Recommended Bibliography for IB 200: Index
History and Philosophy of Systematic Biology
The Hennig Principle
Homology
Characters and Character States
Character Coding
Molecular Data
Classification - Basic Principles
DNA Barcoding
Species Concepts
Phylogenetic Tree Reconstruction
Phenetics
Maximum Likelihood
Bayesian Methods
Phylogenetic Trees: Support and Tree Comparisons
Reticulation and Phylogeography
Morphometrics
Biogeography
Macroevolution
Comparative Methods
Conservation
* = required in 2011 course; other special recommendations starred for direct relevance to the course, basic to the field ("something everyone should have read"), etc.
History and Philosophy of Systematic Biology
Bock, W. J. (1973) Philosophical foundations of classical evolutionary classification Systematic Zoology 22: 375-392 Part of a general symposium on "Contemporary Systematic Philosophies," there are some other interesting papers here.
Brower, A. V. Z. (2000) Evolution Is Not a Necessary Assumption of Cladistics Cladistics 16: 143-154
Cleland, C. L. (2001) Historical science, experimental science, and the scientific method. Geology 29: 987-990
Dayrat, Benoit (2005) Ancestor-descendant relationships and the reconstruction of the Tree of Lif Paleobiology 31: 347-353
Donoghue, M.J. and J.W. Kadereit (1992) Walter Zimmermann and the growth of phylogenetic theory Systematic Biology 41: 74-84
Faith, D. P. and J. W. H. Trueman (2001) Towards an inclusive philosophy for phylogenetic inference Systematic Biology 50: 331-350
Gaffney, E. S. (1979) An introduction to the logic of phylogeny reconstruction, pp. 79-111 in Cracraft, J. and N. Eldredge (eds.) Phylogenetic Analysis and Paleontology Columbia University Press, New York.
Gilmour, J. S. L. (1940) Taxonomy and philosophy, pp. 461-474 in J. Huxley (ed.) The New Systematics Oxford
Hull, D. L. (1974) Philosophy of Biological Sciences. Prentice-Hall, Englewood Cliffs, NJ.
Hull, D. L. (1978) A matter of individuality Phil. of Science 45: 335-360
Hull, D. L. (1978) The principles of biological classification: the use and abuse of philosophy
Hull, D. L. (1984) Cladistic theory: hypotheses that blur and grow, pp. 5-23 in T. Duncan and T. F. Stuessy (eds.) Cladistics: Perspectives on the Reconstruction of Evolutionary History Columbia University Press, New York
* Hull, D. L. (1988) Science as a process: an evolutionary account of the social and conceptual development of science University of Chicago Press. An already classic work on the recent, violent history of systematics; used as data for Hull's general theories about scientific change.
Hull, D. L. (1999) The use and abuse of Sir Karl Popper. Biology and Philosophy 14: 481-504
Kitts, D. B. (1977) Karl Popper, verifiability, and systematic zoology. Systematic Zoology 26: 185-194
Kluge, A. G. (1999) The Science of Phylogenetic Systematics: Explanation, Prediction and Test Cladistics 15: 429-436
Kluge, A. J. (2001) Philosophical conjectures and their refutation Systematic Biology 50: 322-330
Kuhn, T. S. (1970) The Structure of Scientific Revolutions, second edition. University of Chicago Press. A must-read for any scientist.
Mayr, E. (1982) The Growth of Biological Thought. Harvard University Press, Cambridge, Mass.
Laudan, L. (1977) Progress and Its Problems. University of California Press, Berkley.
Losee, J. (1980) A Historical Introduction to the Philosophy of Science. Second edition. Oxford University Press. The best single-volume account of changes since Aristotle in how science proceeds -- strongly recommended.
McKelvey, B. (1982) Organizational Systematics, Univ. of California Press Berkeley
Mishler, B. D. (1989) Untitled review of Hull, D.L. (1988) Science as a process. Systematic Botany 14: 266-268
Mishler, Brent D. (2009). Three centuries of paradigm changes in biological classification: Is the end in sight? Taxon, 58(1), 61-67.
