"PRINCIPLES OF PHYLOGENETICS:  ECOLOGY AND EVOLUTION"

Reading List # 6
Those references preceded by ** are required. Those preceded by * are highly suggested.  The others are suggested too, but we realize you can only read so much.

April 20.   Morphometric comparisons

Arnold, E. N.  1990.  Why do morphological phylogenies vary in quality? An investigation based on comparative history of lizard clades. Proc. R. Soc. Lond., Ser. B 240:135-172.

Bookstein, F. L. 1982.  Foundations of morphometrics.  Ann. Rev. Ecol. Syst. 13:451-470.

Bookstein, F. L. 1991.  Morphometric Tools for Landmark Data. Geometry and Biology.  Cambridge Univ. 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.

Clark, R.B.  1977.  Phylogenetic reconstruction.  Vehr. deutsch. zool. Ges. 1977, 175-181.

Davis, J. I.  1983.  Phenotypic plasticity and the selection of taxonomic characters in Puccinellia (Poaceae). Syst. Bot. 8:341-353.

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).  Syst. Biol. 44(3):343-360.

Fisher, D.C.  1985.  Evolutionary morphology: beyond the analogous, the anecdotal, and the ad hoc.  Paleobiology 11:120-138.

Hickman, C.S.  1980.  Gastropod radulae and the assessment of form in evolutionary paleontology.  Paleobiology 6, 276-294.

Humphries, C. J. (ed.).  1988.  Ontogeny and systematics. Columbia University Press, New York.
 
Klingenberg, C. P., and Ekau, W. (1996). "A combined morphometric and phylogenetic analysis of an ecomorphological trend: Pelagization in Antarctic fishes (Perciformes: Nototheniidae)." Biological Journal of the Linnean Society, 59(2), 143-177.

Kluge, A. G. and R. E. Strauss.  1985.  Ontogeny and systematics. Ann. Rev. Ecol. Syst. 16:247-268.

Kluge, A. J.  1989.  A concern for evidence and a phylogenetic hypothesis of relationships among Epicrates (Boidae, Serpentes). Syst. Zool. 38:7-25.

Lauder, G. V.  1990.  Functional morphology and systematics: studying functional patterns in an historical context. Ann. Rev. Ecol. Syst. 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.

McDade, L.  1990.  Hybrids and phylogenetic systematics. I. Pattrerns of character expression in hybrids and their implications for cladistic analysis. Evol. 44:1685-1700.

Nijhout, H. F.  1990.  Metaphors and the role of genes in development. BioEssays 12:441-446.

Raup, D.M.  1972.  Approaches to morphologic analysis.  In Schopf, T.J.M. (ed.), Models in Paleobiology, 28044.  Freeman, Cooper, San Francisco.

** Rohlf, F. J.  1990.  Morphometrics. Ann. Rev. Ecol. Syst.  21:299-316.

Strauss, R. E. and F. L. Bookstein.  1982.  The truss: Body form reconstructions in morphometrics. Syst. Zool. 31:113-135.

Sultan, S. E.  1987.  Evolutionary implications of phenotypic plasticity in plants. Evol. Biol. 21:127-178.

Thompson, D'A. W.  1942.  On growth and form (Complete Revised Edition, 1992-ab unabridged and unaltered replica of the 1942 edition, paperback).  Dover.  1116 pp.

Wake, D.B.  1983.  Functional and Evolutionary Morphology.  25th Anniv. Issue of Perspectives in Biology and Medicine.

Wiley, E. O.  1981.  Phylogenetics: the theory and practice of phylogenetic systematics. John Wiley and Sons, New York.

**Zelditch, M.L., W.L. Fink, and D.L. Swiderski.  1995.  Morphometrics, homology, and phylogenetics: quantified characters as synapomorphies.  Systematic Biology 44(2):179-189.

Zelditch, M. L. and W. L. Fink.  1996.  Heterochrony and heterotopy: stability and innovation in the evolution of form.  Paleobiol. 22: 241-254.

