Integrative Biology 200B
Readings

Reading List Index
Download Reading List (2009 edition, not including 2011 modifications) as: {printable html} {pdf} {sortable excel}

Recommended Bibliography for IB 200B: Index

History and Philosophy of Systematic Biology
The Hennig Principle
Homology
Characters and Character States
Character Coding
Molecular Data
Classification - Basic Principles
DNA Barcoding
Species Concepts
Phylogenetic Tree Reconstruction
Phenetics
Maximum Likelihood
Bayesian Methods
Phylogenetic Trees: Support and Tree Comparisons
Reticulation and Phylogeography
Morphometrics
Biogeography
Macroevolution
Comparative Methods
Conservation

= required in 2011 course; other special recommendations starred for direct relevance to the course, basic to the field ("something everyone should have read"), etc.

 

History and Philosophy of Systematic Biology

Bock, W. J. (1973) Philosophical foundations of classical evolutionary classification Systematic Zoology 22: 375-392 Part of a general symposium on "Contemporary Systematic Philosophies," there are some other interesting papers here.

Brower, A. V. Z. (2000) Evolution Is Not a Necessary Assumption of Cladistics Cladistics 16: 143-154

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

Dayrat, Benoit (2005) Ancestor-descendant relationships and the reconstruction of the Tree of Lif Paleobiology 31: 347-353

Donoghue, M.J. and J.W. Kadereit (1992) Walter Zimmermann and the growth of phylogenetic theory Systematic Biology 41: 74-84

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

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

Gilmour, J. S. L. (1940) Taxonomy and philosophy, pp. 461-474 in J. Huxley (ed.) The New Systematics Oxford

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

Hull, D. L. (1978) A matter of individuality Phil. of Science 45: 335-360

Hull, D. L. (1978) The principles of biological classification: the use and abuse of philosophy

Hull, D. L. (1984) Cladistic theory: hypotheses that blur and grow, pp. 5-23 in T. Duncan and T. F. Stuessy (eds.) Cladistics: Perspectives on the Reconstruction of Evolutionary History Columbia University Press, New York

* Hull, D. L. (1988) Science as a process: an evolutionary account of the social and conceptual development of science University of Chicago Press. An already classic work on the recent, violent history of systematics; used as data for Hull's general theories about scientific change.

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

Kitts, D. B. (1977) Karl Popper, verifiability, and systematic zoology. Systematic Zoology 26: 185-194

Kluge, A. G. (1999) The Science of Phylogenetic Systematics: Explanation, Prediction and Test Cladistics 15: 429-436

Kluge, A. J. (2001) Philosophical conjectures and their refutation Systematic Biology 50: 322-330

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

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

Laudan, L. (1977) Progress and Its Problems. University of California Press, Berkley.

Losee, J. (1980) A Historical Introduction to the Philosophy of Science. Second edition. Oxford University Press. The best single-volume account of changes since Aristotle in how science proceeds -- strongly recommended.

McKelvey, B. (1982) Organizational Systematics, Univ. of California Press Berkeley

Mishler, B. D. (1989) Untitled review of Hull, D.L. (1988) Science as a process. Systematic Botany 14: 266-268

Mishler, Brent D. (2009). Three centuries of paradigm changes in biological classification: Is the end in sight? Taxon, 58(1), 61-67.

O'Hara, R. J. (1992) Telling the tree: Narrative representation and the study of evolutionary history Biology and Philosophy 7: 135-160

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

de Queiroz, K (1987) Systematics and the Darwinian revolution. Philosophy of Science 55: 238-259

de Queiroz, K. and S. Poe (2001) Philosophy and phylogenetic inference: a comparison of likelihood and parsimony methods in the context of Karl Popper's writings on corroboration. Systematic Biology 50: 305-321

Sober, E. (1988) Reconstructing the past, Chapter 1. MIT Press.

** Sober, E. (2008). Evidence and Evolution: the logic behind the science, Cambridge University Press. Particularly good on philosophy of statistics (frequentism vs. likelihood vs. Bayesian approaches) and their relation to (1) inferring phylogenies and (2) inferring natural selection.

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

Stevens, P. F. (1994) The development of biological systematics. Columbia University Press, New York.

