Source: http://ib.berkeley.edu/courses/ib200b/IB200B_Readings.shtml
Timestamp: 2019-04-25 12:56:01+00:00

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= required in 2011 course; other special recommendations starred for direct relevance to the course, basic to the field ("something everyone should have read"), etc.
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.
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.
Hull, D. L. (1974) Philosophy of Biological Sciences. Prentice-Hall, Englewood Cliffs, NJ.
* 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.
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.
Mishler, Brent D. (2009). Three centuries of paradigm changes in biological classification: Is the end in sight? Taxon, 58(1), 61-67.
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.
Stevens, P. F. (1994) The development of biological systematics. Columbia University Press, New York.
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.
Ax, P. (1987) The phylogenetic system. John Wiley, Chichester.
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.
Lundberg, J. G. and L. A. McDade. (1990) Systematics. pp 65-108 in Methods for Fish Biology, American Fisheries Society.
Hall, B. K. (ed.). (1994) Homology: the hierarchical basis of comparative biology. Academic Press, San Diego. 483 pp.
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.
** Roth, V.L. (1988) The biological basis of homology. In Ontogeny and Systematics. Humpries, C.J. (ed.) Columbia University Press, NY.
** 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.
Wagner, G. P. (ed.). (2001) The character concept in evolutionary biology. Academic Press, San Diego.
* 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.
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.
** 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.
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.
* Miyamoto, M. M. and J. Cracraft (eds.). (1991) Phylogenetic analysis of DNA sequences. Oxford University Press, New York. 358 pp.
Patterson, C. (ed.). (1987) Molecules and Morphology in Evolution: Conflict or Compromise. Cambridge Univ. Press, Cambridge.
Smith, A. B. (1989) RNA sequence data in phylogenetic reconstruction: testing the limits of its resolution.
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.
Ax, P. (1987) The phylogenetic system: The systematization of organisms on the basis of their phylogenesis. John Wiley & Sons, New York.
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.
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.
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.
Eldredge, N. and J. Cracraft. (1980) Phylogenetic patterns and the evolutionary process. New York: Columbia Univ. Press.
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.
evin, D. A. and H. W. Kerster. 1974. Gene flow in seed plants. Evol. Biol. 7: 139-220.
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.
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.
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.
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).
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.
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."
Nelson G, and Platnick, N. (1981) Systematics and Biogeography, Cladistics and Vicariance. New York: Columbia Univ. Press.
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.).
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 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).
Wiley, E. O. (1981) Phylogenetics. The Theory and Practice of Phylogenetic Systematics. (Wiley and Sons: New York).
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).
** Sneath, P.H.A. & Sokal, R.R. (1973) Numerical taxonomy; the principles and practice of numerical classification. W. H. Freeman, San Francisco.
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.
Nylander, Johan A. A.; Ronquist, Fredrik; Huelsenbeck, John P., et al. (2004) Bayesian phylogenetic analysis of combined data. Systematic Biology, 53, 47-67.
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.
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.
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.
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.
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.
Bookstein, F. L. (1991) Morphometric Tools for Landmark Data. Cambridge University Press.
Bookstein, F., B. Chernoff, R. Elder, J. Humphries, G. Smith & R. Strauss. (1985) Morphometrics in Evolutionary Biology. Spec. Pub. 15 Acad. Nat. Sci. Philadelphia.
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.
Humphries, C. J. (1988) Ontogeny and systematics. Columbia University Press, New York.
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.
Thompson, D'A. W. (1942) On growth and form (Complete Revised Edition, 1992: an unabridged and unaltered replica of the1942 edition, paperback). Dover.
Wake, D.B. (1983) Functional and Evolutionary Morphology. 25th Anniv. Issue of Perspectives in Biology and Medicine.
* Wiens, J. J. (2000) Phylogenetic Analysis of Morphological Data. Smithsonian Institution Press, Washington D.C.
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.
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.
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.
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.
Pielou, E. C. (1979) Biogeography. John Wiley and Sons; New York.
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.
Smith, A. B. (1994) Systematics and the fossil record: documenting evolutionary patterns. Blackwell Scientific Publications, Oxford.
Brooks, D.R., & D. McLennan. (1991) Phylogeny, Ecology, and Behavior. University of Chicago Press.
Cliff, A. D., and Ord, J. K. (1973) Spatial Autocorrelation. London: Pion.
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., 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.
** Forey, P.L., C. J. Humphries and P. H. Williams. (1994) Systematics and conservation evaluation, Systematics Association Special Volume No. 50 Clarendon Press, Oxford.
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.
Background image adapted from a phylogeny of all organisms with complete genome sequences.

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