein, Reconstructing evolution of sequences subject to recombination using parsimony, Mathematical Biosciences, vol. 98, no. 2, pp. 185-200, 1990.
Crossref Google Scholar
[21]
J.Hein, A heuristic method to reconstruct the history of sequences subject to recombination, Journal of Molecular Evolution, vol. 36, no. 4, pp. 396-405, 1993.
Crossref Google Scholar
[22]
P.Buneman, The recovery of trees from measures of dissimilarity, in Mathematics in the Archaeological and Historical Sciences, F. R.Hodson, D. G.Kendall, and P. T.Tautu, Ed. Edinburgh, UK: Edinburgh University Press, 1971, pp. 387-395.
[23]
D.Swofford, G.Olsen, P.Waddell, and D.Hillis, Phylogenetic inference, in Molecular Systematics, 1996, pp. 407-513.
[24]
B.Allenand M.Steel, Subtree transfer operations and their induced metrics on evolutionary trees, Annals of Combinatorics, vol. 5, no. 1, pp. 1-15, 2001.
Crossref Google Scholar
[25]
F.Shi, J.Chen, Q.Feng, and J.Wang, Parameterized algorithms for maximum agreement forest on multiple trees, in Proc. 19th Annual International Computing and Combinatorics Conference (COCOON), Hangzhou, China, 2013, pp. 567-578.
Crossref
[26]
J.Hein, T.Jiang, L.Wang, and K.Zhang, On the complexity of comparing evolutionary trees, Discrete Applied Mathematics, vol. 71, no. 1-3, pp. 153-169, 1996.
Crossref Google Scholar
[27]
Y.Yang, A fixed-parameterized algorithm for the maximum agreement forest problem on multifurcating trees, Master dissertation, Central South University, Changsha, China, 2012. .
[28]
R.Downeyand M.Fellows, Parameterized Complexity. New York, USA: Springer, 1999.
Crossref
[29]
J.Chen, Parameterized computation and complexity: A new approach dealing with NP-hardness, Journal of Computer Science and Technology, vol. 20, no. 1, pp. 18-37, 2005.
Crossref Google Scholar
[30]
M.Hallettand C.McCartin, A faster FPT algorithm for the maximum agreement forest problem, Theory of Computing Systems, vol. 41, no. 3, pp. 539-550, 2007.
Crossref Google Scholar
[31]
C.Whiddenand N.Zeh, A unifying view on approximation and FPT of agreement forests, in Proc. Algorithms in Bioinformatics, Philadelphia, PA, USA, 2009, pp. 390-402.
Crossref
[32]
J.Chen, J.Fan, and S.Sze, Parameterized and approximation algorithms for the MAF problem in multifurcating trees, presented at the 39th International Workshop on Graph-Theoretic Concepts in Computer Science, Lübeck, Germany, 2013.
[33]
M.Bordewichand C.Semple, On the computational complexity of the rooted subtree prune and regraft distance, Annals of Combinatorics, vol. 8, no. 4, pp. 409-423, 2005.
Crossref Google Scholar
[34]
G.Hickey, F.Dehne, A.Rau-Chaplin, and C.Blouin, SPR distance computation for unrooted trees, Evolutionary Bioinformatics, vol. 4, pp. 17-27, 2008.
Crossref Google Scholar
[35]
M.Bonetand K. St.John, On the complexity of uSPR distance, IEEE/ACM Transaction on Computational Biology and Bioinformatics, vol. 7, no. 3, pp. 572-576, 2010.
Crossref
[36]
M.Bordewich, C.McCartin, and C.Semple, A 3-approximation algorithm for the subtree distance between phylogenies, Journal of Discrete Algorithms, vol. 6, no. 3, pp. 458-471, 2008.
Crossref Google Scholar
[37]
C.Whidden, R.Beiko, and N.Zeh, Fixed-parameter and approximation algorithms for maximum agreement forests, CoRR. abs/1108.2664, 2011.
Google Scholar
[38]
Z.Chenand L.Wang, HybridNET: A tool for constructing hybridization networks, Bioinformatics, vol. 26, no. 22, pp. 2912-2913, 2010.
Crossref Google Scholar
[39]
E.Rodrigues, M.Sagot, and Y.Wakabayashi, The maximum agreement forest problem: Approximation algorithms and computational experiments, Theoretical Computer Science, vol. 374, nos. 1-3, pp. 91-110, 2007.
Crossref Google Scholar
[40]
M.Bonet, K. St.John, R.Mahindru, and N.Amenta, Approximating subtree distances between phylogenies, Journal of Computational Biology, vol. 13, no. 8, pp. 1419-1434, 2006.
Crossref Google Scholar
[41]
O.Paun, C.Lehnebach, J.Johansson, P.Lockhart, and E.Hrandl, Phylogenetic relationships and biogeography of Ranunculus and allied genera (Ranunculaceae) in the Mediter-ranean region and in the European Alpine System, Taxon, vol. 54, no. 4, pp. 911-932, 2005.
Crossref Google Scholar
Tsinghua Science and Technology
Volume 18 Issue 5,
October 2013
Pages 490-499
DOI: 10.1109/TST.2013.6616522
Cite this article:
Shi F, Feng Q, Chen J, et al. Distances Between Phylogenetic Trees: A Survey. Tsinghua Science and Technology, 2013, 18(5): 490-499. https://doi.org/10.1109/TST.2013.6616522

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Received: 06 August 2013
Revised: 15 August 2013
Accepted: 20 August 2013
Published: 03 October 2013
© The author(s) 2013
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