Recommended readings
Baum, D. A. and A. Larson. 1991. Adaptation reviewed: A phylogenetic methodology for studying
character macroevolution. Systematic Zoology 40:1-18.
Baum, D. A. and M. J. Donoghue. 1995. Choosing between alternative phylogenetic species
concepts. Systematic Botany 20:560-573.
Baum, D. A. and M. J. Donoghue. 2002. Transference of Function, heterotopy, and the evolution
of plant development. Pages 52-69 In Q. C. B. Cronk, R. M. Bateman, and J. A. Hawkins,
(eds.) Developmental Genetics and Plant Evolution, Taylor and Francis, London.
Davis, J. I., and K. C. Nixon. 1992. Populations, genetic variation, and the delimitation of
phylogenetic species. Systematic Biology 41:421-435.
de Queiroz, K. 2005. Different species problems and their resolution. Bioessays 27:1263-1269.
Ereshefksy, M. 1992. Eliminative pluralism. Philosophy of Science 59: 671-690.
Faith, D. P. 2002. Quantifying diversity: A phylogenetic perspective. Conservation Biology
16(1):248-252.
Felsenstein J. 1985. Phylogenies and the comparative method. American Naturalist 125(1): 1-15.
Ghiselin, M. 1974. Radical solution to the species problem. Systematic Zoology 23: 536-544
Gould, S. J. and E. S. Vrba. 1982. Exaptation: a missing term in the science of form. Paleobiology
8:4-15.
Grantham, T. A. 1995. Hierarchical approaches to macroevolution: Recent work on species
selection and the "effect hypothesis." Annu. Rev. Ecol. Syst. 26:301-321.
Greene, H. W. 1986. Diet and Arboreality in the emerald monitor, Varanus prasinus, with
comments on the study of adaptation. Fieldiana Zool. N. Ser. 31:1-12.
Hall. B. K. (2003) Descent with modification: the unity underlying homology and homoplasy as
seen through an analysis of development and evolution. Biological Reviews 78(3): 409-433.
Hennig, W. (1976) Phylogenetic Systematics. Univ. Illinois Press, Champaign-Urbana. (Chap. 1)
Kluge, A. G. (2005) Zoologica Scripta 34(6): 653-663.
Mallet J. (2008) Hybridization, ecological races and the nature of species: empirical evidence for
the ease of speciation. Philosophical Transactions Of The Royal Society B-Biological
Sciences 363(1506): 2971-2986.
Mindell DP, Meyer A. 2001. Homology evolving. Trends in Ecology & Evolution 16(8):434-440.
Nixon, K. C., and Q. D. Wheeler. 1990. An amplification of the phylogenetic species concept.
Cladistics-the International Journal of the Willi Hennig Society 6:211-223.
O’Hara, Robert J. 1997. Population thinking and tree thinking in systematics. Zoologica Scripta,
26(4): 323–32
Orzack S. H., Sober E. 1994. Optimality models and the test of adaptationism. American
Naturalist 143(3):361-380.
Patterson, C. 1982. Morphological characters and homology. Pp. 21-74 in K. A. Joysey and A. E.
Friday (eds.) Problems of Phylogenetic Reconstruction. Academic Press, New York.
Pigliucci, M. 2003. Species as family resemblance concepts: the (dis-)solution of the species
problem? Bioessays 25:596-602.
Pigliucci M. 2008. Is evolvability evolvable? Nature Reviews Genetics 9(1):75-82.
Ree, R. H. Detecting the historical signature of key innovations using stochastic models of
character evolution and cladogenesis. Evolution 59(2): 257-265
Slowinski J. B, and Guyer C. 1993. Testing whether certain traits have caused amplified
diversification - an improved method based on a model of random speciation and extinction.
American Naturalist. 142(6):1019-1024.
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.
Vrba, E. S. and S. J. Gould. 1986. The hierarchical expansion of sorting and selection: sorting and
selection cannot be equated. Paleobiology 12:217-228.
Wagner, G. P. 1989. The origin of morphological characters and the biological basis of homology.
Evolution 43:1157-1171.
Wagner, G. P. and Altenberg L. 1996. Complex adaptations and the evolution of evolvability.
Evolution 50(3): 967-976
West-Eberhard, M. J. 1986. Alternative adaptations, speciation and phylogeny (a review). Proc.
Natl. Acad. Sci. USA 83:1388-1392.
Westoby M., Leishman M. R., Lord J.M. 1995. On misinterpreting the phylogenetic correction.
Journal Of Ecology 83(3): 531-534
Accessory readings
Alberch, P. 1989. The logic of monsters: evidence for internal constraint in development and
evolution. Geobios mémoire spécial no 12:21-57.
