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OJBTM

 Online Journal of Bioinformatics 

Volume 12(2):230-242, 2011.


A least squares method to determine reticulation in eight grass plastomes.

 

Rinku Mathur and Neeru Adlakha

 

Department of Applied Mathematics & Humanities, Sardar Vallabhbhai National Institute of Technology, Surat - 395 007, Gujarat, India.

 

ABSTRACT

 

Mathur R, Adlakha N., A least squares method to determine reticulation in eight grass plastomes, Onl J Bioinform., 12(2):230-242, 2011.  A least squares method was used to determine the evolutionary network amongst 8 grass plastomes. Results suggested the possibility of reticulation events between Oryza and Triticum, non-sister species from different subfamilies and between species belonging to the same subfamily of Bentgrass and Brachypodium. These could be hybridized to obtain a new species that would be more tolerable to extreme weather conditions to produce higher yields. Phylogenetic networks are considered as the structures that are used to understand the evolutionary pathways among the different organisms. Evolutionary relations are due to the preservation of mutations in sequences, occurred due to the non-tree like events like horizontal gene transfer, Homoplasy, sexual hybridization and recombination, etc. The effective and efficient reconstruction of the networks for these events is an challenging task in computational biology. In this article, a new Fuzzy Weighted Least Squares (FWLS) approach is employed to detect these events in commonly known species of grasses. The results obtained by the proposed method predicts the possibility of hybridization or recombination among the inter cluster species i.e., Oryza and Triticum and intra cluster species i.e. Bentgrass and Brachypodium. Results also provide the optimized values of in comparison to the other available least squares method and thus error level is also minimized.

 

Keywords: Phylogenetic Networks, Fuzzy Set, Fuzzy Weighted Least Squares Approach, Subfamilies, Grass Species, Hybridization and Reticulation distance.


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