Integrative Biology 200A
Bibliography

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

 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. (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.

 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

 Mayr, E. (1982) The Growth of Biological Thought. Harvard University Press, Cambridge, Mass.    

 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

 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.   

 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.  

 Cleland, C. L.  (2001) Historical science, experimental science, and the scientific method. Geology 29: 987-990

 Hull, D. L.  (1974) Philosophy of Biological Sciences. Prentice-Hall, Englewood Cliffs, NJ.  

 Hull, D. L.  (1999) The use and abuse of Sir Karl Popper. Biology and Philosophy 14: 481-504

 Kuhn, T. S.  (1970) The Structure of Scientific Revolutions, second edition. University of Chicago Press.   A must-read for any scientist.

 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.

 Stamos, D. N. (1996) Popper, falsifiability, and evolutionary biology. Biology and Philosophy 11: 161-191

The Hennig Principle

 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

 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

Homology

 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

Characters and states

 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

 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

Character coding

* 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

 Sennblad, B and B. Bremer. (2000) Is ther a justification for differential a priori weighting in coding sequences? A case study from rbcL and Apocynaceae s.l. Systematic Biology 49: 101-113

 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

Molecular data

 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

 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

* 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

 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

 Sarich, V. M., C. W. Schmid and J. Marks. (1989) DNA hybridization as a guide to phylogenies: a critical analysis. Cladistics 5: 11749

 Sennblad, B. and B. Bremer. (2000) Is there justification for differential a priori weighting in coding sequences? A case study from rbcL abd Apocynaceae s.l. Systematic Biology 49: 101-113

* 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 K. deQueiroz. (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

 Yang, Z. (1996) Among-site rate variation and its impact on phylogenetic analyses. Trends Ecol. Evolution 11: 367-372

 Zimmer, E. A., R. K. Hamby, M. L. Arnold, D. A. LeBlanc and E. C. Theriot. (1989) Ribosomal RNA phylogenies and flowering plant evolution. pp 205-214 in The Hierarchy of Life (Fernholm, B., K. Bremer and H. Jornvall, ed.). Elsevier, Amsterdam. 205-214 in The Hierarchy of Life (Fernholm, B., K. Bremer and H. Jornvall, ed.). Elsevier, Amsterdam. 

 Zurawski, G. and M. T. Clegg. (1987) Evolution of higher-plant chloroplast DNA-encoded genes: Implications for structure-function and phylogenetic studies. Ann. Rev. Plant Physiol. 38: 391-418

Classification - Basic Principals

 

 Avise, J.C. and G.C. Johns. (1999) Proposal for a standardized temporal scheme of biological classification for extant species.  PNAS 96: 7358-7363

 Ax, P. (1987) The phylogenetic system: The systematization of organisms on the basis of their phylogenesis. John Wiley & Sons, New York.  

 Blackwell, W. H. and M. J. Powell. (1999) Reconciling kingdoms with codes of nomenclature: is it necessary? Systematic Biology 48: 406-412

 Bock, W. J. (1977) Foundations and methods of evolutionary classification. Pages 851-895 in Major patterns in vertebrate evolution (Hecht, M. K., P. C. Goody and B. M. Hecht, ed.). Plenum, New York.  

** de Queiroz, K. (1988) Systematics and the Darwinian revolution.  Phil. Sci.  55: 238-259

 Farris, J. S. (1974) Formal definitions of paraphyly and polyphyly.  Systematic Zoology 23: 548-554

 Hennig, W. (1966) Phylogenetic systematics. University of Illinois Press, Urbana.  

 Lee, M. S. Y. (2001) Snake origins and the need for scientific agreement on vernacular names.  Paleobiology 27: 1-6

 Mayr, E. (1998) Two empires or three?   PNAS 95: 9720-9723

 Nelson, G. (1973) Classification as an expression of phylogenetic relationships.  Systematic Zoology 22: 344-359

 Padian, K. (1999) Charles Darwin's views of classification in theory and practice. Systematic Biology 48: 352-364

 Robeck, H. E., C. C. Maley, and M. J. Donghue. (2000) Taxonomy and temproal diversity patterns. Palebiology 26: 171-187

 Sneath, P. H. A. and R. R. Sokal. (1973) Numerical taxonomy. W.H. Freeman, San Francisco.  

 Wiley, E. O. (1981) Phylogenetics: the theory and practice of phylogenetic systematics. John Wiley and Sons, New York.  

 Woese, C.R. (1998) Default taxonomy: Ernst Mayr's view of the microbial world. P NATL ACAD SCI USA 95  (19) 11043-11046 

Species Concepts  ()   

 Aguilar, J. F., J. A. Rossello, and G. N. Feliner. (1999) Molecular evidence for the compilospecies model of reticulate evolution in Armeria (Plumbaginaceae). Systematic Biology 48: 735-755

 Balakrishnan, Rohini (2005) Species concepts, species boundaries and species identification: A view from the tropics Systematic Biology 54: 689-693

 Bremer, K. and H. E. Wanntorp. (1979) Geographic populations or biological species in phylogeny reconstruction?  Systematic Zoology 28: 220-224

 Brower, A. V. Z. (1999) Delimitation of phylogenetic species with DNA sequences: a critique of Nixon’s population aggregation studies. Systematic Biology 48: 199-213

 Cantino, P. D., H. N. Bryant, K. de Queiroz, M. J. Donoghue, T. Eriksson, D. M. Hillis, and M. S. Y. Lee. (1999) Species names in phylogenetic nomenclature. Systematic Biology 48: 790-808

 Cohan, F. M. (2001) Bacterial species and speciation. Systematic Biology 50: 513-524

 Cracraft, J. (1983) Species concepts and speciation analysis. Curr. Ornith. 1: 159-187

 Cronquist, A. (1978) Once again, what is a species? Pp. 3-20 in Biosystematics in agriculture, ed. J. A. Romberger. Montclair, New Jersey: Allanheld & Osmun.  

 Davis, J. I. (1995) Species concepts and phylogenetic analysis -- introduction.  Systematic Botany 20:  555-559 Introduction to a symposium -- several relevant papers here

 Donoghue, M. J. (1985) A critique of the biological species concept and recommendations for a phylogenetic alternative. Bryologist  88: 172-181

 Ehrlich, P. R. and P. H. Raven. (1969) Differentiation of populations. Science  165: 1228-1232

 Ehrlich, P. R. and R. R. White. (1980) Colorado Checkerspot Butterflies: isolation, neutrality, and the biospecies. Am. Nat. 115: 328-341

 Eldredge, N. and J. Cracraft. (1980) Phylogenetic patterns and the evolutionary process. New York: Columbia Univ. Press.  

 Frost, D. R. and J. W. Wright. (1988) The taxonomy of uniparental species, with special reference to parthenogenetic Cnemidophorus (Squamata: Teiidae).  Systematic Zoology 37: 200-209

 Frost D.R. and Kluge, A.G.. (1994) A consideration of epistemology in systematic biology, with special reference to species. Cladistics 10:  259-294

 Ghiselin, M. T. (1987) Species concepts, individuality, and objectivity.   Biol. Phil. 2: 127-143

 Goldstein, P. Z. and R. DeSalle. (2000) Phylogenetic Species, Nested Hierarchies, and Character Fixation. Cladistics 16:  364-384

 Gould, S. J. (1980) A Quahog is a Quahog. pp 204-213 in The Pandas Thumb. Norton.  

 Grant, V. (1981) Plant speciation. New York: Columbia Univ. Press.  

 Graybeal, A. (1995) Naming species. Systematic Biology 44: 237-250

 Holman, E. W. (1987) Recognizability of sexual and asexual species of rotifers.  Systematic Zoology 36: 381-386

 Hull, D. L. (1987) Genealogical actors in ecological roles. Biol. Phil. 2: 168-184

 Lawrence, J. G. (2001) Catalyzing bacterial speciation: correlating lateral transfer with genetic headroom. Systematic Biology 50:  479-497

Phylogenetic Tree Reconstruction  ()   

 Albert VA, Chase MW, and Mishler BD (1993) Character-state weighting for cladistic analysis of protein-coding DNA sequences. Ann. Missouri Bot. Gard. 80: 752-766

 Albert VA, and Mishler BD (1992) On the rationale and utility of weighting nucleotide sequence data. Cladistics 8: 73-83

 Albert VA, Mishler BD, and Chase MW (1992) Character-state weighting for restriction site data in phylogenetic reconstruction, with an example from chloroplast DNA. pp. 369-403 in PS Soltis, DE Soltis and JJ Doyle (eds.): Molecular Systematics of Plants. New York:Chapman & Hall  

 Anderson, J. S. (2001) The phylogenetic trunk: maximal inclusion of missing data in an analysis of the Lepospondyli (Vertebrata, Tetrapoda). Systematic Biology 50:  170-193

 Bininda-Emonds, O. R. P., M. J. Sanderson. (2001) Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. Systematic Biology 50:  565-579

 Bodenbender, B. E. and D. C. Fisher. (2001) Stratocladistic analysis of blastoid phylogeny. Journal of Paleontology 75:  351-369

 Bremer, B., R. K. Jansen, B. Oxelman, M. Backlund, H. Lantz, and K.-J. Kim. (1999) More characters or more taxa for a robust phylogeny – case study from the coffee family (Rubiaceae). Systematic Biology 48:  413-435

 Brochu, C. A. (1999) Taxon sampling and reverse successive weighting. Systematic Biology 48:  808-814

