Incomplete distance matrices, supertrees and bat phylogeny

Molecular Phylogenetics and Evolution

Volumn 27, Issue 2, 2003, Pages 239-246

  Levasseur, Claudine ^a   Landry, Pierre Alexandre ^a,c   Makarenkov, Vladimir ^a,d   Kirsch, John A W ^b   Lapointe, François Joseph ^a  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

^c UNIVERSITY OF HELSINKI   (Finland)

^d UNIVERSITÉ DU QUÉBEC À MONTRÉAL   (Canada)

Author keywords

Bat phylogeny; Missing data; Phylogenetic trees; Simulations study; Supertrees

Indexed keywords

EID: 0037408485     PISSN: 10557903     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1055-7903(02)00415-3     Document Type: Article

References (34)

1. Buneman, P., 1971. The recovery of trees from measures of dissimilarity. In: Hudson, F.R., Kendall, D.G., Tautu, P. (Eds.), Mathematics in Archeological and Historical Sciences. Edinburgh University Press, Edinburgh, pp. 387-395.
2. Cavalli-Sforza, L.L., Edwards, A.W.F., 1967. Phylogenetic analysis: models and estimation procedures. Evolution 32, 550-570.
3. De Soete, G., 1983. A least squares algorithm for fitting additive trees to proximity data. Psychometrika 48, 621-626.
4. De Soete, G., 1984a. Ultrametric tree representations of incomplete dissimilarity data. J. Classif. 1, 235-242.
5. De Soete, G., 1984b. Additive-tree representations of incomplete dissimilarity data. Qual. Quantity 18, 387-393.
6. Felsenstein, J., 1993. PHYLIP: Phylogeny inference package, version 3.5c. Distributed by the author. University of Washington, Seattle, Washington.
7. Fitch, W.M., Margoliash, E., 1967. Construction of phylogenetic trees. Science 155, 279-284.
8. Gibson, G., 2002. Microarrays in ecology and evolution: a preview. Mol. Ecol. 11, 17-24.
9. Guénoche, A., Grandcolas, S., 1999. Approximations par arbre d'une distance partielle. Math. Info. Sci. Hum. 146, 51-64.
10. Hartigan, J.A., 1967. Representation of similarity matrices by trees. J. Am. Stat. Assoc. 62, 1140-1158.
11. Hein, J., 1989. A tree reconstruction method that is economical in the number of pairwise comparison used. Mol. Biol. Evol. 6, 669-684.
12. Huelsenbeck, J.P., Bull, J.J., Cunningham, C.W., 1996. Combining data in phylogenetic analysis. Trends Ecol. Evol. 11, 152-158.
13. Hutcheon, J.M., Kirsch, J.A.W., Pettigrew, J.D., 1998. Base-compositional biases and the bat problem. III. The question of microchiropteran monophyly. Philos. Trans. R. Soc. Lond. B 353, 607-617.
14. Kim, J., 1993. Improving the accuracy of phylogenetic estimation by combining different methods. Syst. Biol. 42, 331-340.
15. Kluge, A.G., 1989. A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38, 7-25.
16. Landry, P.-A., Lapointe, F.-J., 1997. Estimation of missing distances in path-length matrices: problems and solutions. In: Mirkin, B., McMorris, F.R., Roberts, F.S., Rzhetsky, A. (Eds.), Mathematical Hierarchies and Biology. DIMACS Series in Discrete Mathematics and Theoretical Computer Science. American Mathematical Society, Providence, pp. 209-224.
17. Landry, P.-A., Lapointe, F.-J., Kirsch, J.A.W., 1996. Estimating phylogenies from lacunose distance matrices: additive is superior to ultrametric estimation. Mol. Biol. Evol. 13, 818-823.
18. Lapointe, F.-J., Cucumel, G., 1997. The average consensus procedure: combination of weighted trees containing identical or overlapping sets of taxa. Syst. Biol. 46, 306-312.
19. Lapointe, F.-J., Kirsch, J.A.W., 1995. Estimating phylogenies from lacunose distance matrices, with special reference to DNA hybridization data. Mol. Biol. Evol. 12, 266-284.
20. Levasseur, C., Landry, P.-A., Lapointe, F.-J., 2000. Estimating trees from incomplete distance matrices: a comparison of two methods. In: Kiers, H.A.L., Rasson, J.-P., Groenen, P.J.F., Schader, M. (Eds.), Data Analysis, Classification, and Related Methods. Springer, Berlin, pp. 149-154.
21. Makarenkov, V., Leclerc, B., 1999. The fitting of a tree metric according to a weighted least-squares criterion. J. Classif. 16, 3-26.
22. Mickevich, M.F., 1978. Taxonomic congruence. Syst. Zool. 27, 143-158.
23. Quackenbush, J., 2001. Computational analysis of microarray data. Nat. Rev. Genet. 2, 418-427.
24. Robinson, D.F., Foulds, L.R., 1981. Comparison of phylogenetic trees. Math. Biosci. 53, 131-147.
25. Rzhetsky, A., Nei, M., 1992. A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9, 945-967.
26. Saitou, N., Nei, M., 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
27. Sanderson, M.J., Purvis, A., Henze, C., 1998. Phylogenetic supertrees: assembling the tree of life. Trends Ecol. Evol. 13, 105-109.
28. Sokal, R.R., Rohlf, F.J., 1981. Taxonomic congruence in the Leptopodomorpha re-examined. Syst. Zool. 30, 309-325.
29. Springer, M.S., Kirsch, J.A.W., 1989. Rates of single-copy DNA evolution in phalangeriform marsupials. Mol. Biol. Evol. 6, 331-341.
30. Swofford, D.L., Olsen, G.J., Waddell, P.J., Hillis, D.M., 1996. Phylogenetic inference. In: Hillis, D.M., Moritz, C., Mable, B.K. (Eds.), Molecular Systematics, second ed. Sinauer, Sunderland, pp. 407-514.
31. Swofford, D.L., 1999. PAUP*: Phylogenetic Analysis Using Parsimony (*and other Methods), Version 4. Sinauer Associates, Sunderland, MA.
32. Teeling, E.C., Scally, M., Kao, D.J., Romagnoli, M.L., Springer, M.S., Stanhope, J., 2000. Molecular evidence regarding the origin of echolocation and flight in bats. Nature 403, 188-192.
33. Troyanskaya, O., Cantor, M., Sherlock, G., Brown, P., Hastie, T., Tibshirani, R., Botstein, D., Altman, R.B., 2001. Missing value estimation methods for DNA microarrays. Bioinformatics 17, 520-525.
34. Wiens, J.J., 1998. Does adding characters with missing data increase or decrease phylogenetic accuracy? Syst. Biol. 47, 625-640.