A Maximum Parsimony Model to Reconstruct Phylogenetic Network in Honey Bee Evolution

Authors: Usha Chouhan, K. R. Pardasani

Abstract:

Phylogenies ; The evolutionary histories of groups of species are one of the most widely used tools throughout the life sciences, as well as objects of research with in systematic, evolutionary biology. In every phylogenetic analysis reconstruction produces trees. These trees represent the evolutionary histories of many groups of organisms, bacteria due to horizontal gene transfer and plants due to process of hybridization. The process of gene transfer in bacteria and hybridization in plants lead to reticulate networks, therefore, the methods of constructing trees fail in constructing reticulate networks. In this paper a model has been employed to reconstruct phylogenetic network in honey bee. This network represents reticulate evolution in honey bee. The maximum parsimony approach has been used to obtain this reticulate network.

Keywords: Hybridization, HGT, Reticulate networks, Recombination, Species, Parsimony.

Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1077843

References:

[1] C. Dutta And A. Pan,"Horizontal gene transfer and bacterial diversity" ,J. Biosci. (Suppl. 1) 27 27-33, 2002.
[2] C.T Nguyen,B. Nguyen, W.K.Sung and L. Zhang,-Reconstructing Recombination Network from Sequence Data :The Small Parsimoney Problem",IEEE CS,Cl and EMB Societies & the ACM,Vol.4,No.3,pg 394-401,2007.
[3] D.H. Huson and D. Bryant,"Application of Phylogenetic Networks in Evolutionary Studies", Mol. Biol. Evol. 23(2):254-267. 2006.
[4] G. Jin, L. Nakhleh, S. Snir and T. Tulle,"Efficient parsimony based methods for phylogenetic network Reconstruction",Vol. 23 ECCB, pages e123-e128. 2006.
[5] J. Hein,"Reconstructing evolution of sequences subject to recombination using parsimon",Maths.Biosci.98, 185-200, 1990.
[6] J. Hein,"A heuristic method to reconstruct the history of sequences subject to recombination",J.mol.Evol.36,396-405, 1993.
[7] J. Archer, J. W. Pinney, J. Fan, E. S Loriere," Identifying the Important HIV-1 Recombination Breakpoints", PLoS Comput Biol. 4(9): e1000178, 2008.
[8] M.T Hallet and J. Lagergren,"Efficient algorithms for lateral gene transfer problems. In: Proceedings of the 5th Ann Int Conf Compt Mol Biol (RECOMB 01), New York, and ASM Press. pp 149-156, 2001.
[9] L. Nakhleh, D. Ruth-s,"Gene Trees, species Trees, and species Networks", Lecture notes. RECOMB, San Diego, California USA, 1:1- 24, 2003.
[10] L. Nakhleh,G.J.,F Zhao,"Reconstructing Phylogenetic Networks Using Maximum Parsimony", RECOMB, USA, 1:200-210, 2004.
[11] L. O. Martins,E.Leal,H. Kishino,"Phylogenetic Detection of Recombination with a Bayesian Prior on the Distance between Trees",PLoS One,Volume 3,Issue 7,July 2008,e2651.
[12] V. Makarenkov, P . Legendre and Y. Desdevises,"Modeling phylogenetic relationships using reticulated networks",Zool Scrip 33:89-96, 2004.
[13] V. Makarenkov,"T-Rex: reconstructing and visualizing phylogenetic trees and reticulation networks,",Bioinf 17:664-668, 2001.
[14] V. Makarenkov and P. Legendre ,"From a phylogenetic tree to a reticulated network", J Comput Biol 11:195-212, 2004.
[15] D. Posada and K.A Crandall,"Evaluation of methods for detecting recombination from DNA sequences: Computer simulations", Proc Natl Acad Sci USA 98(24):13757-13762, 2001.
[16] W.K Sung, "Phylogenetic Trees Reconstruction", CS5238: 1-7, 2005.