O'Hara, R. J. (1992) Telling the tree: Narrative representation and the study of evolutionary history Biology and Philosophy 7: 135-160
O'Keefe, F. R. and P. M. Sander (1999) Paleontological paradigms and inferences of phylogenetic pattern: a case study. Paleobiology 25: 518-533
de Queiroz, K (1987) Systematics and the Darwinian revolution. Philosophy of Science 55: 238-259
de Queiroz, K. and S. Poe (2001) Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration. Systematic Biology 50: 305-321
Sober, E. (1988) Reconstructing the past, Chapter 1. MIT Press.
** Sober, E. (2008). Evidence and Evolution: the logic behind the science, Cambridge University Press. Particularly good on philosophy of statistics (frequentism vs. likelihood vs. Bayesian approaches) and their relation to (1) inferring phylogenies and (2) inferring natural selection.
Stamos, D. N. (1996) Popper, falsifiability, and evolutionary biology. Biology and Philosophy 11: 161-191
Stevens, P. F. (1994) The development of biological systematics. Columbia University Press, New York.
Wiley, E. O. (1975) Karl R. Popper, systematics, and classification: a reply to Walter Bock and other evolutionary taxonomists. Systematic Zoology 24: 233-243
Wiley, E. O. (1981) Phylogenetics: The Theory and Practice of Phylogenetic Systematics.
Winsor, Mary Pickard (1995). "The english debate on taxonomy and phylogeny." History and Philosopy of the Life Sciences, 17(2), 227-252.
Ax, P. (1987) The phylogenetic system. John Wiley, Chichester.
Dupuis, C. (1984) Willi Hennig? s impact on taxonomic thought. Annual Review of Ecology and Systematics 15: 1-24
* Farris J.S. (1983) The logical basis of phylogenetic analysis. pp. 7-36 In N Platnick and V Funk (eds.): Advances in Cladistics, Volume 2. NY:Columbia Univ. Press
Forey, P. L., C. J. Humphries, I. L. Kitching, R. W. Scotland, D. J. Siebert, and D. M. Williams. (1992) Cladistics. The Systematics Association Publication No.10, Oxford University Press, New York
Philippe Grandcolas, P., P. Deleporte, L. Desutter-Grandcolas, and C. Daugeron (2001) Phylogenetics and Ecology: As Many Characters as Possible Should Be Included in the Cladistic Analysis. Cladistics 17: 104-110
** Hennig, W. (1965) Phylogenetic systematics. Annual Review of Entomology 10: 97-116
Hennig, W. (1966) Phylogenetic systematics. University of Illinois Press, Urbana.
Kitching, I. J., P. L. Forey, C. J. Humpheries, and D. M. Williams. (1998) Cladistics: The Theory and Practice of Parsimony Analysis. Second Edition. The Systematics Association Publication No. 11 Oxford University Press, Oxford.
Kluge, A.G. (1994) Moving targets and shell games. Cladistics 10: 403-413
Kluge, A. G. (2001) Parsimony with and without Scientific Justification. Cladistics 17: 199-210
Lundberg, J. G. and L. A. McDade. (1990) Systematics. pp 65-108 in Methods for Fish Biology, American Fisheries Society.
Mishler, B. D. and E. De Luna. (1991) The use of ontogenetic data in phylogenetic analyses of mosses. Advances in Bryology 4: 121-167 Especially pages 129-143
**** Mishler, Brent D. (2005). The logic of the data matrix in phylogenetic analysis. In V.A. Albert (ed.), Parsimony, Phylogeny, and Genomics, Oxford University Press, 57-70. doi: 10.1093/acprof:oso/9780199297306.003.0004
Lindberg, D.R. (1992) Systematic Paleontology. Pp. 31-37 In: J. H. Lipps, ed. Fossil Prokaryotes and Protists, Blackwell Scientific Publications, Ltd., Oxford
Pol, D. and M. E. Siddall (2001) Biases in Maximum Likelihood and Parsimony: A Simulation Approach to a 10-Taxon Case. Cladistics 17: 266-281
de Queiroz, K. and J. Gauthier (1992) Phylogenetic taxonomy. Annual Review of Ecology and Systematics 23: 449-480
Wilkinson M. (1994) Three-taxon statements - when is a parsimony analysis is also a clique analysis. Cladistics 10: 221-223
Aboitiz, F. (1988) Homology, a comparative or a historical concept? Acta Biotheoretica 37: 27-29
Bang, R., R. DeSalle, and W. Wheeler. (2000) Transformationalism, taxism, and developmental biology in systematics. Systematic Biology 49: 19-28
Callazo, A. (2000) Developmental variation, homology, and the Pharngula stage. Systematic Biology 49: 3-18
Hall, B. K. (ed.). (1994) Homology: the hierarchical basis of comparative biology. Academic Press, San Diego. 483 pp.
