File:Minimum Evolution-Tree-of-C.cinnamoneus.svg

Evolutionary relationships of Cortinarius cinnamoneus and relatives

The evolutionary history was inferred using the Minimum Evolution method [1]. The optimal tree with the sum of branch length = 0.16207422 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [2]. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Tamura 3-parameter method [3] and are in the units of the number of base substitutions per site. The rate variation among sites was modeled with a gamma distribution (shape parameter = 5). The ME tree was searched using the Close-Neighbor-Interchange (CNI) algorithm [4] at a search level of 2. The Neighbor-joining algorithm [5] was used to generate the initial tree. The analysis involved 38 nucleotide sequences. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 588 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [6].

Type-sequences are in bold print. Incorrect identifications are marked with '**'. All C. cinnamoneus-sequences are reddish brown, correct ones are dark reddish gray, the incorrect pale reddish gray.

The following sequences are taken from the NCBI Nucleotide-Genbank:

• C. aurantiobasis JX045670 Holotypus
• C. cf. cinnamomeus FJ039589
• C. cinnamomeus FJ157025
• C. cinnamomeus FJ717560
• C. cinnamomeus FJ845396
• C. cinnamomeus HQ604650
• C. cinnamomeus AY082608
• C. cinnamomeus AY750159
• C. cinnamomeus EU525963
• C. cinnamomeusJX436890
• C. cinnamomeusJN114080
• C. polaris GU234128
• C. semisanguineus DQ367899
• Cortinarius phoeniceus JN114084.1
• Cortinarius vitiosus NR 119966.1
• All other sequences are taken from the Unite/PlutoF Website (This are all sequences starting with UDB021).

1. Rzhetsky A. and Nei M. (1992). A simple method for estimating and testing minimum evolution trees. Molecular Biology and Evolution 9:945-967.

2. Felsenstein J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39:783-791.

3. Tamura K. (1992). Estimation of the number of nucleotide substitutions when there are strong transition-transversion and G + C-content biases. Molecular Biology and Evolution 9:678-687.

4. Nei M. and Kumar S. (2000). Molecular Evolution and Phylogenetics. Oxford University Press, New York.

5. Saitou N. and Nei M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution 4:406-425.