April 22.  Paleontology and phylogenetic systematics

Cracraft, J.  1981.  Pattern and process in paleobiology:  The role of cladistic analysis in systematic paleontology.  Paleobiology 7:456-468.

** 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.

Doyle, J. A. and M. J. Donoghue.  1987.  The importance of fossils in elucidating seed plant phylogeny and macroevolution.  Rev. Paleobot. Palyn. 50: 63-95.

Fortey, R. A. and R. P. S. Jefferies.  1982.  Fossils and phylogeny--A compromise approach. Pages 197-234 in Problems of Phylogenetic Reconstruction (Joysey, K. A. and A. E. Friday, ed.).  Academic Press, London.

Gauthier, J., A. Kluge and T. Rowe.  1988.  Amniote phylogeny and the importance of fossils.  Cladistics 4: 105-209.

Gingerich, P. D.  1979.  The stratophenetic approach to phylogeny reconstruction in vertebrate paleontology. Pages 41-77 in Phylogenetic Analysis and Paleontology (Cracraft, J. and N. Eldredge, ed.).  Columbia Univ. Press, New York.

Harvey, P. H., R. M. May and S. Nee.  1994.  Phylogenies without fossils.  Evol. 48: 523-529.

** Huelsenbeck, J. P.  1994.  Comparing the stratigraphic record to estimates of phylogeny.  Paleobiol. 20: 470-483.

Patterson, C.  1981.  Significance of fossils in determining evolutionary relationships.  Ann. Rev. Ecol. Syst. 12: 195-223.

Smith, A. B. and D. T. J. Littlewood.  1994.  Paleontological data and molecular phylogenetic analysis.  Paleobiol. 20: 259-273.
 

April 29.  Macroevolution: patterns of diversification and extinction

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. Evol. 36:474-498.

Gilinsky, N.L. and I.J. Good.  1991.  Probabilities of origination, persistence, and extinction of families of marine invertebrate life.  Paleobiology 17(2):145-66

Gould, S. J. and N. Eldredge.  1977.  Punctuated equilibria: the tempo and mode of evolution reconsidered. Paleobiol. 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(4):  411-23.

Hey, J.  1992.  Using phylogenetic trees to study speciation and extinction.  Evol. 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.

Kubo, T. and I. Y.  1995.  Inferring the rates of branching and extinction from molecular phylogenies.  Evol. 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. Syst. Zool. 29:130-142.

** 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.

Patterson, C. and A.B. Smith  1987.  Is the periodicity of extinctions a taxonomic artefact?  [and reply by Sepkoski] Nature 330:248-252.

Raup, D.M. and J.J. Sepkoski  1986.  Periodic extinction of families and genera.  Science.  231:833-836.

Rohde, K.  1996.  Robust phylogenies and adaptive radiations: a critical evaluation of methods used to identify key innovations.  Am. Nat. 148: 481-500.

Schopf, T. M. J.  1981.  Punctuated equilibria and evolutionary stasis. Paleobiol. 7:156-166.

Smith, A.B. & C. Patterson.  1988.  The influence of taxonomic method on the perception of patterns of evolution, Evol. Biol. 23:127-216.

Smith, A. B.  1994.  Systematics and the fossil record: documenting evolutionary patterns.  Blackwell Scientific Publications, Oxford.
 
Stanley, S. M.  1982.  Macroevolution and the fossil record. Evol. 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(2): 153-178.

Wagner, P.J.  1995.  Diversity patterns among early gastropds: contrasting taxonomic and phylogenetic descriptions.  Paloebiology 21(4):410-439.

Williamson, P. G.  1981.  Paleontological documentation of speciation in Cenozoic mollusks from Turkana Basin. Nature 293: 437-443.   [see Biol. Journal Linn. Soc., Volume 26, Number 4, for several papers commenting on Williamson's work.]