Wiley, E. O. (1975) Karl R. Popper, systematics, and classification: a reply to Walter Bock and other evolutionary taxonomists. Systematic Zoology 24: 233-243

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

Winsor, Mary Pickard (1995). "The english debate on taxonomy and phylogeny." History and Philosopy of the Life Sciences, 17(2), 227-252.

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

**** Mishler, Brent D. (2005). The logic of the data matrix in phylogenetic analysis. In V.A. Albert (ed.), Parsimony, Phylogeny, and Genomics, Oxford University Press, 57-70. doi: 10.1093/acprof:oso/9780199297306.003.0004

Lindberg, D.R. (1992) Systematic Paleontology. Pp. 31-37 In: J. H. Lipps, ed. Fossil Prokaryotes and Protists, Blackwell Scientific Publications, Ltd., Oxford

Pol, D. and M. E. Siddall (2001) Biases in Maximum Likelihood and Parsimony: A Simulation Approach to a 10-Taxon Case. Cladistics 17: 266-281

de Queiroz, K. and J. Gauthier (1992) Phylogenetic taxonomy. Annual Review of Ecology and Systematics 23: 449-480

Wilkinson M. (1994) Three-taxon statements - when is a parsimony analysis is also a clique analysis. Cladistics 10: 221-223

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

Fink, William L. (1982). The Conceptual Relationship Between Ontogeny and Phylogeny. Paleobiology, 8(3), 254-264. (JSTOR)

Goldman, N. (1988) Methods of discrete coding of morphological characters for numerical analysis. Cladistics 4: 59-71

Hauser, D. L. and W. Presch. (1991) The effect of ordered characters on phylogenetic reconstruction. Cladistics 7: 243-265

Hibbett, D. S. and M. J. Donoghue (2001) Analysis of character correlations among wood decay mechanisms, mating systems, and substrate ranges in Homobasidiomycetes. Systematic Biology 51: 215-242

Jenner, R. A. (2001) Bilaterian phylogeny and uncritical recycling of morphological data sets. Systematic Biology 50: 730-742

Le Quesne, W. J. (1969) A method of selection of characters in numerical taxonomy. Systematic Zoology 18: 201-205

Lee, D.-C. and H. N. Bryant. (1999) A Reconsideration of the Coding of Inapplicable Characters: Assumptions and Problems. Cladistics 15: 373-378

Lipscomb, D. L. (1992) Parsimony, homology, and the analysis of multistate characters. Cladistics 8: 45-65

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

** Mishler, B. D. (2005) The logic of the data matrix in phylogenetic analysis. In V.A. Albert (ed.), Parsimony, Phylogeny, and Genomics, pp. 57-70. Oxford University Press.

** Mishler, B. D. and E. De Luna. (1991) The use of ontogenetic data in phylogenetic analyses of mosses. Advances in Bryology 4: 121-167

* Neff, N.A. (1986) A rational basis for a priori character weighting. Systematic Zoology 35: 102-109

Monteiro, L. R. (2000) Why morphometrics is special: the problem with using partial warps as characters for phylogenetic analysis. Systematic Biology 49: 796-800

O'Keffe, F. R. and P. J. Wagner. (2001) Inferring and testing hypotheses of cladistic character independence by using character compatibility. Systematic Biology 50: 657-675

Pimentel, R.A. and Riggins, R. (1987) The nature of cladistic data. Cladistics 3: 201-209

Pogue, M. G. and M. F. Mickevich. (1990) Character definitions and character state delineation: the b?te noire of phylogenetic inference. Cladistics 6: 319-361

Rae, T. C. (1998) The logical basis for the use of continuous characters in phylogenetic systematics.? Cladistics 14: 221-228

Schander, C. and P. Sundberg. (2001) Useful characters in gastropod phylogeny: soft information or hard facts? Systematic Biology 50: 136-141

Simmons, M. P. and H. Ochoterena. (2000) Gaps as characters in sequence-based phylogenetic analysis. Systematic Biology 49: 369-381

Simmons, M. P., H. Ochoterena, and T. G. Carr. (2001) Incorporation, relative homoplasy, and effect of gap characters in sequenced-based phylogenetic analysis. Systematic Biology 50: 454-461

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

Slowinski, J. B. (1993) Unordered versus "ordered" characters. Systematic Biology 42: 155-165

Smith, E. N. and R. L. Gutberlet jr. (2001) Generalized frequency coding: a method of preparing polymorphic multistate characters for phylogenetic analysis. Systematic Biology 51: 156-169

* Stevens, P.F. (1991) Character states, morphological variation, and phylogenetic analysis: a review. Systematic Botany 16: 553-583

Strong, E. E. and D. Lipscomb. (1999) Character coding and inapplicable data. Cladistics 15: 363-371

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

Wagner, G. P. (ed.). (2001) The character concept in evolutionary biology. Academic Press, San Diego.