 Camin, J. H. and R. R. Sokal. (1965) A method for deducing branching sequences in phylogeny. Evolution  19: 311-326

 Cavalli-Sforza, L. L. and A. W. F. Edwards. (1967) Phylogenetic analysis: Models and estimation procedures. Evolution 32: 550-570

 CLYDE, W. C. AND D. C. FISHER. (1997) Comparing the fit of stratigraphic and morphologic data in phylogenetic analysis.  Paleobiology 23:  1-19

 Constantinescu, M. and D. Sankoff. (1986) Tree enumeration modulo a consensus. Journal of Classification 3: 349-356

 Donoghue, M. J. and W. P. Maddison. (1986) Polarity assessment in phylogenetic systematics: a response to Meacham.   Taxon 35: 534-545

 Farris, J. S. (1969) A successive approximations approach to character weighting. Systematic Zoology 18: 374-385

 Farris, J. S. (1970) Methods for computing Wagner trees. Systematic Zoology  19: 83-92

 Farris, J. S. (1972) Estimating phylogenetic trees from distance matrices.   American Naturalist 106: 645-668

 Farris, J. S. (1977) Phylogenetic analysis under Dollo's Law. Systematic Zoology 26: 77-88

 Farris J. S.  (1981) Distance data in phylogenetic analysis.  pp. 3-23 in VA Funk and DR Brooks (eds.): Advances in Cladistics: Proceedings of the First Meeting of the Willi Hennig Society. Bronx, New York:New York Botanical Garden  

 Farris, J. S. (1982) Outgroups and parsimony. Systematic Zoology 31: 328-334

 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.  

 Farris, J. S. (1988) Hennig86, version 15 Distributed by the author, Port Jefferson Station, NY. 

 Felsenstein, J. (1978) The number of evolutionary trees. Systematic Zoology 27: 27-33

 Felsenstein, J. (1978) Cases in which parsimony and compatibility will be positively misleading.  Systematic Zoology 27: 401-410

 Felsenstein, J. (1984) The statistical approach to inferring phylogeny and what it tells us about parsimony and compatibility. Pages 169-191 in T. Duncan and T. F. Stuessy (ed.), Cladistics: Perspectives on the Reconstruction of Evolutionary History (Columbia University Press:   

 Fisher, D. C. (1991) Phylogenetic analysis and its application in evolutionary paleobiology. pp 103-121 in Analytical Paleobiology.  

 Fisher, D. C. (1992) Stratigraphic Parsimony. Pages 124-129 in MacClade: Analysis of Phylogeny and Character Evolution, Version 3 (W. P. Maddison and D. R. Maddison, eds.). Sinauer Associates, Sunderland, MA.  

 Fisher, D. C. (1994) Stratocladistics: morphological and temporal patterns and their relation to phylogenetic process. Pages 133-171 in Interpreting the Hierarchy of Nature – from systematic patterns to evolutionary theories (L. Grande and O. Rieppel, eds.). Academic Press, S  

 Fitch, W. M. (1971) Toward defining the course of evolution: minimal change for a specific tree topology. Systematic Zoology 20: 406-416

 Gaffney, E. S. (1979) An introduction to the logic of phylogeny reconstruction. In J Cracraft and N Eldredge (eds.): Phylogenetic Analysis and Paleontology. New York:Columbia University Press, pp. 79-111  

 Gascuel, O., D. Bryant, and F. Denis. (2001) Strengths and limitations of the minimum evolution principle. Systematic Biology 50: 621-627

 Hendy, M. D. and D. Penny. (1982) Branch and bound algorithms to determine minimal evolutionary trees. Mathematical Biosciences 59: 277-290

 Hendy, M. D., M. A. Steel, D. Penny, and I. M. Henderson. (1988) Families of trees and consensus. Pages 355-362 in H. H. Bock (ed.), Classification and Related Methods of Data Analysis (Elsevier: Amsterdam).  

 Hennig, W. (1966) Phylogenetic Systematics. (University of Illinois Press: Urbana, Illinois).  

 Hillis, D. M. (1987) Molecular versus morphological approaches to systematics. Annual Review of Ecology and Systematics 18: 23-42

 Hillis DM, Bull JJ, White ME, Badgett MR, and Molineux IJ. (1992) Experimental phylogenetics: generation of a known phylogeny. Science 255: 589-592

 Houseworth, E. A. and E. P. Martins. (2001) Random sampling of constrained phylogenies: conducting phylogenetic analyses when the phylogeny is partially known. Systematic Biology 50: 628-639

 Huelsenbeck, J. P. (1995) Performance of phylogenetic methods in simulation. Systematic Biology 44: 17-48

 Kim, J. (1996) General inconsistency conditions for maximum parsimony: effects of branch lengths and increasing numbers of taxa. Systematic Biology 45: 363-374

 Kitching, I. J., P. L. Forey, C. J. Humphries, and D. M. Williams. (1998) Cladistics: The Theory and Practice of Parsimony Analysis. Second Edition. Oxford, Oxford University Press.  

 Kluge, A. G. and J. S. Farris. (1969) Quantitative phyletics and the evolution of anurans. Systematic Zoology 18: 1-32

 Kornet, D. J. and H. Turner. (1999) Coding polymorphism for phylogeny reconstruction. Systematic Biology 48: 365-379

 Lake, J. A. (1987) Determining evolutionary distances from highly diverged nucleic acid sequences: operator metrics. J. Mol. Evolution 26: 59-73

 Lundberg, J. G. (1972) Wagner networks and ancestors. Systematic Zoology 21: 398-413

 Maddison, D. R. (1991) The discovery and importance of multiple islands of most-parsimonious trees Systematic Zoology 40: 315-328

 Maddison, W. P. (1989) Reconstructing character evolution on polytomous cladograms. Cladistics 5: 365-377

** Maddison, W. P., and D. R. Maddison. (1992) MacClade: Analysis of Phylogeny and Character Evolution (version 3). Sinauer Associates, Sunderland, MA. Evolution (version 3). Sinauer Associates, Sunderland, MA.: 

 Meacham, C. A. (1984) The role of hypothesized direction of characters in the estimation of evolutionary history. Taxon 33: 26-38

 Meacham, C. A. (1986) More about directed characters: a reply to Donoghue and Maddison. Taxon 35: 538-540

 Mitchell, A., C. Mitter, and J. C. Regier. (2000) More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera). Systematic Biology 49: 202-224

Nelson G, and Platnick, N. (1981) Systematics and Biogeography, Cladistics and Vicariance. New York: Columbia Univ. Press.

 O’Keefe, F. R. and P. M. Sander. (1999) Paleontological paradigms and inferences of phylogenetic pattern: a case study.  Paleobiology 25: 518-533

 Page, R. D. M. (1989) Comments on component-compatibility in historical biogeography. Cladistics 5: 167-182

 Penny, D. and M. D. Hendy. (1985) The use of tree comparison metrics. Systematic Zoology 34: 75-82

 Penny, D., Hendy MD, and Steel MA (1992) Progress with methods for constructing evolutionary trees.  Trends in Ecology and Evolution 7: 73-79

 Pickett KM, Tolman GL, Wheeler WC, et al. (2005) Parsimony overcomes statistical inconsistency with the addition of more data from the same gene. Cladistics 21: 438-445

 Prendini, L. (2001) Species or supraspecific taxa as terminals in cladistic analysis? Groundplans versus exemplars revisited. Systematic Biology 50:  290-300

 Quicke, D. L. J., J. Taylor, and A. Purvis. (2001) Changing the landscape: a new strategy for estimating large phylogenies. Systematic Biology 50:  60-66

 Sankoff, D., R. J. Cedergren, and W. McKay. (1982) A strategy for sequence phylogeny research. Nucleic Acids Research 10: 421-431

 Sankoff, D.D. and R. J. Cedergren. (1983) Simultaneous comparison of three or more sequences related by a tree. Pages 253-263 in D. Sankoff and J. B. Kruskal (ed.), Time Warps, String Edits, and Macromolecules: the Theory and Practice of Sequence Comparison (Addison-Wesley: Reading, Mass.).  

 Sankoff, D.D. and P. Rousseau. (1975) Locating the vertices of a Steiner tree in an arbitrary metric space. Mathematical Programming 9: 240-246

 Simmons, N. B. (2001) Misleading results from the use of ambiguity coding to score polymorphisms in higher-level taxa. Systematic Biology 50:  613-620

 Smith, E. N., and R. L. Gutberlet Jr. (2001) Generalized frequency coding: a method of preparing polymorphic multistate characters for phylogenetic analysis. Systematic Biology 50:  156-169

 Sokal, R. R. and F. J. Rohlf. (1981) Taxonomic congruence in the Leptopodomorpha re-examined. Systematic Zoology 30: 309-325

 Sober, Elliott. (2004) The contest between parsimony and likelihood. Systematic Biology 53: 644-653

 Swofford, D. L. (1991) When are phylogeny estimates from morphological and molecular data incongruent? Pages 295-333 in M. M. a. J. C. Miyamoto (ed.), Phylogenetic Analyis of DNA Sequences (Oxford University Press: New York, N. Y.).  

 Swofford, D. L. and W. P. Maddison. (1987) Reconstructing ancestral character states under Wagner parsimony. Mathematical Biosciences 87: 199-229

 Swofford DL, and Olsen GJ (1990) Phylogeny reconstruction. pp. 411-501 in DM Hillis and C Moritz (eds.): Molecular Systematics (First Edition). Sunderland, MA:Sinauer Associates.  

