@article {7873,
	title = {Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites},
	journal = {Molecular Biology and Evolution},
	volume = {10},
	number = {6},
	year = {1993},
	note = {PDF},
	pages = {1396-1401},
	keywords = {gamma distribution, ML, phylogenetics, rates, substitution rates},
	author = {Yang, Ziheng}
}
@article {7876,
	title = {On the best evolutionary rate for phylogenetic analysis},
	journal = {Systematic Biology},
	volume = {47},
	number = {1},
	year = {1998},
	note = {PDF},
	pages = {125-133},
	keywords = {molecular characters, phylogenetics, rates, substitution rates},
	author = {Yang, Ziheng}
}
@article {7599,
	title = {Correct and incorrect vertebrate phylogenies obtained by the entire mitochondrial DNA sequences},
	journal = {Molecular Biology and Evolution},
	volume = {16},
	number = {5},
	year = {1999},
	note = {PDF},
	pages = {590{\textendash}601},
	keywords = {likelihood, ML, rates},
	author = {Takezaki, Naoko and Gojobori, Takashi}
}
@article {7537,
	title = {Effects of competition on rates of evolution, with special reference to bivalve mollusks and mammals},
	journal = {Systematic Zoology},
	volume = {22},
	number = {4},
	year = {1973},
	note = {PDF},
	pages = {486-506},
	keywords = {bivalvia, competition, diversification, evolution, rates},
	author = {Stanley, Steven M.}
}
@article {7519,
	title = {Likelihood, parsimony, and heterogeneous evolution},
	journal = {Molecular Biology and Evolution},
	volume = {22},
	number = {5},
	year = {2005},
	note = {PDF},
	pages = {1161-1164},
	keywords = {heterotachy, ML, parsimony, phylogenetics, rates},
	author = {Spencer, Matthew and Susko, Edward and Roger, Andrew J.}
}
@article {7328,
	title = {Analysis of rates of morphologic evolution},
	journal = {Annual Review of Ecology, Evolution, and Systematics},
	volume = {34},
	year = {2003},
	note = {PDF},
	pages = {605-632},
	keywords = {evolution, macroevolution, morphological characters, random walk, rates},
	author = {Roopnarine, Peter D.}
}
@inbook {7024,
	title = {Linking macroevolutionary pattern and developmental process in marginellid gastropods},
	booktitle = {Evolutionary patterns: growth, form, and tempo in the fossil record in honor of Alan Cheetham},
	year = {2001},
	note = {PDF},
	pages = {159-195},
	publisher = {University of Chicago Press},
	organization = {University of Chicago Press},
	address = {Chicago and London},
	keywords = {ecology, evodevo, macroevolution, mollusca, morphometrics, ontogeny, rates, speciation},
	author = {Nehm, Ross H.},
	editor = {Jackson, J. B. C. and Lidgard, Scott and McKinney, Frank. K.}
}
@article {6692,
	title = {Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous},
	journal = {Nature},
	volume = {431},
	number = {7011},
	year = {2004},
	note = {PDFTimes Cited: 0ArticleEnglishCited References Count: 30863ti},
	month = {OCT 21},
	pages = {980-984},
	abstract = {All inferences in comparative biology depend on accurate estimates of evolutionary relationships. Recent phylogenetic analyses have turned away from maximum parsimony towards the probabilistic techniques of maximum likelihood and bayesian Markov chain Monte Carlo (BMCMC). These probabilistic techniques represent a parametric approach to statistical phylogenetics, because their criterion for evaluating a topology-the probability of the data, given the tree-is calculated with reference to an explicit evolutionary model from which the data are assumed to be identically distributed. Maximum parsimony can be considered nonparametric, because trees are evaluated on the basis of a general metric-the minimum number of character state changes required to generate the data on a given tree-without assuming a specific distribution(1). The shift to parametric methods was spurred, in large part, by studies showing that although both approaches perform well most of the time(2), maximum parsimony is strongly biased towards recovering an incorrect tree under certain combinations of branch lengths, whereas maximum likelihood is not(3-6). All these evaluations simulated sequences by a largely homogeneous evolutionary process in which data are identically distributed. There is ample evidence, however, that real-world gene sequences evolve heterogeneously and are not identically distributed(7-16). Here we show that maximum likelihood and BMCMC can become strongly biased and statistically inconsistent when the rates at which sequence sites evolve change non-identically over time. Maximum parsimony performs substantially better than current parametric methods over a wide range of conditions tested, including moderate heterogeneity and phylogenetic problems not normally considered difficult.},
	keywords = {accuracy, bias, covariotide model, inference, mitochondrial-DNA, molecules, phylogenetics, rates, sequences, substitution},
	url = {<u><Go to ISI>://000224585600043</u>},
	author = {Kolaczkowski, B. and Thornton, J. W.}
}
@article {5938,
	title = {Testing the relationship between morphological and molecular rates of change along phylogenies},
	journal = {Evolution},
	volume = {56},
	number = {10},
	year = {2002},
	note = {PDF},
	pages = {1921{\textendash}1930},
	keywords = {likelihood, ML, molecular clock, molecules, morphology, phylogenetics, punctuated equilibrium, rates},
	author = {Bromham, Lindell and Woolfit, Megan and Lee, Michael S. Y. and Rambaut, Andrew}
}
@article {5887,
	title = {Testing for equal rates of cladogenesis in diverse taxa},
	journal = {Evolution},
	volume = {57},
	number = {11},
	year = {2003},
	note = {PDF},
	pages = {2469{\textendash}2474},
	keywords = {macroevolution, maximum likelihood, molecular characters, phylogenetics, rates, speciation},
	author = {Bokma, Folmer}
}
