@article {7810,
	title = {Homology and the optimization of DNA sequence data},
	journal = {Cladistics},
	volume = {17},
	year = {2001},
	note = {PDF},
	pages = {S3-S11},
	keywords = {direct optimization, dna, homology, molecules, phylogenetics, poy},
	author = {Wheeler, Ward}
}
@article {7627,
	title = {Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes},
	journal = {Evolution},
	volume = {37},
	number = {2},
	year = {1983},
	note = {PDF},
	pages = {221-244},
	keywords = {mammalia, molecules, phylogenetics, templeton test},
	author = {Templeton, Alan R.}
}
@inbook {7592,
	title = {When are phylogeny estimates from molecular and morphological data incongruent?},
	booktitle = {Phylogenetic analysis of DNA sequences},
	year = {1991},
	note = {xerox},
	pages = {295-333},
	publisher = {Oxford University Press},
	organization = {Oxford University Press},
	address = {New York and Oxford},
	keywords = {congruence, molecules, morphology, phylogenetics},
	author = {Swofford, David L.},
	editor = {Miyamoto, Michael M. and Cracraft, Joel}
}
@article {7423,
	title = {Evidence for the origin of eusociality in the corbiculate bees (Hymenoptera: Apidae)},
	journal = {Journal of the Kansas Entomological Society},
	volume = {74},
	number = {1},
	year = {2001},
	note = {xerox},
	pages = {10-16},
	keywords = {fossils, molecules, morphology, paleontology, phylogenetics, phylogeny},
	author = {Schultz, Ted R. and Engel, Michael S. and Ascher, John S.}
}
@article {7360,
	title = {A theoretical study of the underestimation of brench length by the maximum parsimony principle},
	journal = {Systematic Zoology},
	volume = {38},
	year = {1989},
	pages = {1-6},
	keywords = {molecules, parsimony, phylogenetics, saturation},
	author = {Saitou, N.}
}
@article {7224,
	title = {Species or supraspecific taxa as terminals in cladistic analysis? Groundplans versus exemplars revisited},
	journal = {Systematic Biology},
	volume = {50},
	number = {2},
	year = {2001},
	note = {PDFTimes Cited: 31Editorial MaterialEnglishCited References Count: 84431xn},
	month = {MAR-APR},
	pages = {290-300},
	keywords = {molecules, morphology, phylogenetics, systematics},
	url = {<u><Go to ISI>://000168657200009</u>},
	author = {Prendini, L.}
}
@article {6985,
	title = {Multiple sequence alignment for phylogenetic purposes},
	journal = {Australian Systematic Botany},
	volume = {19},
	year = {2006},
	note = {PDF},
	pages = {479{\textendash}539},
	keywords = {alignment, homology, molecules, multiple sequence alignment, phylogenetics},
	author = {Morrison, David A.}
}
@article {6937,
	title = {Fine scale endemism on coral reefs: archipelagic differentiation in turbinid gastropods},
	journal = {Evolution},
	volume = {59},
	number = {1},
	year = {2005},
	note = {PDF},
	pages = {113-125},
	keywords = {biogeography, ecology, endemism, gastropoda, molecules, mollusca, phylogenetics, phylogeny, reef, speciation, sympatry, turbinidae},
	author = {Meyer, Christopher P. and Geller, Jonathan B. and Paulay, Gustav}
}
@article {6936,
	title = {Molecular systematics of cowries (Gastropoda: Cypraeidae) and diversification patterns in the tropics},
	journal = {Biological Journal of the Linnean Society},
	volume = {79},
	year = {2003},
	note = {PDF},
	pages = {401-459},
	keywords = {biogeography, classification, diversification, gastropoda, molecular clock, molecules, phylogenetics, phylogeny, specialization, taxonomy},
	author = {Meyer, Christopher P.}
}
@article {6824,
	title = {Phylogenetic analysis of molluscan mitochondrial LSU rDNA sequences and secondary structures},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {15},
	number = {1},
	year = {2000},
	note = {PDF},
	month = {April},
	pages = {83-102},
	keywords = {16S, molecules, mollusca, phylogenetics},
	author = {Lydeard, Charles and Holznagel, Wallace E. and Schnare, Murray N. and Gutell, Robin R.}
}
@article {6757,
	title = {The phylogeny of termites (Dictyoptera: Isoptera) based on mitochondrial and nuclear markers: implications for the evolution of the worker and pseudergate castes, and foraging behaviors},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {48},
