Distance-based analysis to reveal vertebrate phylogeny without sequence alignment using complete mitochondrial genomes
Yu, Zuguo, Zhou, Li-Qian, Anh, Vo V., Chu, Ka-Hou, Li, C. P., & Chen, Y. J. (2007) Distance-based analysis to reveal vertebrate phylogeny without sequence alignment using complete mitochondrial genomes. In Callaos, N., Lesso, W., Zinn, C., & Zmazek, B. (Eds.) 11th World Multi-Conference on Systemics, Cybernetics and Informatics: WMSCI 2007, 8-11 July 2007, Florida, USA.
There have been a number of recent attempts to develop methodologies that do not require sequence alignment for deriving species phylogeny based on overall similarities of the complete genomes. The mitochondrial genomes have provided much information on the evolution of this organelle and have been used for phylogenetic reconstruction by various methods with or without sequence alignment. In this paper we introduce three fast algorithms, namely, dynamical language model with correlation distance, Fourier transform with Kullback-Leibler divergence distance, log-correlation distance, for deriving vertebrate phylogeny based on mitochondrial genomes. The distance-based analyses show that the mitochondrial genomes are separated into three major clusters corresponding to mammals, fish, and Archosauria (including birds and reptiles)respectively. The interrelationships among the mitochondrial genomes are roughly in agreement with the current understanding on the phylogeny of vertebrates revealed by the traditional approaches.
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|Item Type:||Conference Paper|
|Keywords:||vertebrate phylogeny, mitochondrial genome, dynamical language model, Fourier transform, correlation distance, Kullback, Leibler divergence distance|
|Subjects:||Australian and New Zealand Standard Research Classification > MATHEMATICAL SCIENCES (010000) > APPLIED MATHEMATICS (010200) > Biological Mathematics (010202)
Australian and New Zealand Standard Research Classification > BIOLOGICAL SCIENCES (060000) > GENETICS (060400) > Molecular Evolution (060409)
|Divisions:||Past > QUT Faculties & Divisions > Faculty of Science and Technology|
|Copyright Owner:||Copyright 2007 (please consult author)|
|Deposited On:||18 Nov 2008|
|Last Modified:||29 Feb 2012 13:40|
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