Open Access Highly Accessed Research article

Molecular phylogeny of the higher and lower taxonomy of the Fusarium genus and differences in the evolutionary histories of multiple genes

Maiko Watanabe1*, Takahiro Yonezawa2, Ken-ichi Lee3, Susumu Kumagai3, Yoshiko Sugita-Konishi1, Keiichi Goto4 and Yukiko Hara-Kudo1

Author Affiliations

1 Division of Microbiology, National Institute of Health Sciences, Kamiyoga 1-18-1, Setagaya-ku, Tokyo 158-8501, Japan

2 School of Life Sciences, Fudan University, 220, Handan Rd. 200433, Shanghai, China

3 Veterinary Medical Science, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan

4 Food Research Laboratories, Mitsui Norin Co., Ltd., Miyabara 223-1, Fujieda-shi, Shizuoka 426-0133, Japan

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BMC Evolutionary Biology 2011, 11:322  doi:10.1186/1471-2148-11-322

Published: 3 November 2011

Additional files

Additional file 1:

Supplementary method S1.

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Additional file 2:

Supplementary figure S1. Maximum likelihood trees of the genus Fusarium and its related genera inferred from 18S rRNA gene (rDNA).

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Additional file 3:

Supplementary figure S2. Maximum likelihood trees of the genus Fusarium and its related genera inferred from internal transcribed spacer region 1.

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Additional file 4:

Supplementary figure S3. Maximum likelihood trees of the genus Fusarium and its related genera inferred from 5.8S rDNA.

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Additional file 5:

Supplementary figure S4. Maximum likelihood trees of the genus Fusarium and its related genera inferred from 28S rDNA. The GTR + I + Γ model was used as the model of the nucleotide substitution. The nodal numbers indicate the bootstrap probability (BP; 1000 replicated). The branch lengths are proportional to the estimated number of nucleotide substitutions. The BP values more than 75% are shown on the nodes. Although the RAxML program inferred the ML tree of 28S rDNA including all 50 strains, it could not be summarized nodal BPs. Therefore, all identical sequences were excluded and remaining 31 sequences were used for the estimation of nodal BPs.

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Additional file 6:

Supplementary method S2.

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Additional file 7:

Supplementary method S3.

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Additional file 8:

Supplementary figure S5. Comparisons of the evolutionary distances by two methods. Number of non-synonymous substitutions per non-per synonymous site (dS). Panel A: Distance method modified Nei-Gojorbori(JC) k = 2.5; panel B: ML method the codon model (pairwise). The estimated synonymous substitution reached plateau from the analysis by Nei Gojobori method. However there was no such tendency from the analysis by the maximum likelihood method. It means that although there were many multiple substitutions at the synonymmous sites, the maximum likelihood effectively correct the numbers of the multiple substitutions.

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