**  Swofford, D. L. (1991) PAUP: Phylogenetic Analysis Using Parsimony, 31 Illinois Nat. Hist. Surv., Champaign, Illinois. 

 Templeton, A. R. (1983a) Convergent evolution and non-parametric inferences from restriction fragment and DNA sequence data. pp 151-179 in B. Weir (ed.), Statistical Analysis of DNA Sequence Data (Marcel Dekker: New York).  

 Templeton, A. R. (1983b) Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and apes. Evolution 37: 221-244

 WAGNER, P. J. (1995) Stratigraphic tests of cladistic hypotheses.  Paleobiology 21:  153-178

 WAGNER, P. J. (1997) Patterns of morphologic diversification among the rostroconchia.  Paleobiology 23:  115-150

 Wiley, E. O. (1981) Phylogenetics. The Theory and Practice of Phylogenetic Systematics. (Wiley and Sons: New York).  

 Wheeler W.C. and Nixon K. (1994) A novel method for economical, diagnosis of cladograms Sankoff optimization. Cladistics 10: 207-213

 Wiley, E. O., D. Siegel-Causey, D. R. Brooks, and V. A. Funk. (1991) The Complete Cladist. A Primer of Phylogenetic Procedures. (University of Kansas Museum of Natural History Special Publ. No. 19, Lawrence, Kansas).  

Phenetics

 Barbujani, G., Oden, N.L., & Sokal, R.R. (1989) Detecting regions of abrupt change in maps of biological variables. Systematic Zoology 38: 37 6-389

 Barrett S.J. & Sneath, P.H.A. (1994) A numerical phenotypic taxonomic study of the genus Neisseria. Microbiology 140: 2867-2891

 Blackwelder, R.E. (1967) A critique of numerical taxonomy. Systematic Zoology 16: 64-72

* Colless, D.H. (1967) An examination of concepts in phenetic taxonomy. Systematic Zoology 16: 6-27

** Farris, J.S. (1967) The meaning of relationship and taxonomic procedure. Systematic Zoology 16: 44-51

 Felsenstein, J. (2001) The troubled growth of statistical phylogenetics. Systematic Biology 50: 465-467

 Huson, Daniel H.; Steel, Mike. (2004) Distances that perfectly mislead. Systematic Biology 53: 327-332

* Jacobson, H.R. & Kistner, D.H. (1975) Numeric analyses of the relationships of genera and species of the subtribe Termitusina (Coleoptera: Staphylinidae).  Systematic Zoology  24: 191-198

* Kim, J., Rohlf, F.J. & Sokal, R.R. (1993) The accuracy of phylogenetic estimation using the neighbor-joining method.  Evolution  47: 471-486

 Mayr, E. (1965) Numerical phenetics and taxonomic theory.  73-97 14: 73-97

 Moss, W. (1968) Experiments with various techniques of numerical taxonomy.  Systematic Zoology 17: 31-47

 Nelson, A.D. and W.J. Elisens. (1999) Polyploid evolution and biogeography in Chelone (Scrophulariaceae): Morphological and isozyme evidence.  American Journal of Botany 86: 1487-1501

 Rasnitsyn, A.P. (1996) Conceptual issues in phylogeny, taxonomy, and nomenclature. CONTRIB ZOOL 66:  3-41

 Rohlf, F.J., Chang, W.S., Sokal, R.R. & Kim, J.Y. (1990) Accuracy of estimated phylogenies effects of tree topology and evolutionary model. Evolution 44: 1671-1684

 Sneath, P. H. A. (1967) Some statistical problems in numerical taxonomy. Statistician 17: 1-12

 Sneath, P. H. A. (1969) Recent trends in numerical taxonomy. Taxon 18: 14-20

* Sneath, P. H. A. (1971) Numerical taxonomy: criticisms and critiques. Biol. J. Linn. Soc. 3:  147-157

 Sneath, P. H. A. (1961) Recent developments in theoretical and quantitative taxonomy. Systematic Zoology 10:  118-139

 Sneath, P.H.A. (1989) Analysis and interpretation of sequence data for bacterial systematics: The view of a numerical taxonomist. Systematic and Applied Microbiology 12: 15-31

 Sneath, P. H. A., and R. R. Sokal (1962) Numerical taxonomy. Nature 193: 855-860

** Sneath, P.H.A. & Sokal, R.R. (1973) Numerical taxonomy; the principles and practice of numerical classification. W. H. Freeman, San Francisco.  

 Sokal, R. R. (1965) Statistical methods in systematics. Biol. Rev. 40: 337-391

 Sokal, R. R. (1966) Numerical taxonomy. Sci. Amer. 215: 106 116

 Sokal, R. R. (1969) Animal taxonomy: theory and practice. Quart. Rev. Biol. 44: 209-211

 Sokal, R. R., J. H. Camin, F. J. Rohlf, and P. H A. Sneath (1965) Numerical taxonomy: some points of view. Systematic Zoology 14: 237-243

* Sokal, R.R., Kim, J.Y. & Rohlf, F.J. (1992) Character and OTU stability in 5 taxonomic groups.  Journal of Classification 9: 117-140

* van der Steen, W.J. & Boontje, W. (1973) Phylogenetic versus phenetic taxonomy: A reappraisal.  Systematic Zoology 22: 55-63

Maximum Likelihood

 Bergsten J. (2005) A review of long-branch attraction. Cladistics 21: 163-193

 Buckley, T. R., C. Simon, and G. K. Chambers. (2001) Exploring among0site variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths, and bootstrap support. Systematic Biology 50:  67-86

 Brinkmann, Henner; Van der Giezen, Mark; Zhou, Yan, et al. (2005) An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Systematic Biology 54: 

 Caterinno, M. S., R. D. Reed, M. M. Kuo, and F. A. H. Sperling. (2001) A partitioned likelihood analysis of swallowtail butterfly phylogeny (Lepidoptera: Papilionidae). Systematic Biology 50: 106-127

 DeBry, R. W. and N. A. Slade. (1985) Cladistic analysis of restriction endonuclease cleavage maps within a maximum-likelihood framework.  Systematic Zoology  34: 21-34

 deQueiroz, 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

 Huelsenbeck, J. P. and B. Rannala. (1997) Maximum likelihood estimation of hpylogeny using stratigraphic data.  Paleobiology 23: 174-180

 Huelsenbeck, J. P. and B. Rannala. (2000) Using stratigraphic information in phylogenetics. pp. 165-191 in J. J. Wiens (ed.), Phylogenetic Analysis of Morphological Data. Washington DC, Smithsonian Institution Press.  

 Faith, D. P. and W. H. Trueman. (2001) Towards an inclusive phylogeny for phylgenetic inference. Systematic Biology 50: 331-350

 Farris, J. S. (2000) Corroboration versus "Strongest Evidence. Cladistics 16: 385-393

** Felsenstein J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evolution 17: 368-376

 Haber, Matthew H. (2005) On probability and systematics: Possibility, probability, and phylogenetic inference. Systematic Biology 54: 831-841

 Kluge, A. G. (2001) Philosophical conjectures and their refutation. Systematic Biology 50: 322-331

 Lewis, P. O. (2001) A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50: 913-925

 Mooers, A. O. and D. Schluter. (1990) Reconstructin ancestor states with maximum likelihood: support for one- and two-rate models. Systematic Biology 48: 612-622

 Pagel, M. (1999) The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Systematic Biology 48: 612-622

 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

 Rogers, J. S. (2001) Maximum likelihood estimation of phylogenetic trees is consistent when substitution rates vary according to the invariable sites plus gamma distribution. Systematic Biology 50: 713-722

 Salter, L. A. (2001) Complexity of the likelihood surface for a large DNA data set. Systematic Biology 50: 970-978

 Salter, L. A. and D. K Pearl. (2001) Stochastic search strategy for estimation of maximum likelihood phylogenetic trees. Systematic Biology 50: 7-18

 Sanderson, M. J. and J. Kim. (2000) Parametric phylogenetics? Systematic Biology 49: 817-829

 Swofford, D. L, P. J. Waddell, J. P. Huelsenbeck, P. G. Foster, P. O. Lewis, and J. S. Rogers. (2001) Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Systematic Biology 50: 525-539

 Wagner, P. J. (1998) A likelihood approach for evaluating estimates of phylogenetic relationships among fossil taxa.  Paleobiology 24: 430-449

 WAGNER, P. J. (1999) The utility of fossil data in phylogenetic analyses: a likelihood example using Ordovician-Silurian species of the Lophospiridae (Gastropoda: Murchisoniina). Amer. Malac. Bull. 15: 1-31

 Wagner, P. J. (2000) Phylogenetic analyses and the fossil record: tests and inferences, hypotheses and models.  Paleobiology 26: 341-371

 Wagner, P. J. (2001) Rate heterogeneity in shell character evolution among lophospirioid gastropods.  Paleobiology 27: 290-310

Bayesian Methods

 Nylander, Johan A. A.; Ronquist, Fredrik; Huelsenbeck, John P., et al. (2004) Bayesian phylogenetic analysis of combined data. Systematic Biology 53: 47-67

 Pagel, Mark; Meade, Andrew; Barker, Daniel. (2004) Bayesian estimation of ancestral character states on phylogenies. Systematic Biology 53: 673-684

 Redelings, Benjamin D.; Suchard, Marc A. (2005) Joint Bayesian estimation of alignment and phylogeny. Systematic Biology 54: 401-418

 Yang, Ziheng; Rannala, Bruce. (2005) Branch-length prior influences Bayesian posterior probability of phylogeny. Systematic Biology 54: 455-470