Baum, D. A. 1998. Individuality and the existence of species through time. Systematic Biology
47:641-653.
Baum, D. A. and K. L. Shaw. 1995. Genealogical perspectives on the species problem.
Monographs in Systematic Botany from the Missouri Botanical Garden 53:289-303.
Baum, D. A. and M. J. Donoghue. 2001. A likelihood framework for the study of adaptation.
Pages 24-44 In: S. Orzack and E. Sober (eds.), Adaptationism and Optimality, Cambridge
University Press, New York.
Bolker, J. A. and R. A. Raff. 1996. Developmental genetics and traditional homology. BioEssays
18:489-494.
de Queiroz, K. 1985. The ontogenetic method for determining character polarity and its relevance
to phylogenetic systematics. Systematic Zoology 34:280-299.
de Queiroz, K. 1999. The general lineage concept of species and the defining properties of the
species category. Pp. 49-89 in R. A. Wilson (eds.) Species: New Interdisciplinary Essays.
MIT Press, Cambridge, MA.
de Quieroz, K. 1997a. The Linnaean hierarchy and the evolutionization of taxonomy, with
emphasis on the problem of nomenclature. Aliso 15:125-144
de Queiroz, K. 1998. The general lineage concept of species, species criteria, and the process of
speciation: A conceptual unification and terminological recommendations. Pages 57-75 in
Endless Forms: Species and speciation (D. J. Howard, and S. H. Berlocher, eds.). Oxford
University Press, New York.
de Queiroz, K. 2007. Species concepts and species delimitation. Systematic Biology 56:879-886.
de Quieroz, K. and J. Gauthier 1992. 1992. Phylogenetic taxonomy. Annu. Rev. Ecol. Syst.
23:449-480
Galis, F. 2001. Key innovations and radiations. Pp. 581-605 in G. P. Wagner (ed.) The Character
Concept in Evolutionary Biology. Academic Press, San Diego.
Gould, S. J. 2001. The interrelationship of speciation and punctuated equilibrium. Pp. 196-217 in J.
B. C. Jackson, S. Lidgard and F. K. McKinney (eds.) Evolutionary Patterns: Growth, Form
and Tempo in the Fossil Record. University of Chicago Press, Chicago.
Gould, S. J. and R. C. Lewontin. 1979. Spandrels of San-Marco and the panglossian paradigm - a
critique of the adaptationist program. Proceedings of the Royal Society of London Series BBiological Sciences 205: 581-598.
Haszprunar, G. 1992. The types of homology and their significance for evolutionary biology and
phylogenetics. Journal of Evolutionary Biology 5:13-24.
Mayr, E. 1982. The Growth of Biological Thought. Harvard Univ. Press, Cambridge. (Pp. 614-616;
233-235)
Mayr, E. 1987. The ontological status of species: scientific progress and philosophical
terminology. Biology and Philosophy 2:145-166.
Miller, A. H. 1949. Some ecologic and morphologic considerations in the evolution of higher
taxonomic categories. Pp. 84-88 in E. Mayr and E. Schuz (eds.) Ornithologie als Biologische
Wissenschaft. Carl Winter/Universitätsverlag, Heidelberg.
Mishler BD, Donoghue MJ. 1982. Species concepts - A case for pluralism. Systematic Zoology
31: 491-503
Müller, G. B. and G. P. Wagner. 1991. Novelty in evolution: restructuring the concept. Annu. Rev.
Ecol. Syst. 22:229-256.
Newman, S. A. and G. B. Müller. 2000. Epigenetic mechanisms of character origination. Journal
of Experimental Zoology 288:304-317.
O’Hara, Robert J. 1988. Homage to Clio, or, toward an historical philosophy for evolutionary
biology. Systematic Zoology, 37(2): 142–155
Paterson, H. E. H. 1981. The continuing search for the unknown and unknowable: a critique of
contemporary ideas on speciation. South African Journal of Science 77:113-119.
Van Valen, L. 1973. A new evolutionary law. Evolutionary Theory 1:1-30.
Van Valen, L. 1976. Ecological species, multispecies, and oaks. Taxon 25: 233-239.
Wagner, G. P. 1988. The significance of developmental constraints for phenotypic evolution by
natural selection. Pp. 222-229 in G. de Jong (ed.) Population Genetics and Evolution,
Springer-Verlag, Berlin.
Wagner, G. P. and B. Y. Misof. 1993. How can a character be developmentally constrained despite
variation in developmental pathways? J. Evol. Biol. 6:449-455.
Wiley, E. O. 1981. Phylogenetics. Wiley & sons, New York. (Pp. 24-34)