MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment
Director of the Center for Evolutionary Functional Genomics in The Biodesign Institute at Arizona State University since 2002. His research interests include development of software, statistical methods and computational tools for comparative sequence analysis. He and Koichiro Tamura are joint first authors of the MEGA3 software.
Molecular evolutionist at the Tokyo Metropolitan University. His research interests are in the area of experimental, theoretical and computational molecular evolution.
Director of the Institute of Molecular Evolutionary Genetics at the Penn State University since 1990. His research interests are in molecular evolutionary genetics and genomics.
Sudhir Kumar, Life Sciences A-351, The Biodesign Institute, Tempe, AZ 85287-4501, USA Tel: +1 (480) 727 6949 Fax: +1 (480) 965 6899 E-mail: s.kumar{at}asu.edu
With its theoretical basis firmly established in molecular evolutionary and population genetics, the comparative DNA and protein sequence analysis plays a central role in reconstructing the evolutionary histories of species and multigene families, estimating rates of molecular evolution, and inferring the nature and extent of selective forces shaping the evolution of genes and genomes. The scope of these investigations has now expanded greatly owing to the development of high-throughput sequencing techniques and novel statistical and computational methods. These methods require easy-to-use computer programs. One such effort has been to produce Molecular Evolutionary Genetics Analysis (MEGA) software, with its focus on facilitating the exploration and analysis of the DNA and protein sequence variation from an evolutionary perspective. Currently in its third major release, MEGA3 contains facilities for automatic and manual sequence alignment, web-based mining of databases, inference of the phylogenetic trees, estimation of evolutionary distances and testing evolutionary hypotheses. This paper provides an overview of the statistical methods, computational tools, and visual exploration modules for data input and the results obtainable in MEGA.
Keywords: evolution, genomics, software, data mining, sequence alignment, distance, phylogenetics, selection
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 L. E. de Vries, H. Christensen, R. L. Skov, F. M. Aarestrup, and Y. Agerso Diversity of the tetracycline resistance gene tet(M) and identification of Tn916- and Tn5801-like (Tn6014) transposons in Staphylococcus aureus from humans and animals J. Antimicrob. Chemother., September 1, 2009; 64(3): 490 - 500. [Abstract] [Full Text] [PDF]
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 R. M. Sakamuri, M. Kimura, W. Li, H.-C. Kim, H. Lee, M. D. Kiran, W. C. Black IV, M. Balagon, R. Gelber, S.-N. Cho, et al. Population-Based Molecular Epidemiology of Leprosy in Cebu, Philippines J. Clin. Microbiol., September 1, 2009; 47(9): 2844 - 2854. [Abstract] [Full Text] [PDF]
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R. Oddone, C. Schweynoch, G. Schonian, C. dos Santos de Sousa, E. Cupolillo, D. Espinosa, J. Arevalo, H. Noyes, I. Mauricio, and K. Kuhls Development of a Multilocus Microsatellite Typing Approach for Discriminating Strains of Leishmania (Viannia) Species J. Clin. Microbiol., September 1, 2009; 47(9): 2818 - 2825. [Abstract] [Full Text] [PDF]
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K. G. Nandasena, G. W. O'Hara, R. P. Tiwari, A. Willems, and J. G. Howieson Mesorhizobium australicum sp. nov. and Mesorhizobium opportunistum sp. nov., isolated from Biserrula pelecinus L. in Australia Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2140 - 2147. [Abstract] [Full Text] [PDF]
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S. K. Panda, V. Jyoti, B. Bhadra, K. C. Nayak, S. Shivaji, F. A. Rainey, and S. K. Das Thiomonas bhubaneswarensis sp. nov., an obligately mixotrophic, moderately thermophilic, thiosulfate-oxidizing bacterium Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2171 - 2175. [Abstract] [Full Text] [PDF]
