Phylogeny Estimation and Hypothesis Testing using Maximum Likelihood

By Ramakant Sharma, Sravanthi Polsani. 2003

663 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/e721e12b6752ad93aae371ba63b13dab12254ee7

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Citations in the corpus

Taxonomy, biogeography and evolution of Euproctus (Amphibia: Salamandridae), with the resurrection of the genus Calotriton and the description of a new endemic species from the Iberian Peninsula (2005, methodology): “ML estimates of divergence times for the combined dataset were obtained after discovery of lineage rate constancy across the tree using the likelihood ratio test (Huelsenbeck & Crandall, 1997).”
Distinguishing importation from diversification of quinolone-resistant Neisseria gonorrhoeae by molecular evolutionary analysis (2007, methodology): “Models of nucleotide substitution were assessed using a maximum likelihood approach [30] with best-fit models selected by Modeltest v3.”
Systematics of Fagaceae: Phylogenetic Tests of Reproductive Trait Evolution (2001, methodology): “We performed hierarchical likelihood ratio tests (see Huelsenbeck and Crandall 1997) starting with a neighbor-joining tree and determined that the model (Posada and CrandallTIM + G 1998), a submodel of the general time reversible model (e.g., Yang 1994), was appropriate for tree estimation.”
Reconstructing routes of invasion using genetic data: why, how and so what? (2010, background): “It may be possible to calculate the likelihood of the tree topology and to carry out statistical tests against alternative tree topologies (Huelsenbeck & Crandall 1997), but it is not possible to determine the likelihood of the history suggested by the topology or the weighting of this history…”
Plio‐Pleistocene climatic oscilations, Holarctic biogeography and speciation in an avian subfamily (2003, methodology): “A ML ratio test (Huelsenbeck & Crandall, 1997) showed that the assumption of the molecular clock was violated preventing a single clock calibration for the whole subfamily.”
Phylogeography of the northern hogsucker, Hypentelium nigricans (Teleostei: Cypriniformes): genetic evidence for the existence of the ancient Teays River (2003, background): “…using a likelihood ratio test, )2logK ¼ )2(logL0 ) logL1) where the likelihood under the null hypothesis (L0) assumes that DNA substitution rates are equal among lineages and the likelihood under the alternative hypothesis (L1) allows substitution rates to vary (Huelsenbeck & Crandall, 1997).”
A STUDY OF THE PSEUDO‐NITZSCHIA PSEUDODELICATISSIMA/CUSPIDATA COMPLEX (BACILLARIOPHYCEAE): WHAT IS P. PSEUDODELICATISSIMA? 1 (2003, methodology): “Use of an optimal model is essential because phylogenetic analyses might otherwise be inaccurate or inconsistent (Swofford et al. 1996, Huelsenbeck and Crandall 1997, Sullivan and Swofford 1997, Lewis 1998, Kelsey et al. 1999, Posada and Crandall 2001).”
TRADITIONAL GENERIC CONCEPTS VERSUS 18S rRNA GENE PHYLOGENY IN THE GREEN ALGAL FAMILY SELENASTRACEAE (CHLOROPHYCEAE, CHLOROPHYTA) (2001, methodology): “This program calculates the likelihood test statistic from the evaluation of a null hypothesis tree under 56 different models of nucleotide evolution (Huelsenbeck and Crandall 1997, Posada and Crandall 1998).”
Phylogeography of the pool frog Rana (Pelophylax) lessonae in the Italian peninsula and Sicily: multiple refugia, glacial expansions and nuclear–mitochondrial discordance (2008, methodology): “To estimate the divergence time between major lineages as they emerged from phylogenetic analyses, we first carried out a likelihood-ratio test according to Huelsenbeck & Crandall (1997) in order to test for the homogeneity of the substitution rates across all clades.”
ModelTest Server: a web-based tool for the statistical selection of models of nucleotide substitution online (2006, background): “The only option within the hierarchical likelihood framework (4,8,9) is the statistical confidence level.”
Biogeography and molecular phylogeny of the genus Schizothorax (Teleostei: Cyprinidae) in China inferred from cytochrome b sequences (2006, methodology): “An LRT (Huelsenbeck & Crandall, 1997) was performed with ML trees with and without a molecular clock constraint using paup*.”
Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. (2004, methodology): “Indeed, posterior probabilities of trees are already being used to estimate phylogenies (Holder and Lewis, 2003; Huelsenbeck et al., 2001, 2002; Larget and Simon, 1999; Mau and Newton, 1997; Mau et al., 1999; Yang and Rannala, 1997).”
Molecular markers for the phylogenetics of mites and ticks (2002, methodology): “In addition to providing new ways of constructing trees, these methods also allow a statistical approach to testing phylogenetic hypotheses ( Huelsenbeck & Crandall, 1997; Huelsenbeck & Rannala, 1997; Goldman et al., 2000; Huelsenbeck et al., 2001; Lewis, 2001b).”
Global stingless bee phylogeny supports ancient divergence, vicariance, and long distance dispersal (2009, background): “Gene fragments were analysed both individually and combined , and partitioned into exon and intron regions when appropriate to account for variable evolutionary rates between gene regions (Huelsenbeck & Crandall, 1997; Schwarz et al., 2004).”
DNA phylogeny of Lacerta (Iberolacerta) and other lacertine lizards (Reptilia: Lacertidae): Did competition cause long‐term mountain restriction? (2004, methodology): “For data set II, the likelihood ratio test (Huelsenbeck & Crandall, 1997) was first used to assess the statistical significance of the difference between the log likelihood of the trees calculated with and without molecular clock assumptions.”
Molecular Systematics and Evolution: Theory and Practice (2002, background): “In addition, an increasing number of empirical and philosophical papers have been published that discuss the different methods of phylogenetic analysis in terms of hypothesis testing (for parsimony [Kluge, 1997] and for maximum-likelihood [Huelsenbeck and Bull, 1996; Huelsenbeck and Crandall, 1997; ”