Multiple Comparisons of Log-Likelihoods with Applications to Phylogenetic Inference

Shimodaira, Hidetoshi; Hasegawa, Masami

doi:10.1093/oxfordjournals.molbev.a026201

Cited by 3,876 publications

(2,671 citation statements)

References 12 publications

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“…This result illustrates that, in this particular case, NNI-based heuristic is trapped in a local maximum because of insufficient tree space exploration conditioned by the BioNJ or MP starting topologies. Note however that the NNI-based and SPR-based ML phylogenetic models are not statistically different according to a SH test (9). Hence, while simultaneous NNIs get trapped in a local maximum, the estimated ML solution is not different from the one found by SPRs from a statistical point of view.…”

Section: Spr Heuristic Searchmentioning

confidence: 90%

Estimating Maximum Likelihood Phylogenies with PhyML

Guindon

Delsuc

Dufayard

et al. 2009

Methods in Molecular Biology

754

600

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Our understanding of the origins, the functions and/or the structures of biological sequences strongly depends on our ability to decipher the mechanisms of molecular evolution. These complex processes can be described through the comparison of homologous sequences in a phylogenetic framework. Moreover, phylogenetic inference provides sound statistical tools to exhibit the main features of molecular evolution from the analysis of actual sequences. This chapter focuses on phylogenetic tree estimation under the maximum likelihood (ML) principle. Phylogenies inferred under this probabilistic criterion are usually reliable and important biological hypotheses can be tested through the comparison of different models. Estimating ML phylogenies is computationally demanding though and careful examination of the results is warranted. This chapter focuses on PhyML, a software that implements recent ML phylogenetic methods and algorithms. We illustrate the strengths and pitfalls of this program through the analysis of a real data set. PhyML v3.0 is available from http://atgc.lirmm.fr/phyml 2 1 Introduction.

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Section: Spr Heuristic Searchmentioning

confidence: 90%

Estimating Maximum Likelihood Phylogenies with PhyML

Guindon

Delsuc

Dufayard

et al. 2009

Methods in Molecular Biology

754

600

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“…To investigate the support for a relationship between the Lipophrys -Coryphoblennius species pair and Salaria, we compared topologies obtained from unconstrained trees with results from phylogenetic inference where Lipophrys -Coryphoblennius and all the species of Salaria were constrained to form a monophyletic group, under the parsimony criterion -using a Wilcoxon signedrank (Templeton, 1983) and Kishino-Hasegawa (K-H; Kishino and Hasegawa, 1989) tests -and, under the likelihood criterion-using Shimodaira-Hasegawa (S-H; Shimodaira and Hasegawa, 1999) and K-H tests to compare constrained and unconstrained ME topologies -as implemented in PAUP * . Tests were performed on the combined mitochondrial and nuclear data set.…”

Section: Dna Analysismentioning

confidence: 99%

Phylogenetic analysis of Peri-Mediterranean blennies of the genus Salaria: Molecular insights on the colonization of freshwaters

Almada

Robalo

Levy

et al. 2009

Molecular Phylogenetics and Evolution

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a b s t r a c tIn this paper, the phylogenetic relationships of the marine blenny Salaria pavo and the freshwater S. fluviatilis and S. economidisi were analyzed using four molecular markers: the mitochondrial 12S rRNA, 16S rRNA, and the control region and the nuclear first intron of the S7 ribosomal protein. The monophyly of Salaria is supported, as well as that of S. pavo and that of all the freshwater members of Salaria. Thus, the present results support a single origin for all freshwater Mediterranean blenniids. Our results reject the placement of the species of Salaria in the genus Lipophrys as proposed in previous studies. Using a molecular clock calibrated with trans-Isthmian geminate blenniid species, the split between the ancestor of the freshwater lineage and the ancestor of S. pavo is tentatively placed in the Middle Miocene (well before the Messinian). The marine S. pavo displays a very low level of intraspecific sequence divergence consistent with a Pleistocene bottleneck. S. fluviatilis is a paraphyletic entity with S. economidisi nested within it. A Moroccan population of S. fluviatilis is more divergent than S. economidisi, both in nuclear and mitochondrial genes. Fish from Israel together with some Turkish samples represent the second oldest split. It is argued that these populations may represent cryptic species. Thus, further studies on the taxonomy of these freshwater blennies are urgently needed.

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“…Alternative phylogenetic topologies were tested using the Templeton Test (Templeton, 1983) and the Shimodaira and Hasegawa (SH) test using 1000 RELL bootstrap replicates (Goldman et al, 2000;Shimodaira and Hasegawa, 1999), both implemented in PAUP* v4.0. To perform the SH tests, a maximum-likelihood tree was found in an unconstrained analysis treating the entire data set as a single partition and using the best-Wt model of evolution.…”

Section: Phylogenetic Analysismentioning

confidence: 99%