Haszprunar, G. (1992) The types of homology and their significance for evolutionary biology and phylogenetics. Journal of Evolutionary Biology 5: 13-24
Lutzoni, L., P. Wagner, V. Reeb, and S. Zoller (2000) Integrating ambiguously aligned regions of DNA sequences without violating positional homology. Systematic Biology 49: 628-651
Patterson, C (1982) Morphological characters and homology. pp. 21-74 in Josey, K.A. and Friday, A.E. (eds.) Problems of Phylogenetic Reconstruction. Academic Press.
Patterson, C (1988) Homology in classical and molecular biology. Mol. Biol. Evolution 5: 603- 625
Roth, V.L. (1984) On homology Bioi. J. Linn. Soc. 22: 13-29
** Roth, V.L. (1988) The biological basis of homology. In Ontogeny and Systematics. Humpries, C.J. (ed.) Columbia University Press, NY.
Roth, V.L. (1991) Homology and hierarchies: Problems solved and unresolved. Journal of Evolutionary Biology 4: 167-194
Scotland, R. W. (2000) Taxic homology and three-taxon statement analysis. Systematic Biology 49: 480-500
Scotland, R. W. and M. A. Carine (2000) Classification or Phylogenetic Estimates? Cladistics 16: 411-419
Stevens, P.F. (1984) Homology and phylogeny: morphology and systematics. Systematic Botany 9: 395-409 Part of a symposium on homology in botany
Wagner, G. P. (1989) The biological homology concept. Ann. Rev. Ecol. Syst. 20: 51-69
Wray, G. A. and C. J. Lowe. (2000) Developmental regulatory genes and echinoderm evolution. Systematic Biology. 49: 28-51
Buschbeck, E. K. (2000) Neurobiological constraints and fly systematics: how different types of neural characters can contribute to a higher level dipteran phylogeny. Evolution 54: 888-898
Chappill, J. A. (1989) Quantitative characters in phylogenetic analysis. Cladistics 5: 217-234
Fink, William L. (1982). The Conceptual Relationship Between Ontogeny and Phylogeny. Paleobiology, 8(3), 254-264. (JSTOR)
Goldman, N. (1988) Methods of discrete coding of morphological characters for numerical analysis. Cladistics 4: 59-71
Hauser, D. L. and W. Presch. (1991) The effect of ordered characters on phylogenetic reconstruction. Cladistics 7: 243-265
Hibbett, D. S. and M. J. Donoghue (2001) Analysis of character correlations among wood decay mechanisms, mating systems, and substrate ranges in Homobasidiomycetes. Systematic Biology 51: 215-242
Jenner, R. A. (2001) Bilaterian phylogeny and uncritical recycling of morphological data sets. Systematic Biology 50: 730-742
Le Quesne, W. J. (1969) A method of selection of characters in numerical taxonomy. Systematic Zoology 18: 201-205
Lee, D.-C. and H. N. Bryant. (1999) A Reconsideration of the Coding of Inapplicable Characters: Assumptions and Problems. Cladistics 15: 373-378
Lipscomb, D. L. (1992) Parsimony, homology, and the analysis of multistate characters. Cladistics 8: 45-65
Mabee, P. M. (1989a) Assumptions underlying the ontogenetic use sequences for determining character state order. Trans. Amer. Fish. Soc. 118: 159-166
** Mishler, B. D. (2005) The logic of the data matrix in phylogenetic analysis. In V.A. Albert (ed.), Parsimony, Phylogeny, and Genomics, pp. 57-70. Oxford University Press.
