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| Abstract.- Modes and rates of molecular evolution, and congruence and combinability for phylogenetic reconstruction, of portions of the nuclear large ribosomal subunit (nLSU-rDNA) and mitochondrial small subunit (mtSSU-rDNA) genes are investigated in the mushroom genus Amanita. The AT content was higher in the mtSSU-rDNA than in the nLSU-rDNA. A transition bias was present in the nLSU-rDNA but not in the mtSSU-rDNA, in which AT substitutions were as frequent as transitions. Among-sites rate variation in nucleotide substitutions at variable sites was present in the nLSU-rDNA, but not in the mtSSU-rDNA. Likelihood ratio tests indicated very different models of evolution for the two molecules. A molecular clock could be rejected for both data sets. Rates of molecular evolution between the two molecules were uncoupled: faster evolutionary rates in the mtSSU-rDNA and nLSU-rDNA were not observed for the same taxa. In separate phylogenetic analyses, the nLSU-rDNA data set had higher phylogenetic resolution. The partition homogeneity test and observation of statistical bootstrap support for branches indicated absence of conflict in the phylogenetic signal between the two data sets; however, tree topologies produced from the separate data sets were not congruent. Heterogeneity in modes and rates of evolution among and between the two molecules pose difficulties for a combined analysis of the two data sets: the use of equally weighted parsimony is not fully satisfactory when rate heterogeneity is present, and it is impractical to determine a model for maximum likelihood analysis that fits simultaneously two heterogeneous data sets. Overall topologies produced from either the separated or combined analyses using various tree-reconstruction methods were identical for nearly all statistically significant branches. |
Figure 2: Phylogenetic relationships in Amanita produced using maximum likelihood, and relative rate tests. Values above branches are bootstrap supports. (a) Single ML tree produced from the the nLSU-rDNA data set. (b) One of the three equally likely trees produced from the mtSSU-rDNA data set.
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