Share This Article:

Technological Perspectives in Phylogeny Research: Revisiting Comparative Analysis of Complete Mitochondrial Genomes for Time-Extended Lineages

Full-Text HTML XML Download Download as PDF (Size:620KB) PP. 470-477
DOI: 10.4236/abb.2014.55057    3,455 Downloads   4,565 Views  
Author(s)    Leave a comment

ABSTRACT

This article seeks to emphasize a simplified approach to phylogeny research using complete mitochondrial genomes alone, while touching upon a number of technological perspectives, such as algorithmic selection, which can help improve accuracy and performance in comparative analysis. My results will show that reliable estimations can be obtained by using mitochondrial markers, even among time-extended taxonomical rankings. Six distinct mammalian groups of taxa were selected for comparison. In all cases, mtDNA models generated reliable phylogeny approximations when compared against other independent data, while rendering exceptional computational performance.


Cite this paper

Rodriguez, T. (2014) Technological Perspectives in Phylogeny Research: Revisiting Comparative Analysis of Complete Mitochondrial Genomes for Time-Extended Lineages. Advances in Bioscience and Biotechnology, 5, 470-477. doi: 10.4236/abb.2014.55057.

References

[1] Lassmann, T. and Sonnhammer, E.L. (2005) Kalign—An Accurate and Fast Multiple Sequence Alignment Algorithm. BMC Bioinformatics, 6, 298. http://dx.doi.org/10.1186/1471-2105-6-298
[2] Allen, A. (1994) Computer Performance Analysis with Mathematica. Academic Press, New York.
[3] DeSalle, R. and Giddings, L.V. (1986) Discordance of Nuclear and Mitochondrial DNA Phylogenies in Hawaiian Drosophila. Proceedings of the National Academy of Sciences, 83, 6902-6906.
http://dx.doi.org/10.1073/pnas.83.18.6902
[4] Rubinoff, D. and Holland, B.S. (2005) Between Two Extremes: Mitochondrial DNA Is Neither the Panacea Nor the Nemesis of Phylogenetic and Taxonomic Inference. Systematic Biology, 54, 952-961.
http://dx.doi.org/10.1080/10635150500234674
[5] Hurst, G.D. and Jiggins, F.M. (2005) Problems with Mitochondrial DNA as a Marker in Population, Phylogeographic and Phylogenetic Studies: The Effects of Inherited Symbionts. Proceedings of the Royal Society B: Biological Sciences, 272, 1525-1534. http://dx.doi.org/10.1098/rspb.2005.3056
[6] Coyne, J. (2012) A New Study of Polar Bears Underlines the Dangers of Reconstructing Evolution Using Mitochondrial DNA. Why Evolution Is True. http://whyevolutionistrue.wordpress.com
[7] Miller, W., Schuster, S.C., Welch, A.J., Ratan, A., Bedoya-Reina, O.C., Zhao, F. and Lindqvist, C. (2012) Polar and Brown Bear Genomes Reveal Ancient Admixture and Demographic Footprints of Past Climate Change. Proceedings of the National Academy of Sciences, 109, E2382-E2390.
http://dx.doi.org/10.1073/pnas.1210506109
[8] Larsen, P.A., Marchán-Rivadeneira, M.R. and Baker, R.J. (2010) Natural Hybridization Generates Mammalian Lineage with Species Characteristics. Proceedings of the National Academy of Sciences, 107, 11447-11452.
http://dx.doi.org/10.1073/pnas.1000133107
[9] Genner, M.J. and Turner, G.F. (2012) Ancient Hybridization and Phenotypic Novelty within Lake Malawi’s Cichlid Fish Radiation. Molecular Biology and Evolution, 29, 195-206. http://dx.doi.org/10.1093/molbev/msr183
[10] Nishihara, H., Satta, Y., Nikaido, M., Thewissen, J.G.M., Stanhope, M.J. and Okada, N. (2005) A Retroposon Analysis of Afrotherian Phylogeny. Molecular Biology and Evolution, 22, 1823-1833. http://dx.doi.org/10.1093/molbev/msi179
[11] Orlando, L., Hänni, C. and Douady, C.J. (2007) Mammoth and Elephant Phylogenetic Relationships: Mammut Americanum, the Missing Outgroup. Evolutionary Bioinformatics Online, 3, 45.
[12] Rohland, N., Reich, D., Mallick, S., Meyer, M., Green, R.E., Georgiadis and Hofreiter, M. (2010) Genomic DNA Sequences from Mastodon and Woolly Mammoth Reveal Deep Speciation of Forest and Savanna Elephants. PLoS Biology, 8, Article ID: e1000564. http://dx.doi.org/10.1371/journal.pbio.1000564
[13] Ripple, J. (1999) Manatees and Dugongs of the World. Voyageur Press, London.
[14] de Jong, W.W., Zweers, A. and Goodman, M. (1981) Relationship of Aardvark to Elephants, Hyraxes and Sea Cows from α-Crystallin Sequences. Nature, 292, 538-540.
[15] Honeycutt, R.L. (2008) Small Changes, Big Results: Evolution of Morphological Discontinuity in Mammals. Journal of biology, 7, 9. http://dx.doi.org/10.1186/jbiol71
[16] Nishihara, H., Satta, Y., Nikaido, M., Thewissen, J.G.M., Stanhope, M.J. and Okada, N. (2005) A Retroposon Analysis of Afrotherian Phylogeny. Molecular biology and evolution, 22, 1823-1833. http://dx.doi.org/10.1093/molbev/msi179
[17] University of Calgary (2009) Is The Hippopotamus The Closest Living Relative to the Whale? Science Daily.
http://www.sciencedaily.com-/releases/2009/03/090318153803.htm
[18] Krause, J., Unger, T., Noçon, A., Malaspinas, A.S., Kolokotronis, S.O., Stiller, M. and Hofreiter, M. (2008) Mitochondrial Genomes Reveal an Explosive Radiation of Extinct and Extant Bears near the Miocene-Pliocene Boundary. BMC Evolutionary Biology, 8, 220. http://dx.doi.org/10.1186/1471-2148-8-220

  
comments powered by Disqus

Copyright © 2017 by authors and Scientific Research Publishing Inc.

Creative Commons License

This work and the related PDF file are licensed under a Creative Commons Attribution 4.0 International License.