Gloeodontia-Maximum Likelihood-Tree
Figure. Molecular Phylogenetic analysis of Gloeodontia by the Maximum Likelihood method
The evolutionary history was inferred by using the Maximum Likelihood method based on the Kimura 2-parameter model [1]. The tree with the highest log likelihood (-5982.7851) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches(only if over 50%). Initial tree for the heuristic search were obtained by applying the Neighbor-Joining method to a matrix of pairwise distances estimated using the Maximum Composite Likelihood (MCL) approach. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.5405)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 60.1162% sites). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 20 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 1461 positions in the final dataset. Evolutionary analyses were conducted in MEGA6 [2].
1. Kimura M. (1980). A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16:111-120.
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.
- List with GenBank Sequences, which were used for the ML-Tree.
- Artomyces pyxidatus DQ389662
- Dentipellis fragilis AF506387
- Echinodontium tinctorium AF506430
- Gloeocystidiellum bisporum AY048875
- Gloeocystidiellum purpureum AF441338
- Gloeodontia columbiensis AF506444
- Gloeodontia discolor AF506445
- Gloeodontia pyramidata AF506446
- Gloeodontia subasperispora AF506404
- Gloiodon nigrescens AF506450
- Gloiodon strigosus AF506449
- Hericium abietis AF506456
- Hericium erinaceum JN649345
- Lactarius volemus AF506413
- Lentinellus cochleatus AF506417
- Lentinellus ursinus AF506419
- Peniophora cinerea subsp. fagicola AF506424
- Peniophora incarnata AF506425
- Stereum subtomentosum AF506482
- Xylobolus frustulatus AF506491
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