** Mishler, B. D. and E. De Luna. (1991) The use of ontogenetic data in phylogenetic analyses of mosses. Advances in Bryology 4: 121-167
* Neff, N.A. (1986) A rational basis for a priori character weighting. Systematic Zoology 35: 102-109
Monteiro, L. R. (2000) Why morphometrics is special: the problem with using partial warps as characters for phylogenetic analysis. Systematic Biology 49: 796-800
O'Keffe, F. R. and P. J. Wagner. (2001) Inferring and testing hypotheses of cladistic character independence by using character compatibility. Systematic Biology 50: 657-675
Pimentel, R.A. and Riggins, R. (1987) The nature of cladistic data. Cladistics 3: 201-209
Pogue, M. G. and M. F. Mickevich. (1990) Character definitions and character state delineation: the b?te noire of phylogenetic inference. Cladistics 6: 319-361
Rae, T. C. (1998) The logical basis for the use of continuous characters in phylogenetic systematics.? Cladistics 14: 221-228
Schander, C. and P. Sundberg. (2001) Useful characters in gastropod phylogeny: soft information or hard facts? Systematic Biology 50: 136-141
Simmons, M. P. and H. Ochoterena. (2000) Gaps as characters in sequence-based phylogenetic analysis. Systematic Biology 49: 369-381
Simmons, M. P., H. Ochoterena, and T. G. Carr. (2001) Incorporation, relative homoplasy, and effect of gap characters in sequenced-based phylogenetic analysis. Systematic Biology 50: 454-461
Simmons, N. P. (2001) Misleading results from the use of ambiguity coding to score polymorphisms in higher-level taxa. Systematic Biology 50: 613-620
Slowinski, J. B. (1993) Unordered versus "ordered" characters. Systematic Biology 42: 155-165
Smith, E. N. and R. L. Gutberlet jr. (2001) Generalized frequency coding: a method of preparing polymorphic multistate characters for phylogenetic analysis. Systematic Biology 51: 156-169
* Stevens, P.F. (1991) Character states, morphological variation, and phylogenetic analysis: a review. Systematic Botany 16: 553-583
Strong, E. E. and D. Lipscomb. (1999) Character coding and inapplicable data. Cladistics 15: 363-371
Wagner, P. J. (2000) Exhaustion of morphologic character states among fossil taxa. Evolution 54: 365-386
Wagner, G. P. (ed.). (2001) The character concept in evolutionary biology. Academic Press, San Diego.
Wagner, P. J. (2000) Exhaustion of morphologic character states among fossil taxa. Evolution 54: 365-386
Wiens, J. J. (1995) Polymorphic characters in phylogenetic systematics. Systematic Biology 44: 482-500
Wiens, J. J. (2001) Character analysis in morphological phylogenetics: problems and solutions. Systematic Biology 50: 689-699
Wilkinson, M. (1992) Ordered versus unordered characters. Cladistics 8: 375-385
* V.A. Albert, B.D. Mishler, and M.W. Chase (1992) Character-state weighting for restriction site data in phylogenetic reconstruction, with an example from chloroplast DNA. In P. Soltis, D. Soltis, and J. Doyle (eds.), Molecular Systematics of Plants, pp. 369-403. Chapman and Hall.