 Zwickl, Derrick J.; Holder, Mark T. (2004) Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Systematic Biology 53: 877-888

Phylogenetic Trees: Support & Tree Comparisons  ()   

 Adams, E. N., III. (1972) Consensus techniques and the comparison of taxonomic trees.  Systematic Zoology 21: 390-397

 Archie, J. W. (1989) Homoplasy excess ratios: new indices for measuring levels of homoplasy in phylogenetic systematics and a critique of the consistency index.  Systematic Zoology 38: 253-269

 Archie, J. W. (1989) A randomization test for phylogenetic information in systematic data.  Systematic Zoology 38: 239-252

 Barrett M, Donoghue MJ, and Sober E.  (1991) Against consensus.  Systematic Zoology 40: 486-493

 Bremer K. (1988) The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42: 795-803

 Bremer, K. (1990) Combinable component consensus. Cladistics 6: 369-372

 Bremer, K. (1994) Branch support and tree stability. Cladistics 10: 295-304

 Brower, A. V. Z., R. DeSalle and A. Vogler. (1996) Gene trees, species trees, and systematics: a cladistic perspective. Annual Review of Ecology and Systematics 27: 423-450

 Bryant, D. (2003) A classification of consensus methods for phylogenetics. in Janowitz, M., Lapointe, F.J., McMorris, F., Mirkin, B. Robers, F. (eds.) Bioconsensus. DIMACS-AMS. 163-184  

 Bull, J. J., J. P. Huelsenbeck, C. W. Cunningham, D. L. Swofford and P. J. Waddell. (1993) Partitioning and combining data in phylogenetic analysis. Systematic Biology 42: 384-397

 Cameron, S. A. and P. Mardulyn. (2001) Multiple molecular data sets suggest independent origins of highly eusocial behavior in bees (Hymenoptera: Apinae). Systematic Biology 50: 194-214

 Cannon, C. H. and P. S. Manos. (2001) Combining and comparing morphometirc shape datya with a molecular phylogeny: the case of fruit type evolution in Bornean Lithocarpus (Fagaceae). Systematic Biology 50: 860-880

 Chavarria, G. and J. M. Carpenter. (1994) Total evidence and the evolution of highly social bees. Cladistics 10: 229-258

 Chippendale, P. T. and J. J. Wiens. (1994) Weighting, partitioning, and combining characters in phylogenetic analysis. Systematic Biology 43: 278-287

 Coddington, J. and Scharff, N. (1994) Problems with zero-length branches. Cladistics 10: 415-423

** de Queiroz, A., M. J. Donoghue and J. Kim. (1995) Separate versus combined analysis of phylogenetic evidence. Annual Review of Ecology and Systematics 26: 657-681

 DeBry, R. W. (2001) Improving interpretation of the decay index for DNA sequence data. Systematic Biology 50: 742-752

 DeBry, R. W. and R. G. Olmstead. (2000) A simulation study of reduced tree-search effort in bootstrap resampling analysis. Systematic Biology 49: 171-179

 Donoghue MJ, Olmstead RG, Smith JF, and Palmer JD. (1992) Phylogenetic relationships of Dipsacales based on rbcL sequences. Ann. Missouri Bot. Gard. 79: 333-345

 Farris, J. S. (1989a) The retention index and homoplasy excess. Systematic Zoology 38: 406-407

 Farris, J. S. (1989b) The retention index and the rescaled consistency index. Cladistics 5: 417-419

 Farris J.S., Kallersjo, M., Kluge, A.G. and Bult, C. (1994) Testing significance of incongruence. Cladistics 10: 315-319

 Farris, J. S., M. Kallersjo, and J. E. De Laet. (2001) Branch Lengths Do Not Indicate Support-Even in Maximum Likelihood. Cladistics 17: 298-299

** Felsenstein, J. (1985) Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39: 783-791

 Flook, P. K., S. Klee, and C. H. F. Rowell. (1999) Combined molecular phylogenetic analysis of the Orthoptera (Arthropoda, Insecta) and implications for their higher systematics. Systematic Biology 48: 233-253

 Flores-Villela, O., K. M. Kjer, M. Benabib, and J. W. Sites Jr. (2000) Multiple data sets, congruence, and hypothesis testing for the phylogeny of basal groups of the lizard genus Sceloporus (Squamata, Phyrnosomatidae). Systematic Biology 49: 713-739

 Gatesy, J. (2000) Linked branch support and tree stability. Systematic Biology 49: 800-808

 Gatesy, J. and P. Arctander. (2000) Hidden morphological support for the phylogenetic placement of Pseudoryx nghetinhensis with bovine bovids: a combined analysis of gross anatomical evidence and DNA sequences from five genes. Systematic Biology 49: 515-538

 Goldman, N., J. P. Anderson, and A. G. Rodrigo. (2000) Likelihood-based tests of topologies in phylogenetics. Systematic Biology 49: 652-670

 Goloboff P. (1991) Homoplasy and the choice among cladograms. Cladistics 7: 215-232

 Grandcolas, P., P.-L. Deleporte, L. Desutter-Grandcolas, C. Daugeron. (2001) Phylogenetics and Ecology: As Many Characters as Possible Should Be Included in the Cladistic Analysis. Cladistics 17: 104-110

 Graham LE, Delwiche CF, and Mishler BD. (1991) Phylogenetic connections between the "green algae" and the "bryophytes". Advances in Bryology 4: 213-244

 Grant, T, and A. G. Kluge. (2003) Data exploration in phylogenetic inference: scientific, heuristic, or neither. Cladistics:  19: 379-418

 Huelsenbeck, J. P. (1991) Tree-length distribution skewness: an indicator of phylogenetic information.  Systematic Zoology 40: 257-270

 Huelsenbeck, J.P. (1995) Performance of phylogenetic methods in simulation. Systematic Biology 44: 17-48

 Huelsenbeck, J. P. and J. J. Bull. (1996) A likelihood ratio test to detect conflicting phylogenetic signal. Systematic Biology 45: 92-98

* Huelsenbeck, J. P., J. J. Bull and C. W. Cunningham. (1996) Combining data in phylogenetic analysis. Trends Ecol. Evolution 11: 152-158

 Joy, T. and J. E. Conn. (2001) Molecular and morphological phylogenetic analysis of an insular radiation of Pacific black flies. Systematic Biology 50: 18-38

 Kallersjo M, Farris JS, Kluge AG, and Bult C. (1992) Skewness and permutation. Cladistics 8: 275-287

 Kennedy, Martyn; Holland, Barbara R.; Gray, Russell D., et al. (2005) Untangling long branches: Identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks. Systematic Biology 54: 620-633

 Kjer, K. M., R. J. Blahnik, and R. W. Holzenthal. (2001) Phylogeny fo Trichoptera (caddisflies): characterization of signal and noise within multiple data sets. Systematic Biology 50: 758-780

 Klassen GJ, Mooi RD, and Locke A. (1991) Consistency indices and random data.  Systematic Zoology 40: 446-457

 Kluge A. J. (1989) A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes).  Systematic Zoology 38: 39654

 Kress, W. J., L. M. Price, W. J. Hahn, and E. A. Zimmer. (2001) Unraveling the evolutionary radiation of the families of the Zingiberales using morphological and molecular evidence. Systematic Biology 50: 926-944

 Lee, M. S. Y. (2000) Tree robustness and clade significance. Systematic Biology 49: 829-836

 Levaseur, C. and F.-J. Lapointe. (2001) War and peace in phylogenetics: a rejoinder on total evidence and consensus. Systematic Biology 50: 881-891

 McCracken, K. G., J. Harshman, D. A. McClellan, and A. D. Afton. (1999) Data set incongruence and correlated character evolution: an example of functional convergence in the hind-limbs of stifftail diving ducks. Systematic Biology 48: 683-714

 McLennan, D. A. and M. Y. Mattern. (2001) The Phylogeny of the Gasterosteidae: Combining Behavioral and Morphological Data Sets. Cladistics 17: 11-27

 Mishler BD, Donoghue MJ, and Albert VA. (1991) The decay index as a measure of relative robustness within a cladogram [abstract]. Hennig X [Annual meeting of the Willi Hennig Society], Toronto, Ontario.  

