Maximum Likelihood-Tree-of-C.cinnamoneus
Molecular Phylogenetic analysis of Cortinarius cinnamoneus by the Maximum Likelihood method
The evolutionary history was inferred by using the Maximum Likelihood method based on the Tamura 3-parameter model [1]. The tree with the highest log likelihood (-1442.8567) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches (the bootstrap test was performed with 1000 replicates). A user-specified Minimum Evolution-tree was used as an initial tree in the heuristic search. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.1184)). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved only 29 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 591 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [2].
Type-sequences are in bold print. Incorrect identifications are marked with '**'. All C. cinnamoneus-sequences are reddish brown, correct ones are dark reddish brown, the incorrect pale reddish brown.
1. 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.
2. Tamura K., Stecher G., Peterson D., Filipski A., and Kumar S. (2013). MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology and Evolution30: 2725-2729.
The following sequences are taken from the [NCBI Nucleotide-Genbank https://www.ncbi.nlm.nih.gov/nuccore/]:
- 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 from the Unite/PlutoF Website
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