V.A. Albert and B.D. Mishler (1992) On the rationale and utility of weighting nucleotide sequence data. Cladistics 8: 73-83
** V.A. Albert, M.W. Chase, and B.D. Mishler (1993) Character-state weighting for cladistic analysis of protein-coding DNA sequences. Annals Missouri Botanical Garden 80: 752-766
Broughton, R. E., S. E. Stanley, and R. T. Durrett. (2000) Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analysis. Systematic Biology 49: 617-627
Carpenter J.M. (1994) Successive weighting, reliability and evidence. Cladistics 10: 215-220
Farris, J. S. (1969) A successive approximations approach to character weighting. Systematic Zoology 18: 374-385
Freudenstein, J. V., Pickett, K. M., Simmons, M. P. and Wenzel, J. W. (2003) From basepairs to birdsongs: Phylogenetic data in the age of genomics. Cladistics 19: 333-347
Goloboff, P. A. (1993) Estimating character weights during tree searches. Cladistics 9: 83-91
Taran Grant, Arnold G. Kluge (2004) Transformation Series as an Ideographic Character Concept. Cladistics 20: 23? 31
Kirchoff, B. K.; Richter, S. J.; Remington, D. L., et al. (2004) Complex data produce better characters. Systematic Biology 53: 1-17
Liebherr, J. K. and Zimmerman, E. C. (1998) Cladistic analysis, phylogeny and biogeography of the Hawaiian Platynin (Coleoptera: Carabidae). Systematic Entomology 23: 137-172
Maddison, W. P. (1993) Missing data versus missing characters in phylogenetic analysis. Systematic Biology 42: 576-581
Nixon K. C. and Davis J. I. (1991) Polymorphic taxa, missing values and cladistic analysis. Presented at: Annual meeting of the Botanical Society of America with the American Institute of Biological Sciences, San Antonio, Texas, USA, AUGUST 4-8. American Journal of Botany 78: 206
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Wheeler, Q.D. ( ) Character weighting and cladistic analysis. Systematic Zoology 35: 110-123
Whitehead D. R. and Ball G. E. (1975) Classification of the Middle American Genus (Cyrtolaus: Coleoptera: Carabidae pterostichini). Quaestiones Entomologicae 11: 591-619
Wilkinson, M. (1994) Weights and ranks in numerical phylogenetics. Cladistics 10: 321-329
Yeates, D. K. (1995) Groundplans and exemplars: Paths to the tree of life. Cladistics 11: 343-357
Albert, V. A. and B. D. Mishler. (1992) On the rationale and utility of weighting nucleotide sequence data. Cladistics 8: 73-83
Albert, V. A., B. D. Mishler and M. W. Chase. (1992) Character-state weighting for restriction site data in phylogenetic reconstruction, with an example from chloroplast DNA. Pages 369-403 in Molecular Systematics of Plants (Soltis, P. S., D. E. Soltis and J. J. Doyle, ed.). Chapman & Hall, New York.
Avise, J. C., J. Arnold, R. M. Ball, E. Bermingham, T. Lamb, J. E. Neigel, C. A. Reeb and N. C. Saunders. (1987) Intraspecific phylogeography: the mitochondrial DNA bridge between population genetics and systematics. Annual Review of Ecology and Systematics 18: 489-522
Avise, J. C. (1989) Gene trees and organismal histories: a phylogenetic approach to population biology. Evolution 43: 1192-1208
Baker, R. H., G. S. Wilkinson, R. DeSalle. (2001) Phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae). Systematic Biology 50: 87-105
Bledsoe, A. H. and R. J. Raikow. (1990) A quantitative assessment of congruence between molecular and nonmolecular estimates of phylogeny. J. Mol. Evolution 30: 247-259
Bremer, K. (1988) The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42: 795-803
Broughton, R. E., S. E. Stanley, and R. T. Durrett. (2000) Quantification of homoplasy for nucleotide transitions and transversions and a reexamination of assumptions in weighted phylogenetic analyses. Systematic Biology 49: 617-627
Brower, Andrew V. Z., Schawaroch, Valerie (1996). "Three steps of homology assessment." Cladistics, 12(3), 265–272. doi: 10.1111/j.1096-0031.1996.tb00014.x
Bruns, T. D., T. J. White and J. W. Taylor. (1991) Fungal molecular systematics. Annu. Rev. Ecol. Syst. 22: 525-564
Collins, Timothy M.; Fedrigo, Olivier; Naylor, Gavin J. P. (2005) Choosing the best genes for the job: The case for stationary genes in genome-scale phylogenetics. Systematic Biology 54: 493-500
* Cracraft, J. (1987) DNA hybridization and avian phylogenetics. Evolutionary Biology 21: 47-96
Creer S, Malhotra A, Thorpe RS, et al. (2005) Targeting optimal introns for phylogenetic analyses in non-model taxa: experimental results in Asian pitvipers. Cladistics 21: 390-395
DeBry, R. W. (1999) Maximum likelihood analysis of gene-based and structure-based process partitions, using mammalian mitochondrial genomes. Systematic Biology 48: 286-299
DeSalle, R. and D. A. Grimaldi. (1991) Morphological and molecular systematics of the Drosophilidae. Annual Review of Ecology and Systematics 22: 447-475
** Donoghue, M. J. and M. J. Sanderson. (1992) The suitability of molecular and morphological evidence in reconstructing plant phylogeny. Pages 340-368 in Molecular Systematics of Plants (Soltis, P. S., D. E. Soltis and J. J. Doyle, ed.). Chapman & Hall, New York.