 Mishler, B. D., L. A. Lewis, M. A. Buchheim, K. S. Renzaglia, D. J. Garbary, C. F. Delwiche, F. W. Zechman, T. S. Kantz and R. L. Chapman. (1994) Phylogenetic relationships of the "green algae" and "bryophytes". Ann. Mo. Bot. Gard. 81: 451-483

 Miyamoto MM. (1985) Consensus cladograms and general classifications. Cladistics 1: 186-189

 Miyamoto, M.M. and M.W. Fitch. (1995) Testing species phylogenies and phylogenetic methods with congruence. Systematic Biology 41: 64-76

 Mort, M. E., P. S. Soltis, D. E. Soltis, and M. L. Mabry. (2000) Comparison of methods for estimating internal support on phylogenetic trees. Systematic Biology 49: 160-171

 Nee, Sean. (2004) Extinct meets extant: simple models in paleontology and molecular phylogenetics.  Paleobiology 30: 172-178

 Penny, D. and M. D. Hendy. (1985) The use of tree comparison metrics.  Systematic Zoology 34: 75-82

 Poe S, Chubb AL. (2004) Birds in a bush: Five genes indicate explosive evolution of avian orders. Evolution 58: 404-415

 Quicke, D. L. J. and R. Belshaw. (1999) Incongruence between morphological data sets: an example from the evolution of endoparasitism among parasitic wasps (Hymenoptera: Braconidae). Systematic Biology 48: 436 - 454

 Rohlf, F. J. (1982) Consensus indices for comparing classifications Mathematical Biosciences  59: 131-144

 Sanderson MJ, and Donoghue MJ (1989)  Patterns of variation in levels of homoplasy. Evolution 43: 1781-1795

** Sanderson, M.J. (1995) Objections to boostraping phylogenies: a critique. Systematic Biology 44: 299-320

 Sanderson, M. J., and M. Wojciechowski. (2000) Improved bootstrap confidence limits in large scale phylogenies, with an example from neo-astragalus (Leguminoseae). Systematic Biology 49: 671-685

 Sharkey, M. J. and J. W. Leathers. (2001) Majority Does Not Rule: The Trouble with Majority-Rule Consensus Trees. Cladistics 17: 282-284

 Sorensen MV, Sterrer W, Giribet G. (2006) Gnathostomulid phylogeny inferred from a combined approach of four molecular loci and morphology. Cladistics 22: 32-58

 Steel, M., A. W. M. Dress, and S. Bocker. (2000) Simple but fundamental limitations on supertree and consensus tree methods. Systematic Biology 49: 363-368

 Sullivan, J. and D. L. Swofford. (2001) Should we use model-based methods for phylogenetic inference when we know that assumptions about among site rate variation and nucleotide substitution pattern are violated? Systematic Biology 50: 723-729

 Summral, C. D., C. A. Brochu, and J. W. Merck Jr. (2001) Global lability, regional resolution, and majority rule consensus bias.  Paleobiology 27: 254-261

 Swofford, D. L. (1991) When are phylogeny estimates from molecular and morphological data incongruent? Pp. 295-333 in M. M. Miyamoto &J. Cracraft (ed.), Phylogenetic analysis of DNA sequences. Oxford University Press, New York.  

 Weiblen, G. D. (2001) Phylogenetic relationships of fig wasps pollinating functionally dioecious Ficus based on mitochondrial DNA sequences and morphology. Systematic Biology 50: 243-267

 Wiens, J. J. and B. D. Hollingsworth. (2000) War of the iguanas: conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards. Systematic Biology 49: 143-159

 Wilkinson, M. (1994) Common cladistic information and its consensus representation: reduced Adams and reduced cladistic trees and profiles. Systematic Biology 43: 343-368

 Wilkinson, M. and J. L. Thorley. (2001) Efficiency of strict consensus trees. Systematic Biology 50: 610-612

 Wilkinson, M., J. L. Thorley, and P. Upchurch. (2000) A chain is no stronger than its weakest link: double decay analysis of phylogenetic hypotheses. Systematic Biology 49: 754-776

 Wood, S.W. (1994) Monophyly and comparisons between trees. Cladistics 10: 339-346

 Yolder, A. D., J. A. Irwin, and B. A. Payseur. (2001) Failure of the ILD to determine data combinability for slow loris phylogeny. Systematic Biology 50: 408-424

 Zandler, R. H. (2001) A conditional probability of reconstruction measure for internal cladogram branches. Systematic Biology 50: 425-437

Reticulation and Phylogeography

 Arnold, M. L., C. M. Buckner and J. J. Robinson. (1991) Pollen-mediated introgression and hybrid speciation in Louisiana irises. PNAS 88: 1398-1402

 Arnold, M. L., J. J. Robinson, C. M. Buckner and B. D. Bennet. (1992) Pollen dispersal and interspecific gene flow in Louisiana irises. Heredity 68: 399-404

 Avise, J. C. (1989) Gene trees and organismal histories: a phylogenetic approach to population biology. Evolution 43: 1192-1208

 Avise, J. C. and R. M. Ball. (1990) Principles of geneological concordance in species concepts and biological taxonomy. Oxford Surveys in Evolutionary Biology 7: 45-67

* Baum, D. (1992) Phylogenetic species concepts.  Trends in Ecology and Evolution 7: 1-2

 Baum, D. A., and K. L. Shaw. (1995) Genealogical perspectives on the species problem. Pages 289-303 in Experimental and molecular approaches to plant biosystematics. Monographs in systematics, Volume 53 (P. C. Hoch and A. G., Stevenson, eds.). Missouri Botanical Garden, St, Louis.  

 Carstens BC, Brunsfeld SJ, Demboski JR, et al. (2005) Investigating the evolutionary history of the Pacific Northwest mesic forest ecosystem: Hypothesis testing within a comparative phylogeographic framework. Evolution 59: 1639-1652 

 Crandall, K. A. (1994) Intraspecific cladogram estimation: accuracy at higher levels of divergence. Systematic Biology 43: 222-235

 Doyle, J. J. (1992) Gene trees and species trees: Molecular systematics as one-character taxomony. Systematic Botany 17: 144-163

 Funk, V. A. (1985) Phylogenetic patterns and hybridization Ann. Missouri Bot. Gard. 72: 681-715

 Gadgil and L. L. Cavalli-Sforza. (1995) Demographic history of India and mtDNA sequence diversity. Am. J. Hum. Genet. 56: 979-992

 Goodman, M., J. Czelusniak, G. W. Moore, A. E. Romero-Herrera, and G. Matsuda. (1979) Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences.  Systematic Zoology 28: 132-163

 Heads M. (2005) Dating nodes on molecular phylogenies: a critique of molecular biogeography. Cladistics 21: 62-78 

 Heiser, C. B. (1973) Introgression re-examined. Bot. Rev. 39: 347-366

* Hudson, R. R. (1991) Gene genealogies and the coalescent process. Oxford Surveys in Evolutionary Biology 7: 1-44

 Hudson, R. R., M. Slatkin and W. P. Maddison. (1992) Estimation of levels of gene flow from DNA sequence data. Genetics 132: 583-589

 James JK, Abbott RJ. (2005) Recent, allopatric, homoploid hybrid speciation: The origin of Senecio squalidus (Asteraceae) in the British Isles from a hybrid zone on Mount Etna, Sicily. Evolution 59: 2533-2547

 Kidwell, M. G. (1993) Lateral transfer in natural populations of eukaryotes. Annu. Rev. Genet. 27  235-256 

 Maddison, W. P. (1997) Gene trees in species trees. Systematic Biology 46: 523-536

 Mason-Gamer, Roberta J.  (2004) Reticulate evolution, introgression, and intertribal gene capture in an allohexaploid grass. Systematic Biology 53: 25-37 

 McDade, L. (1990) Hybrids and phylogenetic systematics. I. Patterns of character expression in hybrids and their implications for cladistic analysis. Evolution 44: 1685-1700

** McDade, L. A. (1992) Hybrids and phylogenetic systematics II. The impact of hybrids on cladistic analysis. Evolution 46: 1329-1346

 McDade, L. A. (1995) Hybridization and phylogenetics. in Experimental and molecular approaches to plant biosystematics (Hoch, P. C. and A. G. Stephenson, ed.  Missouri Botanical Garden, St. Louis. 

 McDade, L A. (1997) Hybrids and phylogenetic systematics III. Comparison with distance methods. Systematic Botany 22: 669-683

 Mountain, J. L., J. M. Hebert, S. Bhattacharyya, P. A. Underhill, C. Ottolenghi, M. Nason, J. D., N. C. Ellstrand and M. I. Arnold. (1992) Patterns of hybridization and introgression in populations of oaks, manzanitas, and irises. Am. J. Bot.  79: 101-111

 Nieto, F.G., A.J. Fuertes, and J.A. Rossello. (2001) Can extensive reticulation and concerted evolution result in a cladistically structured mmolecular data set? Cladistics 17: 301-312

 Ree RH. (2005) Detecting the historical signature of key innovations using stochastic models of character evolution and cladogenesis. Evolution 59: 257-265 

 Rieseberg, L. H. (1991) Homoploid reticulate evolution in Helianthus (Asteraceae): evidence from ribosomal genes. Amer. J. Bot 78: 1218-1237

 Rieseberg, L. H., R. Carter and S. Zona. (1990) Molecular tests of the hypothesized hybrid origin of two diploid Helianthus species (Asteraceae). Evolution 44: 1498-1511

 Schlefer, E. K., M. A. Romano, S. I. Guttman and S. B. Ruth. (1986) Effects of twenty years of hybridization in a disturbed habitat on Hyla cinerea and Hyla gratiosa. J. of Herpetology 20: 210-221

 Skala, Z. and Zrzavy J. (1994) Phylogenetic reticulations and cladistics - discussion of methodological concepts. Cladistics 10: 305-313

 Slatkin, M. and W. Maddison. (1989) A cladistic measure of gene flow inferred from the phylogenies of alleles. Genetics 123: 603-613

 Slatkin, M. and W. Maddison. (1990) Detecting isolation by distance using phylogenies of genes. Genetics 126: 249-260

 Vrana, P. and W. Wheeler. (1992) Individual organisms as terminal entities: laying the species problem to rest. Cladistics 8: 67-72

 Wagner, W. H. (1983) Reticulistics: the recognition of hybrids and their role in cladistics and classification. Pages 63-79 in Advances in Cladistics, Volume 2 (Platnick, N. I. and V. A. Funk, ed.) Columbia University Press, New York.  