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

Wiens, J. J. (1995) Polymorphic characters in phylogenetic systematics. Systematic Biology 44: 482-500

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

Wilkinson, M. (1992) Ordered versus unordered characters. Cladistics 8: 375-385

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

#include file="menu.htm"

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

Brower, Andrew V. Z., Schawaroch, Valerie (1996). "Three steps of homology assessment." Cladistics, 12(3), 265272. doi: 10.1111/j.1096-0031.1996.tb00014.x

Bruns, T. D., T. J. White and J. W. Taylor. (1991) Fungal molecular systematics. Annu. Rev. Ecol. Syst. 22: 525-564

Collins, Timothy M.; Fedrigo, Olivier; Naylor, Gavin J. P. (2005) Choosing the best genes for the job: The case for stationary genes in genome-scale phylogenetics. Systematic Biology 54: 493-500

* Cracraft, J. (1987) DNA hybridization and avian phylogenetics. Evolutionary Biology 21: 47-96

Creer S, Malhotra A, Thorpe RS, et al. (2005) Targeting optimal introns for phylogenetic analyses in non-model taxa: experimental results in Asian pitvipers. Cladistics 21: 390-395

DeBry, R. W. (1999) Maximum likelihood analysis of gene-based and structure-based process partitions, using mammalian mitochondrial genomes. Systematic Biology 48: 286-299

DeSalle, R. and D. A. Grimaldi. (1991) Morphological and molecular systematics of the Drosophilidae. Annual Review of Ecology and Systematics 22: 447-475

** Donoghue, M. J. and M. J. Sanderson. (1992) The suitability of molecular and morphological evidence in reconstructing plant phylogeny. Pages 340-368 in Molecular Systematics of Plants (Soltis, P. S., D. E. Soltis and J. J. Doyle, ed.). Chapman & Hall, New York.

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

Fleissner, Roland; Metzler, Dirk; Von Haeseler, Arndt. (2005) Simultaneous statistical multiple alignment and phylogeny reconstruction. Systematic Biology 54: 548-561

Giribet G. (2005) Generating implied alignments under direct optimization using POY . Cladistics 21: 396-402

Givnish, T. J. and K. J. Sytsma (1997). Homoplasy in molecular vs. morphological data: the likelihood of correct phylogenetic inference. Molecular (1997) Evolution and Adaptive Radiation. (T. J. Givnish and K. J. Sytsma, eds). Cambridge, Cambridge University Press: 55-101

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

Hillis, D. M., J. J. Bull, M. E. White, M. R. Badgett and I. J. Molineux. (1992) Experimental phylogenetics: generation of a known phylogeny. Science 255: 589-592

Hillis, D.M. (1995) Approaches for assessing phylogenetic accuracy. Systematic Biology 44: 39523

Hillis, D. M., C. Moritz and B. K. Mable (eds.). (1996) Molecular Systematics, second edition. Sinauer, Sunderland, MA. 655 pp.

Hillis, D. M. and J. J. Wiens. (2000) Molecules versus morphology in systematics: conflicts, artifacts, and misconceptions. pp. 1-19 in J. J. Wiens (ed.), Phylogenetic Analysis of Morphological Data. Washington DC, Smithsonian Institution Press.