	year = {2008},
	note = {PDF},
	pages = {615-627},
	keywords = {arthropoda, behavior, molecules, phylogenetics, phylogeny, poy, sensitivity, termites},
	author = {Legendre, Fr{\'e}d{\'e}ric and Whiting, Michael F. and Bordereau, Christian and Cancello, Eliana, M. and Evans, Theodore A. and Grandcolas, Philippe}
}
@inbook {6761,
	title = {Maximum likelihood as an alternative to parsimony for inferring phylogeny using nucleotide sequence data},
	booktitle = {Molecular Systematics of Plants II},
	year = {1998},
	note = {xerox},
	pages = {132-163},
	publisher = {Kluwer},
	organization = {Kluwer},
	address = {Boston},
	keywords = {ML, molecules, phylogenetics},
	author = {Lewis, Paul O.},
	editor = {Soltis, D. E. and Soltis, P. S. and Doyle, J. J.}
}
@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.}
}
@inbook {6658,
	title = {The neutral theory as a basis for understanding the mechanism of evolution and variation at the molecular level},
	booktitle = {Molecular evolution, protein polymorphism and the neutral theory},
	year = {1982},
	pages = {3-56},
	publisher = {Springer},
	organization = {Springer},
	address = {Berlin},
	keywords = {evolution, molecular evolution, molecules, phylogenetics},
	author = {Kimura, M.},
	editor = {Kimura, M.}
}
@article {6669,
	title = {Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea},
	journal = {Journal of Molecular Evolution},
	volume = {29},
	year = {1989},
	pages = {170-179},
	keywords = {likelihood, molecules, phylogenetics},
	author = {Kishino, Hirohisa and Hasegawa, Masami}
}
@book {6652,
	title = {The simple fool{\textquoteright}s guide to PCR},
	year = {1989},
	note = {DO NOT HAVE},
	pages = {23},
	publisher = {University of Hawaii},
	organization = {University of Hawaii},
	address = {Honolulu, Hawaii},
	keywords = {16S, molecules, pcr, phylogenetics},
	author = {Kessing, B. and Croom, H. and Martin, A. and McIntosh, C. and Owen Mcmillan, W. and Palumbi, S.}
}
@inbook {6511,
	title = {Discriminating between phylogenetic signal and random noise in DNA sequences},
	booktitle = {Phylogenetic analysis of DNA sequences},
	year = {1991},
	pages = {278-294},
	publisher = {Oxford University Press},
	organization = {Oxford University Press},
	address = {New York and Oxford},
	keywords = {molecules, noise, phylogenetics},
	author = {Hillis, David M.},
	editor = {Miyamoto, Michael M. and Cracraft, Joel}
}
@article {6353,
	title = {Maximum likelihood inference of phylogenetic trees, with special reference to a Poisson process model of DNA substitution and to parsimony analysis},
	journal = {Systematic Zoology},
	volume = {39},
	number = {4},
	year = {1990},
	note = {PDF},
	pages = {345-361},
	keywords = {likelihood, ML, molecules, phylogenetics},
	author = {Goldman, Nick}
}
@article {6331,
	title = {A phylogeny of megachiropteran bats (Mammalia: Chiroptera: Pteropodidae) based on direct optimization analysis of one nuclear and four mitochondrial genes},
	journal = {Cladistics},
	volume = {19},
	year = {2003},
	note = {PDF},
	pages = {496-511},
	keywords = {bats, chiroptera, mammalia, molecules, phylogenetics, phylogeny, poy},
	author = {Giannini, Norberto P. and Simmons, Nancy B.}
}
@article {6169,
	title = {Ribosomal RNA secondary structure: compensatory mutations and implications for phylogenetic analysis},
	journal = {Molecular Biology and Evolution},
	volume = {10},
	number = {1},
	year = {1993},
	note = {PDF},
	pages = {256-267},
	keywords = {28S, molecules, phylogenetics, rDNA, secondary structure},
	author = {Dixon, Michael T. and Hillis, David M.}
}
@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 {5791,
	title = {Assessing the relative contribution of molecular and morphological characters in sumultaneous analysis trees},
	journal = {Molecular Phylogenetics and Evolution},
	volume = {9},
	number = {3},
	year = {1998},
	note = {PDF},
	pages = {427-436},
	keywords = {combined data analyses, molecules, morphology, phylogenetics},
	author = {Baker, Richard H. and Yu, Xiaobo and DeSalle, Rob}
}