 Williams ST, Reid DG. (2004) Speciation and diversity on tropical rocky shores: A global phylogeny of snails of the genus Echinolittorina. Evolution 58: 2227-2251

 Woodruff, D. S. and S. J. Gould. (1987) Fifty years of interspecific hybridization: genetics and morphometrics of a controlled experiment on the land snail Cerion in the Florida Keys. Evolution 41: 1022-1043

Morphometrics

 

 Adams, D.C. and M.S. Rosenberg (1998) Partial warps, phylogeny, and ontogeny: A comment on Fink and Zelditch (1995). Systematic Biology 47: 168-173 

 Arnold, E. N (1990) Why do morphological phylogenies vary in quality? An investigation based on comparative history of lizard clades. Proceedings of the Royal Society of London B  240: 135-172

 Bang, R., R. DeSalle, and W. Wheeler (2000) Transformationalism, taxism, and developemntal biology in systematics. Systematic Biology 49: 

 Baker, R. H. and Wilkinson, G. S. (2001) Phylogenetic analysis of secual dimorphism and eye-span allometry in stalk-eyed flies (Diopsidae). Evolution 55: 1373-1385

 Bookstein, F. L. (1982) Foundations of morphometrics. Annual Review of Ecology and Systematics 13: 451-470

 Bookstein, F. L. (1991) Morphometric Tools for Landmark Data. Cambridge University Press.  

 Bookstein, F.L. (1998) A hundred years of morphometrics. Acta Zoologica 44: 7-59

 Bookstein, F., B. Chernoff, R. Elder, J. Humphries, G. Smith & R. Strauss. (1985) Morphometrics in Evolutionary Biology. Spec. Pub. 15 Acad. Nat. Sci. Philadelphia. 

 Briggs, Derek E. G.; Fortey, Richard A. (2005) Wonderful strife: systematics, stem groups, and the phylogenetic signal of the Cambrian radiation.  Paleobiology 31: 94-112

 Collazo, A. (2000) Developmental variation, homology, and the pharyngula stage. Systematic Biology 49: 3-18

 Davis, J. I. (1983) Phenotypic plasticity and the selection of taxonomic characters in Puccinellia (Poaceae). Systematic Botany 8: 341-353

 Donoghue, M. J., J. A. Doyle, J. Gauthier, A. Kluge and T. Rowe. (1989) The importance of fossils in phylogeny reconstruction. Annu. Rev. Ecol. Syst. 20: 431-460

 Duarte, L. C., L. R. Monteiro, F. J. Von Zuben, S. F. Dos Reis. (2000) Variation in mandible shape in Thrichomys apereoides (Mammalia: Rodentia): geometric morphometric analysis of a complex morphological Structure. Systematic Biology 49: 563-578

 Finarelli, John A.; Clyde, William C. (2004) Reassessing hominoid phylogeny: evaluating congruence in the morphological and temporal data. Paleobiology 30: 614-651

 Fink, W. L. (1988) Phylogenetic analysis and the detection of ontogenetic patterns. pp. 71-91 in M. L. McKinney (ed.) Heterochrony in Evolution. Plenum Press, New York.  

 Fink, W.L. and M.L. Zelditch. (1995) Phylogenetic analysis of ontogenetic shape transformations: a reassessment of the Piranha genus Pygocentrus (Teleostei). Systematic Biology 44: 343-360

 Fisher, D.C. (1985) Evolutionary morphology: beyond the analogous, the anecdotal, and the ad hoc.  Paleobiology 11: 120-138

 Gaubert, Philippe; Wozencraft, W. Chris; Cordeiro-Estrela, Pedro, et al.  (2005) Mosaics of convergences and noise in morphological phylogenies: What's in a viverrid-like carnivoran? Systematic Biology 54: 865-894

 Gauthier, J., A. Kluge and T. Rowe. (1988) Amniote phylogeny and the importance of fossils. Cladistics 4: 105-209

 Gibson GD, Gibson AJF. (1900) Heterochrony and the evolution of poecilogony: Generating larval diversity Evolution 58: 2704-2717

 Guralnick, R.P.and D.R Lindberg. (1999) Integrating developmental evolutionary patterns and mechanisms: A case study using the gastropod radula. Evolution 53:  

 Guralnick, R. P. and D. R. Lindberg. (2001) Reconnecting cell and animal lineages: what do cell lineages tell us about the evolution and development of spiralia? Evolution 55: 1501-1519

 Hickman, C.S. (1980) Gastropod radulae and the assessment of form in evolutionary paleontology.  Paleobiology  6, 276-294: 

 Humphries, C. J. (1988) Ontogeny and systematics. Columbia University Press, New York.  

 Klingenberg, C. P. and L. J. Leamy. (2001) Quantitative genetics of geometric shape in the mouse mandible. Evolution 55: 2342-2352

 Kluge, A. G. and R. E. Strauss. (1985) Ontogeny and systematics. Annual Review of Ecology and Systematics 16: 247-268

 Kluge, A. J. (1989) A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes).  Systematic Zoology 38: 7-25

 Lauder, G. V. (1990) Functional morphology and systematics: studying functional patterns in an historical context. Annual Review of Ecology and Systematics 21: 317-340

 Mabee, P. M. (1989) Assumptions underlying the use of ontogenetic sequences for determining character state order. Trans. Amer. Fish. Soc. 118: 159-166

 Mabee, P. M., K. L. Olmstead, and C. C. Cubbage. (2000) An experimental study of intrspecific variation, developmental timing, and heterochrony in fishes. Evolution 54: 2091-2106

 MacLeod, N. (1999) Generalizing and extending the eigenshape method of shape space visualization and analysis.  Paleobiology 25: 107-138

 Magwene, P. M. (2001) Comparing ontogenetic trajectories using growth process data. Systematic Biology 50: 640-666

 McDade, L. (1990) Hybrids and phylogenetic systematics. I. Pattrerns of character expression in hybrids and their implications for cladistic analysis. Evolution 44: 1685-1700

 Mead, A. J. (2000) Sexual dimorphism and paleoecology in Teloceras, a North American Miocene rhinoceros.  Paleobiology 26: 689-706

 Muller, M. and Q. C. B. Cronk. (2001) Evolution of a morpholgoical novelty: a phylogenetic analysis of growth patterns in Streptocarpus (Geseneriaceae). Evolution 55: 918-929

 Monteiro, L. R. (1999) Multivariate regression models and geometric morphometrica: the search for causal factors in the analysis of shape. Systematic Biology 48: 192-199

 Monteiro, L. R. (2000) Why morphometrics is special: the problem with using partial warps as characters for phylogenetic inference. Systematic Biology 49: 796-799

 Nijhout, H. F. (1990) Metaphors and the role of genes in development BioEssays 12: 441-446

 O'Keefe, F. R., O. Rieppel, and P. M. Sander. (1999) Shape disassociation and inferred heterochrony in a clade of pachypleurosaurs (Reptilia, Sauropterygia).  Paleobiology 25: 504-517

 Raup, D.M. (1972) Approaches to morphologic analysis. In Schopf, T.J.M. (ed.), Models in pproaches to morphologic analysis. In Schopf, T.J.M. (ed.), Models in Paleobiology, 28044. Freeman, Cooper, San Francisco.  

 Renaud, S., M. Benammi, and J.-J.. Jaeger. (1999) Morphological evolution of the murin rodent Paraethomys in response to climativ variations (Mio-Liocene of North Africa).  Paleobiology 25: 369-382

** Rohlf, F. J. (1990) Morphometrics. Annual Review of Ecology and Systematics 21: 29-316

 Rohlf, F.J., A. Loy A, & M. Corti. (1996) Morphometric analysis of old world talpidae (Mammalia, Insectivora) using partial-warp scores. Systematic Biology 45: 344-362

 Rohlf, F.J. (1998) On applications of geometric morphometrics to studies of ontogeny and phylogeny. Systematic Biology 47: 147-158

 Rohlf, F. J. (2001) Comparative methods for the analysis of continuous variables: geometric interpretations. Evolution 55: 2143-2160

 Roth-Nebelsick, A., G. Grimm, V. Mosbrugger, H. Hass, and H. Kerp. (2000) Morphometric analysis of Rhynia and Asteroxylon: testing functional aspects of early land plant evolution.  Paleobiology 26: 405-418

 Samadi, S., P. David, and P. Jarne. (2000) Variation of shell shape in the clonal snail Melanoides tuberculata and its consequences for the interpretation of fossil series. Evolution 54: 492-502

 Slice, D. E. (2001) Landmark coordinates aligned by procrustes analysis do not lie in Kendall's shape space. Systematic Biology 50: 141-149

 Smith, E. N. and R. L. Gutberlet. (2001) Generalized frequency coding: a method of preparing polymorphic multistate characters for phylogenetic analysis. Systematic Biology 50: 159-169

 Smith, Nathan D., Turner, Alan H. (2005) Morphology's role in phylogeny reconstruction: Perspectives from paleontology. Systematic Biology 54: 166-173

 Strauss, R. E. and F. L. Bookstein. (1982) The truss: Body form reconstructions in morphometrics.  Systematic Zoology 31: 113-135

 Sultan, S. E. (1987) Evolutionary implications of phenotypic plasticity in plants. Evolutionary Biology 21: 127-178

 Swiderski, D.L. and M.L. Zelditch. (1998) Why morphometrics is not special: Coding quantitative data for phylogenetic analysis. Systematic Biology 47: 508-519

 Thompson, D'A. W. (1942) On growth and form (Complete Revised Edition, 1992: an unabridged and unaltered replica of the1942 edition, paperback). Dover.  

 Walker, J. A. (2000) Ability of geometric morphometric methods to estimate a known covariance matrix Systematic Biology 49: 686-696

 Wake, D.B. (1983) Functional and Evolutionary Morphology. 25th Anniv. Issue of Perspectives in Biology and Medicine.  