Doyle, J. J. (1992) Gene trees and species trees: molecular systematics as one-character taxonomy. Systematic Botany 17: 144-163
Fleissner, Roland; Metzler, Dirk; Von Haeseler, Arndt. (2005) Simultaneous statistical multiple alignment and phylogeny reconstruction. Systematic Biology 54: 548-561
Giribet G. (2005) Generating implied alignments under direct optimization using POY . Cladistics 21: 396-402
Givnish, T. J. and K. J. Sytsma (1997). Homoplasy in molecular vs. morphological data: the likelihood of correct phylogenetic inference. Molecular (1997) Evolution and Adaptive Radiation. (T. J. Givnish and K. J. Sytsma, eds). Cambridge, Cambridge University Press: 55-101
Hillis, D. M. (1987) Molecular versus morphological approaches to systematics. Annual Review of Ecology and Systematics 18: 23-42
Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett and I. J. Molineux. (1992) Experimental phylogenetics: generation of a known phylogeny. Science 255: 589-592
Hillis, D.M. (1995) Approaches for assessing phylogenetic accuracy. Systematic Biology 44: 39523
Hillis, D. M., C. Moritz and B. K. Mable (eds.). (1996) Molecular Systematics, second edition. Sinauer, Sunderland, MA. 655 pp.
Hillis, D. M. and J. J. Wiens. (2000) Molecules versus morphology in systematics: conflicts, artifacts, and misconceptions. pp. 1-19 in J. J. Wiens (ed.), Phylogenetic Analysis of Morphological Data. Washington DC, Smithsonian Institution Press.
Huelsenbeck, J. P. and R. Nielsen. (1999) Effect of non-independent substitution on phylogenetic accuracy. Systematic Biology 49: 317-328
Laamanen TR, Meier R, Miller MA, et al. (2005) Phylogenetic analysis of Themira (SepsidaeDiptera): sensitivity analysis, alignment, and indel treatment in a multigene study. Cladistics 21: 258-271
Lutzoni, F., P. Wagner, V. Reeb and S. Zoller. (2000) Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Systematic Biology 49: 628-651
Macey, J. R., J. A. Schulte II, and A. Larson. (2000) Evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards. Systematic Biology 49: 257-277
Mindell, D. P. and R. L. Honeycutt. (1990) Ribosomal RNA in vertebrates: evolution and phylogenetic applications. Annual Review of Ecology and Systematics 21: 541-566
** Mishler, B. D. (1994) The cladistic analysis of molecular and morphological data. American Journal of Physical Anthropology 94: 143-156
Mishler, B. D., K. Bremer, C. J. Humphries and S. P. Churchill. (1988) The use of nucleic acid sequence data in phylogenetic reconstruction. Taxon 37: 391-395
Morrison, David A. (2009). Why Would Phylogeneticists Ignore Computerized Sequence Alignment?, Systematic Biology, 58(1), 150-158. doi: 10.1093/sysbio/syp009
* Miyamoto, M. M. and J. Cracraft (eds.). (1991) Phylogenetic analysis of DNA sequences. Oxford University Press, New York. 358 pp.
Nei, M. and F. Tajima. (1987) Problems arising in phylogenetic inference from restriction-site data. Mol. Biol. Evolution 4: 320-323
Palmer, J. D., R. K. Jansen, H. J. Michaels, M. W. Chase and J. R. Manhart. (1988) Chloroplast DNA variation and plant phylogeny. Ann. Mo. Bot. Gard. 75: 1180-1206
Palmer, J. D. and L. A. Herbon. (1988) Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J. Mol. Evolution 28: 87-97
Patterson, C. (ed.). (1987) Molecules and Morphology in Evolution: Conflict or Compromise. Cambridge Univ. Press, Cambridge.