Huelsenbeck, J. P. and R. Nielsen. (1999) Effect of non-independent substitution on phylogenetic accuracy. Systematic Biology 49: 317-328

Laamanen TR, Meier R, Miller MA, et al. (2005) Phylogenetic analysis of Themira (SepsidaeDiptera): sensitivity analysis, alignment, and indel treatment in a multigene study. Cladistics 21: 258-271

Lutzoni, F., P. Wagner, V. Reeb and S. Zoller. (2000) Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology. Systematic Biology 49: 628-651

Macey, J. R., J. A. Schulte II, and A. Larson. (2000) Evolution and phylogenetic information content of mitochondrial genomic structural features illustrated with acrodont lizards. Systematic Biology 49: 257-277

Mindell, D. P. and R. L. Honeycutt. (1990) Ribosomal RNA in vertebrates: evolution and phylogenetic applications. Annual Review of Ecology and Systematics 21: 541-566

** Mishler, B. D. (1994) The cladistic analysis of molecular and morphological data. American Journal of Physical Anthropology 94: 143-156

Mishler, B. D., K. Bremer, C. J. Humphries and S. P. Churchill. (1988) The use of nucleic acid sequence data in phylogenetic reconstruction. Taxon 37: 391-395

Morrison, David A. (2009). Why Would Phylogeneticists Ignore Computerized Sequence Alignment?, Systematic Biology, 58(1), 150-158. doi: 10.1093/sysbio/syp009

* Miyamoto, M. M. and J. Cracraft (eds.). (1991) Phylogenetic analysis of DNA sequences. Oxford University Press, New York. 358 pp.

Nei, M. and F. Tajima. (1987) Problems arising in phylogenetic inference from restriction-site data. Mol. Biol. Evolution 4: 320-323

Palmer, J. D., R. K. Jansen, H. J. Michaels, M. W. Chase and J. R. Manhart. (1988) Chloroplast DNA variation and plant phylogeny. Ann. Mo. Bot. Gard. 75: 1180-1206

Palmer, J. D. and L. A. Herbon. (1988) Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J. Mol. Evolution 28: 87-97

Patterson, C. (ed.). (1987) Molecules and Morphology in Evolution: Conflict or Compromise. Cambridge Univ. Press, Cambridge.

Patterson, C., D. M. Williams and C. J. Humphries. (1993) Congruence between molecular and morphological phylogenies. Annual Review of Ecology and Systematics 24: 153-188

Penny, D., M. Hasegawa, P. J. Waddell, and M. D. Hendy. (1999) Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition. Systematic Biology 48: 76-93

Phillips, Aloysius; Janies, Daniel; Wheeler, Ward (2000). "Multiple Sequence Alignment in Phylogenetic Analysis." Molecular Phylogenetics and Evolution, 16(3), 317-330. doi: 10.1006/mpev.2000.0785

Pisani, Davide. (2004) Identifying and removing fast-evolving sites using compatibility analysis: An example from the arthropoda. Systematic Biology 53: 978-989

Posada, D. and K. A. Crandall. (2001) Selecting the best fit model of nucleotide substitution. Systematic Biology 50: 580-601

Saitou, N. and M. Nei. (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evolution 4: 406-425

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

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 de Queiroz, K. (2000) Phylogenetic relationships among the phyrnosomatid sand lizards inferred from mitochondrial DNA sequences generated by heterogeneous evolutionary processes. Systematic Biology 49: 592-612

Xia, X. (2000) Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses. Systematic Biology 49: 87-100

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 Principles

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

evin, D. A. and H. W. Kerster. 1974. Gene flow in seed plants. Evol. Biol. 7: 139-220.

Levin, D. A. 1979. The nature of plant species. Science 204:381-384.

Lidén, M. and B. Oxelman. 1989. Species -- pattern or process? Taxon 38: 228-232.

Mattern, M. Y. and D. A. McLennan. 2000. Phylogeny and Speciation of Felids. Cladistics 16: 232-253.

Mayr, E. 1970. Populations, species, and evolution. Cambridge, Mass.: Harvard Univ. Press.

Mayr, E. 1982. The Growth of Biological Thought. Harvard University Press, Cambridge, Mass. Especially Chapter 6, on "Microtaxonomy, the science of species"

Mayr, E. 1984. Species concepts and their application. (reprinted) Pages 531-540 in Conceptual Issues in Evolutionary Biology (Sober, E., ed.). MIT press, Cambridge, Mass.

McKitrick, M. C. and R. M. Zink. 1988. Species concepts in ornithology. Condor 90:1-14.

Miller, W. 2001. The structure of species, the outcomes of speciation and the ‘species problem’: ideas for paleobiology. Palaegeography, Palaeoclimatology, Palaeoecology 176: 1-10.

Mishler, B. D. and M. J. Donoghue. 1982. Species concepts: a case for pluralism. Syst. Zool. 31:491-503.