 Webster, Mark; Zelditch, Miriam Leah (2005) Evolutionary modifications of ontogeny: heterochrony and beyond.  Paleobiology 31: 354-372

 Wiley, E. O. (1981) Phylogenetics: the theory and practice of phylogenetic systematics. John Wiley and Sons, New York.  

* Wiens, J. J. (2000) Phylogenetic Analysis of Morphological Data. Smithsonian Institution Press, Washington D.C.  

 Wiens, J. J. (2001) Character analysis in morphological phylogenetics: problems and soultions. Systematic Biology 50:  689-699

 Wiens, John J.; Bonett, Ronald M.; Chippindale, Paul T. (2005) Ontogeny discombobulates phylogeny: Paedomorphosis and higher-level salamander relationships. Systematic Biology 54: 91-110

 Wiens, John J. (2004) The role of morphological data in phylogeny reconstruction. Systematic Biology 53: 653-661

 Young NM, Hallgrimsson B. (2005) Serial homology and the evolution of mammalian limb covariation structure. Evolution 59: 2691-2704

** Zelditch, M.L., W.L. Fink, and D.L. Swiderski. (1995) Morphometrics, homology, and phylogenetics: quantified characters as synapomorphies. Systematic Biology 44: 179-189

 Zelditch, M. L. and W. L. Fink. (1996) Heterochrony and heterotopy: stability and innovation in the evolution of form. Paleobiology 22: 241-254

 Zelditch, M.L., W.L. Fink, D.L. Swiderski, and B.L. Lundrigan. (1998) On applications of geometric morphometrics to studies of ontogeny and phylogeny: A reply to Rohlf. Systematic Biology 47: 159-167

 Zelditch, M. L. and W. L. Fink. (1998) Partial warps, phylogeny and ontogeny: A reply to Adams and Rosenberg. Systematic Biology 47: 345-348

 Zelditch, M. L., H. D. Sheets, and W. L. Fink. (2000) Spatiotemporal reorganization of growth rates in the evolution of ontogeny. Evolution 54: 1363-1371

Biogeography

 Alroy, J. (1995) Continuous track analysis: a new phylogentic and biogeographic method. Systematic Biology  44: 152-178

 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

 Baldwin, B. G., D. W. Kyhos and J. Dvorak. (1990) Chloroplast DNA evolution and adaptive radiation in the Hawaiian silversword alliance (Asteraceae-Madiinae). Ann. Mo. Bot. Gard. 77: 96-109

 Baldwin, B. G. and R. H. Robichaux. (1995) Historical biogeography and ecology of the Hawaiian silversword alliance (Asteraceae): New molecular phylogenetic perspectives.Pp. 259-287 In Wagner, W. L. and V. Funk (Eds.) Hawaiian Biogeography, evolution on a Hot Spot Archipelago. Smithsonian Institution Press, Washington. 

 Baldwin, B. G., and Sanderson, M. J. (1998) Age and rate of diversification of the Hawaiian silversword alliance (Compositae). PNAS 95: 9402-9406

 Ball, I.R. (1976) Nature and formulation of biogeographical hypotheses.  Systematic Zoology 24: 407-430

** Brooks, D.R., & D. McLennan. (1991) Phylogeny, Ecology, and Behavior. University of Chicago Press. Pp. 206-248  

* Brooks, D. R. (1990) Parsimony analyisis in historical biogeography and coevolution: Methodological and theoretical update.  Systematic Zoology 39: 14-30

 Carpenter, J M. (1996) Phylogeny and biogeography of Polistes. Pp. 18-57 in Turillazzi, S. and M. J. West-Eberhard (Ed.). Natural history and evolution of paper-wasps; Proceedings of the International Workshop, Castiglioncello, Italy, October 4-7, 1993. Oxford University Press:  

 Coscaron, M D C; Morrone, J J. (1997) Cladistics and biogeography of the assassin bug genus Melanolestes Stal (Heteroptera: Reduviidae).  Proceedings of the Entomological Society of Washington 99:  55-59

 Cracraft, J. (1995) Cladistic analysis and vicariance biogeography. pp. 104-112 in Slatkin, M. (Ed.). Exploring evolutionary biology: Readings from American Scientist. Sinauer Associates, Inc.: Sunderland, Massachusetts, USA.  

 De Meyer, M. (1996) Cladistic and biogeographic analyses of Hawaiian Pipunculidae (Diptera) revisited. Cladistics 12: 291-303

 Emerson, B C; Wallis, G P; Patrick, B H. (1997) Biogeographic area relationships in southern New Zealand: A cladistic analysis of Lepidoptera distributions. Journal of Biogeography 24: 89-99

 Enghoff, H. (1995) Historical biogeography of the Holarctic: Area relationships, ancestral areas, and dispersal of non-marine animals. Cladistics 11: 223-263

 Evans, B J; Morales, J C; Picker, M D; Kelley, D B; Melnick, D J. (1997) Comparative molecular phylogeography of two Xenopus species, X. gilli and X. laevis, in the south-western Cape Province, South Africa. Molecular Ecology 6: 333-343

 Grant, P. R.  (1998) Radiations, communities, and biogeography. Pp. 196-209. in P. R. Grant, eds. Evolution on islands. Oxford University Press, Oxford.  

 Gray, J. and A.J. Boucot (eds. (1979) Historical Biogeography, Plate Tectonics, and the Changing Environment, Oregon State University Press, Corvallis, Oregon.  

 Kluge, A. G. (1988) Parsimony in vicariance biogeography: a quantitative method and a greater Antillean example.  Systematic Zoology 37: 315-328

 Linder, H P; Crisp, M D.  (1995) Nothofagus and Pacific biogeography. Cladistics 11: 5-32

 Lydeard, C. M.C. Wooten, and A. Meyer. (1995) Molecules, morphology and area cladeograms: a cladistic and biogeographic analysis of Gambusia (Teleostei: Poecilliiae) Systematic Biology 44: 221-236

 Morrone J.J. and Carpenter, J.M. (1994) In search of a method for cladistic biogeography - an comparison of component analysis, brooks parsimony analysis, and three area statements. Cladistics 10: 99-153

 Nelson, G. (1985) A decade of challenge the future of biogeography Earth Sciences History 4: 187-196

 Nelson, G. and N. Platnick. (1981) Systematics and biogeography, cladistics and vicariance. Columbia Univ. Press, New York.  

 Nelson, G. and Rosen, D.E. (1981) Vicariance biogeography: a critique. ColumbiaUniversity Press, New York.  

 Nelson, G and Ladiges, P. Y.   (1996) Paralogy in cladistic biogeography and analysis of paralogy free subtrees. American Museum Novitates 3167: 1-58

 Page, R. D. M. (1989) Comments on component-compatibility in historical biogeography. Cladistics 5: 167-182

 Page, R. D. M. (1994) Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Systematic Biology 43: 58-77

 Page, R.D.M. (1994) Parallel phylogenies - reconstructing the history of host-parasite assemblages. Cladistics 10: 155-173

 Pielou, E. C. (1979) Biogeography. John Wiley and Sons; New York.  

 Rosen, D. E. (1975) A vicariance model of Caribbean biogeography.  Systematic Zoology 24: 431-464

 Rosen, D. E. (1978) Vicariant patterns and historical explanation in biogeography.  Systematic Zoology 27: 159-188

 Rosen, D. E. (1979) Fishes from the upland and intermontane basins of Guatemala: revisionary studies and comparative geography. Bull. Amer. Mus. Nat. Hist. 162: 267-376

** Sanmartin, I.; Ronquist, F.    (2002) New solutions to old problems: Widespread taxa, redundant distributions and missing areas in event-based biogeography. Animal Biodiversity and Conservation 25 : 75-93

 Siddall, M E. (1996) Phylogenetic covariance probability: Confidence and historical associations. Systematic Biology 45: 48-66

 Springer, V. G. (1982) Pacific plate biogeography, with special reference to shorefishes. Systematic Biology 45: 1-167

 Swenson, U. and K. Bremer. (1997) Pacific Biogeography of the Asteraceae genus Abrotanella (Senecioneae, Belnnospermatinae).  Systematic Botany 22: 493-508

** van Veller, Marco G. P.; Brooks, D. R.; Zandee, M. (2003) Cladistic and phylogenetic biogeography: The art and the science of discovery. Journal of Biogeography 30 : 319-329

 Vermeij, G. J. (1978) Biogeography and adaptation. Harvard University Press; Cambridge.  

 Wagner, W. L. and V. A. Funk (1995) Hawaiian biogeography: Evolution on a hot spot archipelago. Smithsonian Institution Press: Washington, DC.  

 Weston, P H; Crisp, M D. (1994) Cladistic biogeography of waratahs (Proteaceae:Embothrieae) and their allies across the Pacific. Australian  Systematic Botany 7: 225-249

 Wiley, E. O. (1981) Phylogenetics: the theory and practice of phylogenetic systematics. John Wiley and Sons, New York.  

