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Integrative Biology 200B Spring 2007

"PRINCIPLES OF PHYLOGENETICS: ECOLOGY AND EVOLUTION"

Most important recommended readings are in bold face; required readings also have two asterisks

May 1: MACROEVOLUTION: PATTERNS OF DIVERSIFICATION AND EXTINCTION

Alroy, J. 2000. Understanding the dynamics of trends within evolving lineages. Paleobiology 26: 319-329.

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.

Elbe, G. J. 2000. Contrasting evolutionary flexibility in sister groups: disparity and diversity in Mesozoic atelostomate echinoids. Paleobiology 26: 56-79.

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.

Jablonski, D. 2000. Micro- and macroevolution: scale and heirarchy in evolutionary biology and paleobiology. Paleobiology 26 (supplement to 4): 15-52.

Jeffery, C. H. 2001. Heart urchins at the Cretaceous/Tertiary boundary: a tale of two clades. Paleobiology 27: 104-125.

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.

McShea, D. W. 2000. Trends, tools, and terminology. Paleobiology 26: 330-333.

** 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.

Norris, R. D. 2000. Pelagic species diversity, biogeography, and evolution. Paleobiology 26 (supplement to 4): 236-258.

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.

Robeck, H. E., C. C. Maley, and M. J. Donoghue. 2000. Taxonomy and temporal diversity patterns. Paleobiology 26: 171-187.

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

Roopnarine, P. D., G. Byars, and P. Fitzgerald. 1999. Anagenetic evolution, stratophenetic patterns and random walk models. Paleobiology 25: 41-57.

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

Shubin, N. H. and C. R. Marshall. 2000. Fossils, genes, and the origin of novelty. Paleobiology 26 (supplement to 4): 324-340.

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.

Smith, L. H. and B. S. Lieberman. 1999. Disparity and constraint in the olenelloid trilobites and the Cambrian rasiation. Paleobiology 25: 459-470.

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.

Wagner, P. J. 1996. Contrasting the underlying patterns of active trends in morphological evolution. Evolution 50: 990-1007.

Wagner, P. J. 2000. Exhaustion of morphologic character states among fossil taxa. Evolution 54: 365-386.

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.]