Reconstruction of Certain Phylogenetic Networks from Their Tree-Average Distances

Bulletin of Mathematical Biology

Volumn 75, Issue 10, 2013, Pages 1840-1878

  Willson, Stephen J ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

Metric; Network; Phylogenetic network; Phylogeny; Tree; Tree average distance

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; HYBRIDIZATION; MATHEMATICAL PHENOMENA; MOLECULAR EVOLUTION; PHYLOGENY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; HYBRIDIZATION, GENETIC; MATHEMATICAL CONCEPTS; MODELS, GENETIC; PHYLOGENY;

EID: 84885078909     PISSN: 00928240     EISSN: 15229602     Source Type: Journal    
DOI: 10.1007/s11538-013-9872-z     Document Type: Article

References (30)

1. Bandelt, H.-J., & Dress, A. (1992). Split decomposition: a new and useful approach to phylogenetic analysis of distance data. Mol. Phylogenet. Evol., 1, 242-252.
2. Baroni, M., Semple, C., & Steel, M. (2004). A framework for representing reticulate evolution. Ann. Comb., 8, 391-408.
3. Baroni, M., Semple, C., & Steel, M. (2006). Hybrids in real time. Syst. Biol., 55, 46-56.
4. Boc, A., & Makarenkov, V. (2003). New efficient algorithm for detection of horizontal gene transfer events. In G. Benson, R. D. Page (Eds.), Lecture notes in computer science: Vol. 2812. Proceedings of the WABI03 (pp. 190-201).
5. Bryant, D., & Moulton, V. (2004). Neighbor-net: an agglomerative method for the construction of phylogenetic networks. Mol. Biol. Evol., 21, 255-265.
6. Cardona, G., Rosselló, F., & Valiente, G. (2009). Comparison of tree-child phylogenetic networks. IEEE/ACM Trans. Comput. Biol. Bioinform., 6(4), 552-569.
7. Choy, C., Jansson, J., Sadakane, K., & Sung, W.-K. (2005). Computing the maximum agreement of phylogenetic networks. Theor. Comput. Sci., 335(1), 93-107.
8. Desper, R., & Gascuel, O. (2002). Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J. Comput. Biol., 9(5), 687-705.
9. Desper, R., & Gascuel, O. (2004). Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol., 21(3), 587-598.
10. Doolittle, W. F., et al. (2003). How big is the iceberg of which organella genes in nuclear genomes are but the tip? Philos. Trans. R. Soc. Lond. B, Biol. Sci., 358, 39-47.
11. Eslahchi, C., Habibi, M., Hassanzadeh, R., & Mottaghi, E. (2010). MC-net: a method for the construction of phylogenetic networks based on the Monte-Carlo method. BMC Evol. Biol., 10, 254. doi: 10. 1186/1471-2148-10-254.
12. Gascuel, O., & Steel, M. (2006). Neighbor-joining revealed. Mol. Biol. Evol., 23, 1997-2000.
13. Gusfield, D., Eddhu, S., & Langley, C. (2004). Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. J. Bioinform. Comput. Biol., 2, 173-213.
14. Hasegawa, M., Kishino, H., & Yano, K. (1985). Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol., 22, 160-174.
15. Huson, D. H., & Bryant, D. (2006). Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol., 23(2), 254-267.
16. Huson, D., Rupp, R., & Scornavacca, C. (2010). Phylogenetic networks: concepts, algorithms and applications. Cambridge: Cambridge University Press.
17. van Iersel, L. J. J., Keijsper, J. C. M., Kelk, S. M., Stougie, L., Hagen, F., & Boekhout, T. (2009). Constructing level-2 phylogenetic networks from triplets. IEEE/ACM Trans. Comput. Biol. Bioinform., 6(43), 667-681.
18. Jukes, T. H., & Cantor, C. R. (1969). Evolution of protein molecules. In S. Osawa & T. Honjo (Eds.), Evolution of life: fossils, molecules (pp. 79-95). Tokyo: Springer.
19. Kimura, M. (1980). A simple model for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol., 16, 111-120.
20. Lake, J. A. (1994). Reconstructing evolutionary trees from DNA and protein sequences: paralinear distances. Proc. Natl. Acad. Sci. USA, 91, 1455-1459.
21. Marcussen, T., Jakobsen, K., Danihelka, J., Ballard, H., Blaxland, K., Brysting, A., & Oxelman, B. (2012). Inferring species networks from gene trees in high-polyploid North American and Hawaiian violets (Viola, Violacae). Syst. Biol., 61, 107-126.
22. Moret, B. M. E., Nakhleh, L., Warnow, T., Linder, C. R., Tholse, A., Padolina, A., Sun, J., & Timme, R. (2004). Phylogenetic networks: modeling, reconstructibility, and accuracy. IEEE/ACM Trans. Comput. Biol. Bioinform., 1, 13-23.
23. Nakhleh, L., Warnow, T., & Linder, C. R. (2004). Reconstructing reticulate evolution in species-theory and practice. In P. E. Bourne & D. Gusfield (Eds.), Proceedings of the eighth annual international conference on computational molecular biology (pp. 337-346). RECOMB '04, San Diego, California, March 27-31, 2004. New York: ACM.
24. Saitou, N., & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
25. Semple, C., & Steel, M. (2003). Phylogenetics. Oxford: Oxford University Press.
26. Steel, M. A. (1994). Recovering a tree from the leaf colorations it generates under a Markov model. Appl. Math. Lett., 7(2), 19-23.
27. Wang, L., Zhang, K., & Zhang, L. (2001). Perfect phylogenetic networks with recombination. J. Comput. Biol., 8, 69-78.
28. Wang, L., Ma, B., & Li, M. (2000). Fixed topology alignment with recombination. Discrete Appl. Math., 104(1-3), 281-300.
29. Willson, S. J. (2010). Properties of normal phylogenetic networks. Bull. Math. Biol., 72, 340-358.
30. Willson, S. J. (2012). Tree-average distances on certain phylogenetic networks have their weights uniquely determined. Algorithms Mol. Biol., 7, 13. doi: 10. 1186/1748-7188-7-13.