Macroevolution

 Alroy, J. (2000) Understanding the dynamics of trends within evolving lineages.  Paleobiology 26: 319-329

 Brooks, D. R. and D. A. McLennan. (1993) Comparative study of adaptive radiations with an example using parasitic flatworms (Platyhelminthes, Cercomeria). Am. Nat. 142: 755-778

 Charlesworth, B., R. Lande and M. Slatkin. (1982) A neo-Darwinian commentary on macroevolution. Evolution 36: 474-498

 Elbe, G. J. (2000) Contrasting evolutionary flexibility in sister groups: disparity and diversity in Mesozoic atelostomate echinoids.  Paleobiology 26: 56-79

 Gilinsky, N.L. and I.J. Good. (1991) Probabilities of origination, persistence, and extinction of families of marine invertebrate life.  Paleobiology 17: 145-66

 Gould, S. J. and N. Eldredge. (1977) Punctuated equilibria: the tempo and mode of evolution reconsidered.  Paleobiology 3: 115-151

 Gould, S.J., N.L. Gilinsky & R.Z. German (1987) Asymmetry and the direction of evolutionary time. Science 236: 1437-1441

 Gould, S.J. (1991) The disparity of the Burgess Shale arthropod fauna and the limits of cladistic analysis: why we must strive to quantify morphospace.  Paleobiology 17: 411-23

 Hey, J. (1992) Using phylogenetic trees to study speciation and extinction. Evolution 46: 627-640

 Jablonski, D., J.J. Sepkoski, Jr., D.J. Bottjer, and P.M. Sheehan. (1983) Onshore-offshore patterns in the evolution of Phanerozoic shelf communities. Science 222: 1123-1125

 Jablonski, D. (1986) Background and mass extinctions: the alternation of macroevolutionary regimes.   Science 231: 129-133

 Jablonski, D. (1987) Heritability at the species level: Analysis of geographic ranges of cretaceous mollusks. Science 238: 360-363

 Jablonski, D. (2000) Micro- and macroevolution: scale and heirarchy in evolutionary biology and and paleobiology. Paleobiology 26: 15-52

 Jeffery, C. H. (2001) Heart urchins at the Cretaceous/Tertiary boundary: a tale of two clades.  Paleobiology 27: 104-125

 Kubo, T. and I. Y. (1995) Inferring the rates of branching and extinction from molecular phylogenies. Evolution 49: 694-704

** Lemen, C.A. and P.W. Freeman. (1989) Testing macroevolutionary hypotheses with cladistic analysis: evidence against rectangular evolution. Evolution 43: 1538-1554

 Levington, J. S. and C. M. Simon. (1980) A critique of the punctuated equilibria model and implications for the detection of speciation in the fossil record.  Systematic Zoology 29: 130-142

 McShea, D. W. (2000) Trends, tools, and terminology.  Paleobiology 26: 330-333

** Mindell, D. P., J. W. Sites Jr. and D. Graur. (1989) Speciational evolution: A phylogenetic test with allozymes in Sceloporus (Reptilia). Cladistics 5: 49-61

 Norris, R.D. (1991) Biased extinction and evolutionary trends.  Paleobiology 17: 388-99

 Norris, R. D. (2000) Pelagic species diversity, biogeography, and evolution.  Paleobiology 26: 236-258

 Patterson, C. and A.B. Smith (1987) Is the periodicity of extinctions a taxonomic artefact? Nature 330: 248-252 and reply by Sepkoski 

 Raup, D.M. and J.J. Sepkoski (1986) Periodic extinction of families and genera. Science. 231: 833-836

 Robeck, H. E., C. C. Maley, and M. J. Donoghue. (2000) Taxonomy and temporal diversity patterns.  Paleobiology 26: 171-187

 Rohde, K. (1996) Robust phylogenies and adaptive radiations: a critical evaluation of methods used to identify key innovations.  Am. Nat. 148: 481-500

 Roopnarine, P. D., G. Byars, and P. Fitzgerald. (1999) Anagenetic evolution, stratophenetic patterns and random walk models.  Paleobiology 25: 41-57

 Schopf, T. M. J. (1981) Punctuated equilibria and evolutionary stasis. Paleobiology 7: 156-166

 Shubin, N. H. and C. R. Marshall. (2000) Fossils, genes, and the origin of novelty.  Paleobiology  26 : 324-340

 Smith, A.B. & C. Patterson. (1988) The influence of taxonomic method on the perception of patterns of evolution. Evolutionary Biology 23: 127-216

 Smith, A. B. (1994) Systematics and the fossil record: documenting evolutionary patterns. Blackwell Scientific Publications, Oxford.  

 Smith, L. H. and B. S. Lieberman. (1999) Disparity and constraint in the olenelloid trilobites and the Cambrian rasiation.  Paleobiology 25: 459-470

 Stanley, S. M. (1982) Macroevolution and the fossil record. Evolution 36: 460-473

 Stidd, B. M. (1985) Are punctuationists wrong about the modern synthesis? Phil. Sci. 52: 98-109

 Van Valen, L.M. and V.C. Maiorana. (1985) Patterns of origination. Evol. Theory 7: 107-125

 Vrba, E.S. (1980) Evolution, species and fossils: how does life evolve? S. Afr. J. Sci. 76: 61-84

 Wagner, P.J. (1995) Stratigraphic tests of cladistics hypotheses.  Paleobiology 21: 153-178

 Wagner, P.J. (1995) Diversity patterns among early gastropds: contrasting taxonomic and phylogenetic descriptions. Paloebiology 21: 410-439

 Wagner, P. J. (1996) Contrasting the underlying patterns of active trends in morphological evolution. Evolution 50: 990-1007

 Wagner, P. J. (2000) Exhaustion of morphologic character states among fossil taxa. Evolution 54: 365-386

 Williamson, P. G. (1981) Paleontological documentation of speciation in Cenozoic mollusks from Turkana Basin.   Nature 293: 437-443

Comparative Methods

 Brooks, D.R., & D. McLennan. (1991) Phylogeny, Ecology, and Behavior. University of Chicago Press.  

 Burt, A. (1989) Comparative methods using phylogenetically independent contrasts. Oxford Surveys in Evolutionary Biology 6: 33-53

 Cheverud, J., and M. Dow. (1985) An autocorrelation analysis of the effect of lineal fission on genetic variation among social groups. Amer. J. Phys. Anthropol. 67: 113-121

 Cheverud, J. M., M. M. Dow, and W. Leutenegger. (1985) The quantitative assessment of phylogenetic constraints in comparative analyses: Sexual dimorphism in body weight among primates.  Evolution 39: 1335-1351

 Cliff, A. D., and Ord, J. K. (1973) Spatial Autocorrelation. London: Pion.  

 Coddington, J. (1988) Cladistic tests of adaptational hypotheses. Cladistics 4: 3-22

 de Queiroz, K. (1996) Including the characters of interest during tree reconstruction and the problems of circularity and bias in studies of character evolution. Am. Nat. 148: 700-708

 Donoghue, M.J. (1989) Phylogenies and analysis of evolutionary sequences, with examples from seed plants. Evolution 43: 1137-1156

 Felsenstein, J. (1985) Phylogenies and the comparative method. Am. Nat. 125: 1-15

 Funk, V.A. and D.R. Brooks. (1990) Phylogenetic systematics as the basis of comparative biology. Smithsonian Institution Press.  

 Harvey, P.H. and M.D. Pagel. (1991) The comparative method in evolutionary biology. Oxford University Press.  

 Martins, E. P. (1996) Phylogenies, spatial autoregression, and the comparative method: A computer simulation test.  Evolution 50: 1750-1765

 Martins, E. P., and Hansen, T. F. (1997) Phylogenies and the comparative method: A general approach to incorporating phylogenetic information into the analysis of interspecific data. Am. Nat.  

 Miles, D. B. and A. E. Dunham. (1993) Historical perspectives in ecology and evolutionary biology: the use of phylogenetic comparative analyses. Annual Review of Ecology and Systematics 24: 587-619

 Sillin-Tullberg, B. (1988) Evolution of gregariousness in aposematic butterfly larvae: a phylogenetic analysis. Evolution 42: 293-305

 Vogl, C., and G. P. Wagner. (1990) Interspecific variability in randomly evolving clades: models for testing hypotheses on the relative evolutionary flexibility of quantitative traits. Systematic Zoology 39: 109-123

Conservation

*** Crozier, R.H., Dunnett, L.J. and Agapow, P.M. (2005) Phylogenetic biodiversity assessment based on systematic nomenclature. Evolutionary Bioinformatics Online 1: 11-36

 Faith, D. P. (1992a) Conservation evaluation and phylogenetic diversity. Biological Conservation 61: 1-10

 Faith, D. P. (1992b) Systematics and conservation: on predicting the feature diversity of subsets of taxa. Cladistics 8: 361-373

** Forey, P.L., C. J. Humphries and P. H. Williams. (1994) Systematics and conservation evaluation, Systematics Association Special Volume No. 50 Clarendon Press, Oxford.  

 Mishler, B.D. (1995) Plant systematics and conservation: science and society. Madrono 42: 103-113

 Moritz,C., J. L. Patton, C. J. Schneider, and T. B. Smith. (2000) DIVERSIFICATION OF RAINFOREST FAUNAS: An Integrated Molecular Approach Annu. Rev. Ecol. Syst.  31: 533-563

 Polhemus, D. A.  (1997) Phylogenetic analysis of the Hawaiian damselfly genus Megalagrion (Odonata: Coenagrionidae): Implications for biogeography, ecology, and conservation biology. Pacific Science 51: 395-412

 Tyler, H. A., Brown, K. S., Jr., and Wilson, K. H. (1994) Swallowtail butterflies of the Americas: A study in biological dynamics, ecological diversity, biosystematics, and conservation.  

 Vane-Wright, R. I., C. J. Humphries and P. H. Williams (1991) What to protect? -- Systematics and the agony of choice. Biological Conservation 55 235-254