Mishler, B. D. 1985. The morphological, developmental, and phylogenetic basis of species concepts in bryophytes. Bryol. 88:207-214.

**Mishler, B. D. and R. N. Brandon. 1987. Individuality, pluralism, and the phylogenetic species concept. Biol. Phil. 2:397-414.

Mishler, B. D. and A. F. Budd. 1990. Species and evolution in clonal organisms -- introduction. Syst. Bot. 15:79-85.

Nelson, G. J. and N. I. Platnick. 1981. Systematics and biogeography: cladistics and vicariance. New York: Columbia Univ. Press.

**Nixon, K. C. and Q. D. Wheeler. 1990. An amplification of the phylogenetic species concept. Cladistics 6:211-223.

Otte, D. and J. A. Endler (eds.). 1989. Speciation and Its Consequences. Sinauer Associates, Sunderland, Mass.

Paterson, H. E. H. 1985. The recognition concept of species. Pp. 21-29 in Species and speciation , ed. E. S. Vrba. Pretoria: Transvaal Museum.

Ridley, M. 1989. The cladistic solution to the species problem. Biol. Phil. 4:1-16.

Rosen, D. E. 1978. Vicariant patterns and historical explanation in biogeography. Syst. Zool. 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.Simpson, G. G. 1961. Principles of animal taxonomy. New York: Columbia Univ. Press.

Schander, C. and M. Thollesson. 1995. Phylogenetic taxonomy - some comments. Zoologica Scripta 24(3):263-268.

Sokal, R. R. and T. J. Crovello. 1984. The biological species concept: a critical evaluation. (reprinted) Pages 541-566 in Conceptual Issues in Evolutionary Biology (Sober, E., ed.). MIT Press, Cambridge, Mass.

Templeton, A.R. 1989. The meaning of species and speciation: a genetic perspective. Pp. 3-27 in Speciation and its consequences, ed. D. Otte and J. A. Endler. Sunderland, Mass.: Sinauer Associates.

Theriot, E. 1992. Custers, species concepts, and morphological evolution of diatoms. Syst. Biol. 41:141-157.

Van Valen, L. M. 1976. Ecological species, multispecies, and oaks. Taxon 25:233-239.

Van Valen, L. M. 1982. Integration of species: stasis and biogeography. Evol. Theory 6:99-112.

Vrba, E. S. (ed.). 1985. Species and Speciation. Transvaal Museum, Pretoria. A collected work with a number of good papers.

Wheeler, Q. D. and Meier, R. 2000. Species Concepts and Phylogenetic Theory. Columbia Unviersity Press, New York.

Wiens, J. J. and T. A. Penkrot. 2002. Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Systematic Biology 51: 69-91.

Wiley, E. O. 1978. The evolutionary species concept reconsidered. Syst. Zool. 27:17-26.

Wilson, R. A. (ed.). 1999. Species: New Interdisciplinary Essays. MIT Press, Cambridge.

Winston, J. E. 1999. Describing Species. Columbia University Press, New York.

Wu, C.-I. 2001. The genic view of the process of speciation. Journal of Evolutionary Biology 14:851-865. Also check out the many comments and Wu's reply in the same issue.

DNA Barcodes

Hebert, Paul D. N.; Gregory, T. Ryan. The promise of DNA barcoding for taxonomy. Systematic Biology 54 (5) 2005

Wheeler QD. Losing the plot: DNA "barcodes" and taxonomy. Cladistics 21 (4): 405-407 2005

Will, Kipling W.; Mishler, Brent D.; Wheeler, Quentin D.. The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biology 54 (5) OCT 2005

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. (2002) MacClade: Analysis of Phylogeny and Character Evolution (version 4). Sinauer Associates, Sunderland, MA. Chapter 3, "Overview of Phylogenetic Inference." Chapter 4, "Reconstructing Character Evolution Using Parsimony."

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

Huelsenbeck, John P.; Larget, Bret; Miller, Richard E.; Ronquist, Fredrik (2002). Potential Applications and Pitfalls of Bayesian Inference of Phylogeny. Systematic Biology, 51(5), 673-688. doi:10.1080/10635150290102366 (Scholar)

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 and 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

Background image adapted from a phylogeny of all organisms with complete genome sequences.

Last update Spring 2011
by Nicholas J. Matzke