Maximum-likelihood trees

Figure 5 A maximum-likelihood tree evolutionary model.

Figure 2 Maximum likelihood tree. Distance analysis was performed using PUZZLE 4.0.2 (Strimmer and von Haeseler, 1996). Because of the unequal rate of nucleotide substitution among the positions, the matrix of maximum likelihood distances was computed using the model of Tamura and Nei (1993) with gamma distance corrections for substitution rate heterogeneity.

Yang, Z., Goldman, N., and Rriday, A. (1995). Maximum likelihood trees from DNA sequences A pecuhar statistical problem. Syst. Biol. 44, 384-399. 

Pleurocarpy/non-pleurocarpy sensu Newton and De Luna (1999) was optimized onto one of the 24 most parsimonious trees (henceforth referred to as tree A) obtained from the molecular analysis in Bell and Newton (2004). In addition, the effects on optimization of using a slightly different topology (tree B), in which Leptotheca gaudichaudii is sister to Orthodontium lineare (as in the maximum likelihood tree in Bell and Newton, 2004), were explored. No other conflicts between topologies obtained under parsimony and likelihood criteria in Bell and Newton (2004) signiflcantly... 

Figure 4 Phylogenetic relationships among Claviceps species based on rDNA ITSl region. A—maximum likelihood tree ...

On the other side, maximum likelihood tree (out of 211 tested) placed Australian C. phalaridis basal to the group 2, whereas American C. paspali and C. citrina were closer to the ancestors of group 1. The branches with zero length were collapsed to polytomies. The neighbor-joining tree resembles the ML tree (with the exception of C. phalaridis) and their log likelihoods were almost identical (ML=-990.245 NJ =-990.256). The NJ tree branches supported by less than 50% bootstraps were reduced to polytomies. 

The most commonly used techniques for estimating trees for sequences may be grouped into three categories (1) distance methods, (2) maximum parsimony, and (3) maximum likelihood based methods. There are other methods but they are not widely used. Further, each of these categories covers many variations and even distinct methods with different properties and assumptions. These methods have often been divided different ways (different from the three categories here) such as cladistic versus phenetic, character-based versus non-character-based, method-based versus criterion-based, and others. These divisions may merely reflect particular predjudices by the person making them and can be artificial. 

Strimmer K., and von Haeseler, A. (1996). Quartet puzzling a quartet maximum-likelihood method for reconstructing tree topologies. Mol. Biol. Evol. 13, 964—969. 

Arisue N, Hasegawa M, Hashimoto T (2005) Root of the eukaryota tree as inferred from combined maximum likelihood analyses of multiple molecular sequence data. Mol Biol Evol 22 409-420... 

Fig. 5.2. Phylogeny of monopisthocotylean Monogenea based on SSU rDNA. The tree topology is from a Bayesian analysis with nodal support indicated, from top to bottom, for maximum likelihood (bootstrap%, n = 100), maximum parsimony (bootstrap%, n = 1000) and Bayesian inference (posterior probabilities). Figure from Matejusova etal. (2003).

Fig. 10.4. Maximum likelihood phylogenetic trees of (a) pyruvate ferredoxin oxidoreductase (PFO) and (b) Fe-hydrogenase genes. Trees and branch support were obtained as in Fig. 10.3. Branch support above branches is shown only for those nodes with greater than 85% bootstrap support. Anaerobic eukaryotes are shown in bold...

Figure 3 Phylogenetic relationship of the Cordyceps fungi based on the total sequence data. A tandemly concatenated nuclear and mitochondrial rDNA data set (4272 nucleotide sites) was subjected to neighbor-joining (NJ), maximum-likelihood quartet puzzling (ML-PUZZLE) and maximum parsimony (MP) analyses. The strict consensus tree of the three analyses is presented. Numbers at the nodes are bootstrap values (%) obtained by the NJ (left), ML-PUZZLE (center), and MP (right) methods, respectively. Shown on the right side are host organisms, names of the clades, and morphological types of the stromata.

Pairwise distance is calculated using maximum-likelihood estimators of substitution rates. The most popular distance tree-building programs have a limited number of substitution models, but PAUP 4.0 implements a number of models, including the actual model estimated from the data using maximum likelihood, as well as the log-det distance method. 

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