Boidinia-Maximum-Likelihood-Tree

Figure. Figure. Molecular Phylogenetic analysis of Boidinia and Gloeopeniophorella by 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 (-4514.2002) is shown. The percentage of trees in which the associated taxa clustered together is shown next to the branches. A Strict Consensus Maximum-Parsimony 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 = 0.5454)). The rate variation model allowed for some sites to be evolutionarily invariable ([+I], 59.4678% sites). The tree is drawn to scale, with branch lengths measured in the number of substitutions per site. The analysis involved 19 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 1167 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

• Boidinia_granulata AY048880
• Boidinia_propinqua AF506379
• Lactarius_volemus AF506413
• Boidinia_sp. AF506378
• Boidinia_aculeata AF506433
• Gloeopeniophorella_convolvens AF506435
• Gloeopeniophorella_laxa AF506440
• Russula_nauseosa AF506462
• Boidinia_furfuracea AF506376
• Pseudoxenasma_verrucisporum AF506426
• Hericium_americanum AF506458
• Hericium_abietis AF506456
• Gloeocystidiellum_porosum AF310099
• Lactarius_leonis AF506411
• Russula_violacea AF506465
• Lactarius_subemboratus AF506412