Patterson, C., D. M. Williams and C. J. Humphries. (1993) Congruence between molecular and morphological phylogenies. Annual Review of Ecology and Systematics 24: 153-188
Penny, D., M. Hasegawa, P. J. Waddell, and M. D. Hendy. (1999) Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition. Systematic Biology 48: 76-93
Phillips, Aloysius; Janies, Daniel; Wheeler, Ward (2000). "Multiple Sequence Alignment in Phylogenetic Analysis." Molecular Phylogenetics and Evolution, 16(3), 317-330. doi: 10.1006/mpev.2000.0785
Pisani, Davide. (2004) Identifying and removing fast-evolving sites using compatibility analysis: An example from the arthropoda. Systematic Biology 53: 978-989
Posada, D. and K. A. Crandall. (2001) Selecting the best fit model of nucleotide substitution. Systematic Biology 50: 580-601
Saitou, N. and M. Nei. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evolution 4: 406-425
Sanderson, M. J. and M. J. Donoghue. (1989) Patterns of variation in levels of homoplasy. Evolution 43: 1781-1795
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* Sibley, C. G. and J. E. Ahlquist. (1986) Reconstructing bird phylogeny by comparing DNAs. Sci. Am. 254: 82-92
Simmons, M. P. (2000) A Fundamental Problem with Amino-Acid-Sequence Characters for Phylogenetic Analyses. Cladistics 16: 274-282
Simmons, M. P. and H. Ochoterena. (2000) Gaps as characters in sequence-based phylogenetic analyses. Systematic Biology 49: 369-381
Simmons, M. P., H. Ochoterena, and T. G. Carr. (2001) Incorporation, relative homoplasy, and effect of gap characters in sequence-based phylogenetic analyses. Systematic Biology 50: 454-462
Slowinski, J. B. and B. S. Arbogast. (1999) Is the rate of molecular evolution inversely related to body size? Systematic Biology 48: 396-399
Smith, A. B. (1989) RNA sequence data in phylogenetic reconstruction: testing the limits of its resolution.
Smith, R. L. and K. J. Sytsma. (1990) Evolution of Populus nigra (sect. Aigeiros): introgressive hybridization and the chloroplast contribution of Populus alba (sect. Populus ). Am. J. Bot. 77 1176-1187
Springer, M. S., H. M. Amrine, A. Burk, and M. J. Stanhope. (1999) Additional support for Afrotheria and Paenungulata, the performance of mitochondrial versus nuclear genes, and the impact of data partitions with heterogeneous base composition. Systematic Biology 48: 65-75
Steel, M., D. Huson, and P. J. Lockhart. (2000) Invariable sites models and their use in phylogeny reconstruction. Systematic Biology 49: 225-232
Sytsma, K. J., J. F. Smith and L. D. Gottlieb. (1990) Phylogenetics in Clarkia (Onagraceae): restriction site mapping of chloroplast DNA. Systematic Botany 15: 280-295
Sytsma, K. J. (1990) DNA and morphology: inference of plant phylogeny. Trends Ecol. Evolution 5: 104-110
Terry MD, Whiting MF. (2005) Comparison of two alignment techniques within a single complex data set: POY versus Clustal. Cladistics 21: 272-281
Van Dijk, M. A. M., E. Paradis, F. Catzeflis, and W. W. De Jong. (1999) The virtues of gaps: Xenarthran (edentate) monophyly supported by a unique deletion in aA-Crystallin. Systematic Biology 48: 94-106
Waddell, P. J., Y. Cao, J. Hauf, M. Hasegawa. (1999) Using novel phylogenetic methods to evaluate mammalian mtDNA, including amino acid-invariant sites-LogDet plus site stripping, to detect internal conflicts in the data, with special reference to the positions of hedgehog, armadillo, and elephant. Systematic Biology 48: 31-53
Wheeler, W. C. (1995) Sequence alginment, parameter sensistivity and the phylogenetic analysis of molecular data. Systematic Biology 44: 321-331
Wheeler, W. C. (2001) Homology and the Optimization of DNA Sequence Data. Cladistics 17: S3-S11
Wilgenbusch, J. and de Queiroz, K. (2000) Phylogenetic relationships among the phyrnosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes. Systematic Biology 49: 592-612
Xia, X. (2000) Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses. Systematic Biology 49: 87-100
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Classification - Basic Principles
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