Title: Modified evolutionary model with insertion and deletion (Indel) for phylogenetic tree construction
Authors: Asim Kumar Mahadani; Goutam Sanyal; Pradosh Mahadani; Partha Bhattacharjee
Addresses: Department of Computer Science and Engineering, National Institute of Technology, Durgapur, West Bengal, India ' Department of Computer Science and Engineering, National Institute of Technology, Durgapur, West Bengal, India ' Crop Improvement Division, ICAR - National Rice Research Institute, Cuttack, Odisha, India ' CSIR - Central Mechanical Engineering Research Institute, Durgapur, West Bengal, India
Abstract: Estimation of biological relationship among various taxa is usually measured on some evolutionary models. Majority of the existing evolutionary models ignore insertion and deletion (Indel) event which reduces the computational difficulties but at the same time it causes loss of valuable phylogenetic information. In this study, we developed a modified Jukes-Cantor (M J-C) model to include the insertion and deletion (Indel) information in phylogenetic technique. Utility of modified Jukes-Cantor model was tested in existing phylogenetic methods (UPGMA and NJ). 24 Indel rich chloroplast DNA sequences (trnH-psbA) of different citrus species are used as a dataset in phylogenetic tree construction. In comparison to J-C model, the proposed modified Jukes-Cantor model shows significant improvement in branch support (bootstrap) value in phylogenetic trees, considering Indel information. This new modified J-C model may accelerate the phylogenetic study on Indel-rich DNA sequences. The Indels would be important for phylogenetic tree reconstruction, especially when low level of divergence is found in the studied taxa.
Keywords: Indel; gap; J-C model; evolutionary model; genetic distance; phylogenetics.
International Journal of Data Mining and Bioinformatics, 2018 Vol.21 No.1, pp.43 - 69
Received: 12 Feb 2018
Accepted: 04 Sep 2018
Published online: 09 Oct 2018 *