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Reading List 2
The required readings are marked with two asterisks**. Highly recommended readings
are marked with one asterisk*; the rest are for background information and to allow
you an entrance into the literature.

Jan. 24: The Hennig Principle: synapomorphy. Intro to parsimony


Ax, P. 1987. The phylogenetic system. John Wiley, Chichester.

Dupuis, C. 1984. Willi Hennig’s impact on taxonomic thought. Ann. Rev. Ecol. Syst. 15:



*Farris J.S. 1983. The logical basis of phylogenetic analysis. In N Platnick and V Funk

(eds.): Advances in Cladistics, Volume 2. NY.:Columbia Univ. Press, pp. 7-36.


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. Ann. Rev. 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(4): 403-413.


Kluge, A. G. 2001. Parsimony with and without Scientific Justification. Cladistics 17:



Lundberg, J. G. and L. A. McDade. 1990. Systematics. Pages 65-108 in Methods for

Fish Biology, American Fisheries Society.


Mishler, B. D. and E. De Luna. 1991. The use of ontogenetic data in phylogenetic

analyses of mosses. Advances in Bryology 4:121-167. [especially pages 129-143]


Lindberg, D.R. Systematic paleontology, pp. 31-37.


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. Ann. Rev. Ecol. Syst. 23:



Wilkinson M. 1994. Three-taxon statements - when is a parsimony analysis is also a

clique analysis. Cladisitcs 10(2): 221-223

Jan. 26: Homology


Aboitiz, F. 1988. Homology, a comparative or a historical concept? Acta Biotheoretica



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. J. Evol. Biol. 5(1):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



Patterson, C. 1988. Homology in classical and molecular biology. Mol. Biol. Evol.

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. J. Evol.

Biol. 4:167-194.


Scotland, R. W. 2000. Taxic homology and thre-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. Syst. Bot.

9:395-409. [Part of symposium on homology in botany]


Wagner, G. P. 1989. The biological homology concept. Ann. Rev. Ecol. Syst. 20:51-



Wray, G. A. and C. J. Lowe. 2000. Developmental regulatory genes and echinoderm

evolution. Systematic Biology. 49: 28-51.