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M. Otoguro, S. Ratnakomala, Y. Lestari, R. D. Hastuti, E. Triana, Y. Widyastuti, and K. Ando Streptomyces baliensis sp. nov., isolated from Balinese soil Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2158 - 2161. [Abstract] [Full Text] [PDF]
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M. K. Kim, S. Srinivasan, Y.-J. Kim, and D.-C. Yang Castellaniella ginsengisoli sp. nov., a {beta}-glucosidase-producing bacterium Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2191 - 2194. [Abstract] [Full Text] [PDF]
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S. Qin, G.-Z. Zhao, J. Li, W.-Y. Zhu, L.-H. Xu, and W.-J. Li Jiangella alba sp. nov., an endophytic actinomycete isolated from the stem of Maytenus austroyunnanensis Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2162 - 2165. [Abstract] [Full Text] [PDF]
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Y.-R. Cao, Y. Jiang, J.-Y. Wu, L.-H. Xu, and C.-L. Jiang Actinopolymorpha alba sp. nov., isolated from a rhizosphere soil Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2200 - 2203. [Abstract] [Full Text] [PDF]
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X.-W. Xu, Y.-H. Wu, C.-S. Wang, X.-G. Wang, A. Oren, and M. Wu Croceicoccus marinus gen. nov., sp. nov., a yellow-pigmented bacterium from deep-sea sediment, and emended description of the family Erythrobacteraceae Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2247 - 2253. [Abstract] [Full Text] [PDF]
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H.-Y. Weon, S.-H. Yoo, Y.-J. Kim, C.-M. Lee, B.-Y. Kim, Y.-A. Jeon, S.-B. Hong, R. Anandham, and S.-W. Kwon Rudaea cellulosilytica gen. nov., sp. nov., isolated from soil Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2308 - 2312. [Abstract] [Full Text] [PDF]
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H.-Y. Xu, L.-P. Chen, S.-Z. Fu, H.-X. Fan, Y.-G. Zhou, S.-J. Liu, and Z.-P. Liu Zhangella mobilis gen. nov., sp. nov., a new member of the family Hyphomicrobiaceae isolated from coastal seawater Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2297 - 2301. [Abstract] [Full Text] [PDF]
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P. Anil Kumar, T. N. R. Srinivas, V. Thiel, M. Tank, Ch. Sasikala, Ch. V. Ramana, and J. F. Imhoff Thiohalocapsa marina sp. nov., from an Indian marine aquaculture pond Int J Syst Evol Microbiol, September 1, 2009; 59(9): 2333 - 2338. [Abstract] [Full Text] [PDF]
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C. Henke-Gendo, G. Harste, B. Juergens-Saathoff, F. Mattner, H. Deppe, and A. Heim New Real-Time PCR Detects Prolonged Norovirus Excretion in Highly Immunosuppressed Patients and Children J. Clin. Microbiol., September 1, 2009; 47(9): 2855 - 2862. [Abstract] [Full Text] [PDF]
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 C. Ampomah-Dwamena, T. McGhie, R. Wibisono, M. Montefiori, R. P. Hellens, and A. C. Allan The kiwifruit lycopene beta-cyclase plays a significant role in carotenoid accumulation in fruit J. Exp. Bot., September 1, 2009; 60(13): 3765 - 3779. [Abstract] [Full Text] [PDF]
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E. F. Walton, R.-M. Wu, A. C. Richardson, M. Davy, R. P. Hellens, K. Thodey, B. J. Janssen, A. P. Gleave, G. M. Rae, M. Wood, et al. A rapid transcriptional activation is induced by the dormancy-breaking chemical hydrogen cyanamide in kiwifruit (Actinidia deliciosa) buds J. Exp. Bot., September 1, 2009; 60(13): 3835 - 3848. [Abstract] [Full Text] [PDF]
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 L. B. Geyer and H.A. Lessios Lack of Character Displacement in the Male Recognition Molecule, Bindin, in Altantic Sea Urchins of the Genus Echinometra Mol. Biol. Evol., September 1, 2009; 26(9): 2135 - 2146. [Abstract] [Full Text] [PDF]
