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Reading List 6
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.

February 28: Classification I - basic principles (monophyly & information content)


Avise, J.C. and G.C. Johns. 1999. Proposal for a standardized temporal scheme of biological classification for extant species. P NATL ACAD SCI USA 96: (13) 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. Syst. Zool. 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? P NATL ACAD SCI USA 95: (17) 9720-9723.


Nelson, G. 1973. Classification as an expression of phylogenetic relationships. Syst. Zool. 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.

March 2: Classification: 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

Species concepts, species boundaries and species identification: A view from the tropics

Systematic Biology 54 (4) : 689-693 AUG 2005


Bremer, K. and H. E. Wanntorp. 1979. Geographic populations or biological species in phylogeny reconstruction? Syst. Zool. 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. 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. Syst. Bot. 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). Syst. Zool. 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(3): 259-294


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


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


Gould, S. J. 1980. A Quahog is a Quahog. Pages 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(2):237-250.


Häuser, C. L. 1987. The debate about the biological species concept -- a review. Z. Zool. Syst. Evolut.-forsch. 25:241-257.


Holman, E. W. 1987. Recognizability of sexual and asexual species of rotifers. Syst. Zool. 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.


Levin, 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.)

March 7: DNA  Barcodes


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


EA Herre. Barcoding helps biodiversity fly. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 (11): 3949-3950 March 14 2006


Alex Smith, Norman E. Woodley, Daniel H. Janzen, Winnie Hallwachs, and Paul D. N. Hebert. DNA barcodes reveal cryptic host-specificity within the presumed polyphagous members of a genus of parasitoid flies (Diptera: Tachinidae). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 103 (10): 3567-3662 March 7 2006


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

March 14: Classification V - Phylogenetic taxonomy


Cantino, P. D., H. N. Bryant, K. De Quieiroz, M. J. Donoghue, T. Eriksson, D. M. Hillis, and M. S. Y. Lee. Species names in phylogenetic nomenclature. Systematic Biology 48: 790-807.


Queiroz, K. D. 1994. Replacement of an essentialistic perspective on taxonomic definitions as exemplified by the definition of "Mammalia". Systematic Biology 43: 497-510.


**de Queiroz, K. and J. Gauthier. 1992. Phylogenetic taxonomy. Ann. Rev. Ecol. Syst. 23:449-480.


de Queiroz, K. and J. Gauthier. 1994. Toward a phylogenetic system of nomenclature. Trends Ecol. Evol. 9: 27-31.


Gauthier, J. and K. de Queiroz. 2001. Feathered dinosaurs, flying dinosaurs, crown dinosaurs and the name "Aves." pp. 7-42 in J. Gauthier and L. F. Gall (eds.), New Perspectives on the Origin and Early Evolution of Birds. Peabody Museum of Natural History, New Haven.


Lee, M. S. Y. and P. S. Spencer. 1997. Crown-clades, key characters, and taxonomic stability: when is an amniote not an amniote? pp. 61-84 in S. S. Sumida and K. L. M. Martin (eds.) Amniote Origins: Completing the Transition to Land. Academic Press, New York.


Lee, M.S.Y. 1998. Phylogenetic uncertainty, molecular sequences, and the definition of taxon names. SYST BIOL 47: (4) 719-726.


Lee, M.S.Y. 1999. Reference taxa and phylogenetic nomenclature. TAXON 48: (1) 31-34.


Moore, G. 1998. A comparison of traditional and phylogenetic nomenclature. TAXON 47: (3) 561-579.


Nixon, K. C., and J. M. Carpenter. 2000. On the Other "Phylogenetic Systematics." Cladistics 16: 298-318.


Pickett KM. The new and improved PhyloCode, now with types, ranks, and even polyphyly: a conference report from the First International Phylogenetic Nomenclature Meeting . CLADISTICS 21 (1): 79-82 FEB 2005


Pleijel, F. 1999. Phylogenetic taxonomy, a farewell to species, and a revision of Heteropodarke. Systematic Biology 48: 755-789.


Sereno, P.C. 1999. Definitions in phylogenetic taxonomy: Critique and rationale. SYST BIOL 48: (2) 329-351.


Sereno, Paul C. The logical basis of phylogenetic taxonomy. Systematic Biology 54 (4) : 595-619 AUG 2005


Scotland, R. W. and M. A. Carine. 2000. Classification or Phylogenetic Estimates? Cladistics 16: 411-419.

Wheeler QD. Taxonomic triage and the poverty of phylogeny. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY OF LONDON SERIES B-BIOLOGICAL SCIENCES 359 (1444): 571-583 APR 29 2004