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      Sequestrate Lactarius species from tropical Africa: L. angiocarpus sp. nov. and L. dolichocaulis comb. nov.

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      Mycological Research
      Cambridge University Press (CUP)

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          Abstract

          Lactarius angiocarpus sp. nov. is described from miombo woodlands in Zambia. It is the third sequestrate representative of the Russulaceae described from tropical Africa. Morphological characters and DNA sequence data support its placement in Lactarius subgen. Plinthogali. Molecular kinship analyses confirm a multiple origin of sequestrate Russulaceae spp. As none of the previously sequenced sequestrate Russulaceae spp. has been assigned to the Plinthogali clade, the placement of L. angiocarpus indicates an additional point of origin of derivative sporocarp types within the Russulaceae. Within the same subgenus, another tropical African sequestrate species, L. dolichocaulis comb. nov. (syn. Arcangeliella dolichocaulis) is recognized.

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          The general stochastic model of nucleotide substitution.

          DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.
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            Markov Chasin Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees

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              Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence.

              Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap.
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                Author and article information

                Journal
                Mycological Research
                Mycological Research
                Cambridge University Press (CUP)
                09537562
                September 2004
                September 2004
                : 108
                : 9
                : 1042-1052
                Article
                10.1017/S0953756204000784
                15506016
                67c064cb-0b2c-4952-bff6-9a7f899f0e91
                © 2004

                http://www.elsevier.com/tdm/userlicense/1.0/

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