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N. Georgelis, J. R. Shaw, and L. C. Hannah Phylogenetic Analysis of ADP-Glucose Pyrophosphorylase Subunits Reveals a Role of Subunit Interfaces in the Allosteric Properties of the Enzyme Plant Physiology, September 1, 2009; 151(1): 67 - 77. [Abstract] [Full Text] [PDF]
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N. Puillandre, C. Cruaud, and Yu. I. Kantor CRYPTIC SPECIES IN GEMMULOBORSONIA (GASTROPODA: CONOIDEA) J. Mollus. Stud., August 25, 2009; (2009) eyp042v1. [Abstract] [Full Text] [PDF]
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 A. Tatarenkov, S. M. Q. Lima, D. S. Taylor, and J. C. Avise Long-term retention of self-fertilization in a fish clade PNAS, August 25, 2009; 106(34): 14456 - 14459. [Abstract] [Full Text] [PDF]
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M. M. Van der Merwe, M. W. Kinnear, L. G. Barrett, P. N. Dodds, L. Ericson, P. H. Thrall, and J. J. Burdon Positive selection in AvrP4 avirulence gene homologues across the genus Melampsora Proc R Soc B, August 22, 2009; 276(1669): 2913 - 2922. [Abstract] [Full Text] [PDF]
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D. Dong, G. He, S. Zhang, and Z. Zhang Evolution of Olfactory Receptor Genes in Primates Dominated by Birth-and-Death Process Gen Biol Evol, August 20, 2009; 2009(0): 258 - 264. [Abstract] [Full Text] [PDF]
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G. Margos, S. A. Vollmer, M. Cornet, M. Garnier, V. Fingerle, B. Wilske, A. Bormane, L. Vitorino, M. Collares-Pereira, M. Drancourt, et al. A New Borrelia Species Defined by Multilocus Sequence Analysis of Housekeeping Genes Appl. Envir. Microbiol., August 15, 2009; 75(16): 5410 - 5416. [Abstract] [Full Text] [PDF]
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K. R. Elmer, C. Reggio, T. Wirth, E. Verheyen, W. Salzburger, and A. Meyer Pleistocene desiccation in East Africa bottlenecked but did not extirpate the adaptive radiation of Lake Victoria haplochromine cichlid fishes PNAS, August 11, 2009; 106(32): 13404 - 13409. [Abstract] [Full Text] [PDF]
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S. Tasumi, C. A. Velikovsky, G. Xu, S. A. Gai, K. D. Wittrup, M. F. Flajnik, R. A. Mariuzza, and Z. Pancer High-affinity lamprey VLRA and VLRB monoclonal antibodies PNAS, August 4, 2009; 106(31): 12891 - 12896. [Abstract] [Full Text] [PDF]
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M. G. Shehata, A. M. Samy, S. A. Doha, A. R. Fahmy, R. M. Kaldas, B. D. Furman, and J. T. Villinski First Report of Leishmania tropica from a Classical Focus of L. major in North-Sinai, Egypt Am J Trop Med Hyg, August 1, 2009; 81(2): 213 - 218. [Abstract] [Full Text] [PDF]
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C. Li, L. Lu, X. Wu, C. Wang, P. Bennett, T. Lu, and D. Murphy Complete genomic sequences for hepatitis C virus subtypes 4b, 4c, 4d, 4g, 4k, 4l, 4m, 4n, 4o, 4p, 4q, 4r and 4t J. Gen. Virol., August 1, 2009; 90(8): 1820 - 1826. [Abstract] [Full Text] [PDF]
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L. Bernad, N. Duran-Vila, and S. F. Elena Effect of citrus hosts on the generation, maintenance and evolutionary fate of genetic variability of citrus exocortis viroid J. Gen. Virol., August 1, 2009; 90(8): 2040 - 2049. [Abstract] [Full Text] [PDF]
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F. Ntziora, D. Paraskevis, C. Haida, E. Magiorkinis, E. Manesis, G. Papatheodoridis, S. Manolakopoulos, A. Beloukas, S. Chryssoy, G. Magiorkinis, et al. Quantitative Detection of the M204V Hepatitis B Virus Minor Variants by Amplification Refractory Mutation System Real-Time PCR Combined with Molecular Beacon Technology J. Clin. Microbiol., August 1, 2009; 47(8): 2544 - 2550. [Abstract] [Full Text] [PDF]
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