Modified indel treatment for accurate Phylogenetic Tree construction

Abstract

Phylogenetic tree reconstruction has become very rapid-growing field because of its application in the broad range of biological areas. Phylogenetic reconstruction is enhanced by different statistical approaches. Lots of studies have suggested the acceptance of Gap (indel), in evolutionary tree because it contains huge phylogenetic information. We used simulation studies that explore the relative performance of different Indel (gap) treating approaches in a phylogenetic analysis with respect to the accuracy of the phylogenetic tree. We evaluated the approaches using indel rich highly similar ten Polychilos species DNA sequences. Our results indicate that Jukes-Cantor(J-C) with indel model(Indel as a separate state in J-C nucleotide substitution model) performs better than all other indel treating methods (Completely removing the indels, gaps as fifth state in an evolutionary model, combined indel distance and Nucleotide distance, gaps as missing data,) in phylogenetic tree construction using the selected dataset. We have used bootstrapping method and Robinson-Foulds distance method to test the phylogenetic trees constructed utilizing the gap incorporation techniques. The phylogenetic tree constructed with the framework of J-C with indel model shows 81% accuracy while other shows less accuracy.