An Accurate Method for Phylogeny Tree Reconstruction Based on a Modified Wild Dog Algorithm

Authors: Essam Al Daoud

Abstract:

This study solves a phylogeny problem by using modified wild dog pack optimization. The least squares error is considered as a cost function that needs to be minimized. Therefore, in each iteration, new distance matrices based on the constructed trees are calculated and used to select the alpha dog. To test the suggested algorithm, ten homologous genes are selected and collected from National Center for Biotechnology Information (NCBI) databanks (i.e., 16S, 18S, 28S, Cox 1, ITS1, ITS2, ETS, ATPB, Hsp90, and STN). The data are divided into three categories: 50 taxa, 100 taxa and 500 taxa. The empirical results show that the proposed algorithm is more reliable and accurate than other implemented methods.

Keywords: Least squares, neighbor joining, phylogenetic tree, wild dogpack.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1123839

References:

[1] J. Gatesy, M. S. Springer, "Phylogenetic analysis at deep timescales: unreliable gene trees, bypassed hidden support, and the coalescence/ concatalescence conundrum. Molecular Phylogenetics and Evolution vol. 80, no. 11, pp231–266, 2014.
[2] M. Riester, C. S. Attolini, R. J. Downey, S. Singer, F. Michor, "A Differentiation-Based Phylogeny of Cancer Subtypes," Plos Comp. Biol., vol. 6, no. e1000777, pp1-14, 2010.
[3] A. Dereeper, V. Guignon, G. Blanc, S. Audic, S. Buffet, F. Chevenet, J.-F. Dufayard, S. Guindon, V. Lefort, M. Lescot, J.-M. Claverie and O. Gascuel, "Phylogeny.fr: robust phylogenetic analysis for the non-specialist," Nucleic Acids Research, vol. 36, pp465–469, 2008.
[4] S. Kumar, M., Nei, J., Dudley, K., Tamura, "MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences," BriefBioinform., vol 9, pp. 299–306, 2008.
[5] S. Roch, "Toward extracting all phylogenetic information from matrices of evolutionary distances," Science, vol 327, pp1376-1379, 2010.
[6] P. J. Waddell, H. Kishino, R. Ota, "Phylogenetic Methodology for Detecting Protein Complexes," Mol. Biol. Evol., vol 24, pp650-659, 2007.
[7] O. Gascuel, M. Steel, "Neighbor-Joining Revealed," Molecular Biology and Evolution, vol23, no 11, pp1997-2000, 2006.
[8] E. Al Daoud, "A Modified Optimization Algorithm Inspired by Wild Dog Packs," International Journal of Science and Advanced Technology, vol. 4, no. 9, pp: 25-28, 2014.
[9] E. Al Daoud, R. Alshorman, F. Hanandeh, "A New Efficient Meta-Heuristic Optimization Algorithm Inspired by Wild Dog Packs," International Journal of Hybrid Information Technology, vol. 7, no. 6, pp: 83-100, 2014.
[10] R. Mihaescu, L. Pachter, "Combinatorics of least-squares trees," Proc. Nat. Acad. Sci., vol. 105, pp13206-13207, 2008.
[11] C. C. Ribeiro, D.S. Vianna, "A hybrid genetic algorithm for the phylogeny problem using path-relinking as a progressive crossover strategy," International Transactions in Operational Research, vol. 16, no. 5, pp641–657, 2009.
[12] E. Al Daoud, "An Efficient Algorithm for Finding a Fuzzy Rough Set Reduct Using an Improved Harmony Search," I.J. Modern Education and Computer Science, vol. 7, no. 2, pp16-23, 2015.