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
April
24. PALEONTOLOGY AND PHYLOGENETIC
SYSTEMATICS
Benton, M. J. R. Hitchin, and M. A. Wills.
1999. Assessing congruence
between cladistic and stratigraphic
data. Systematic Biology 48: 581-595.
Bloch, J. I., D. C.
Fisher, K. D. Rose, and P. D. Gingerich.
2001. Stratocladistic
analysis of Paleocene Carpolestidae (Mammalia, Plesiadapiformes) with
description of a new Late Tiffinian genus. Journal of Vertebrate Paleontology 21:
119-131.
Bodenbender, B. E. and D. C.
Fisher. 2001. Stratocladistic analysis of blastoid
phylogeny. Journal of Paleontology 75:
351-369.
Brochu, C. A., H. N. Bryant, J. M. Theodor, M. A. O’Leary, J. M. Adrain,
C. D. Sumrall. Modern phylogenetics in paleontology: comments on Vermeij 1999. Paleobiology 27: 174-176.
Cracraft, J. and N. Eldredge
(eds.).
1979. Phylogenetic Analysis and
Paleontology.
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.
Fisher, D. C. 1991.
Phylogenetic analysis and it application in evolutionary paleobiology. Pages 103-122 in N. L. Gilinsky and P. W.
Signor (eds.) Analytical Paleobiology. Short Courses in
Paleontology 4; Paleontological Society.
Fisher, D. C. 1992. Stratigraphic parsimony.
Pages 124-129 in W. P. Maddison
and D. R. Maddison, MacClade
Version 3.0. Sinauer Associates,
Fisher, D. C. 1994. Stratocladistics: morphological and temporal patterns and
their relation to phylogenetic process.
Pages 85-132 in L. Grande and O. Rieppel
(eds.) Interpreting the Heirarchy of Nature. Academic Press,
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,
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.).
Geiger, D. L., K.
Fitzhugh, and C. E. Thacker. 2001.
Timeless characters: a response to Vermeij
(1999). Paleobiology
27: 177-178.
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.
Novacek, M. J.
2001. Character distributions are
phylogenetic evidence. Paleobiology 27: 172-173.
O’Leary, M. A. 1999.
Parsimony analysis of total evidence from extinct and extant taxa and
the cetacean-artiodactyl question (Mammalia, Ungulata). Cladistics 15:
315-330.
O’Leary, M. A. and J.
H. Geisler. 1999. The position of Cetacea
within Mammalia: phylogenetic analysis of
morphological data from extinct and extant taxa. Systematic Biology 48: 455-490.
O’Leary, M. A. and M.
D. Uhen. 1999.
The time of origin of whales and the role of behavior changes in the
terrestrial-aquatic transition. Paleobiology 25: 534-556.
O’Keefe, F. R. and P.
M. Sander. 1999.. Paleontological
paradigms and inferences of phylogenetic pattern: a case study. Paleobiology 25:
518-533.
Patterson, C. 1981.
Significance of fossils in determining evolutionary relationships. Ann. Rev. Ecol. Syst.
12: 195-223.
Rieppel, O. and R. R. Reisz. 1999.
The origin and early evolution of turtles. Annual reviews of Ecology and Systematics 30: 1-22.
Siddall, M. E.
1998. Stratigraphic
Fit to Phylogenies: A Proposed Solution.
Cladistics 14: 201-20
Smith, A. B. Systematics and the fossil record.
Blackwell Scientific Publications,
Smith, A. B. 2000. Stratigraphy in phylogeny reconstruction. Journal of Paleontology 74: 763-766.
Smith, A. B. and D. T.
J. Littlewood. 1994. Paleontological
data and molecular phylogenetic analysis.
Paleobiol. 20: 259-273.
Vermeij, G. J.
1999. A serious matter with
character-taxon matrices. Paleobiology 25: 431-433.
Vermeij, G. J.
2001. Time and the comparative
method. Paleobiology
27: 179-180.
Vermeij, J. G. and S. J.
Carlson. 2000.
The muricid gastropod subfamily Rapaninae: phylogeny and ecological history. Paleobiology 26:
19-46.
Wanger, P. J.
1995. Stratigraphic
tests of cladistic hypotheses. Paleobiology 21:
153-178.
Wagner, P. J. 1998.
Phylogenetic analyses and the quality of the fossil record. Pages 165-188 in S. K.
Donovan and C. R. C. Paul (eds.) The Adequacy of the Fossil Record. John Wiley and Sons,
Wagner, P. J. 1999. The utility of fossil data in phylogenetic
analyses: a likelihood example using Ordovician-Silurian species of the Lophospiridae (Gastropoda: Murchinsoniina).
American Malacological Bulletin 15: 1-31.
Wagner, P. J. 2000.
Likelihood tests of hypothesized durations: determining and
accommodating biasing factors. Paleobiology 26: 431-449.
Wagner, P. J. 2000.
Phylogenetic analysis and the fossil record: tests and inferences,
hypotheses and models. Paleobiology 26 (supplement to 4) 341-371.
Wagner, P. J. 2000.
The quality of the fossil record and the accuracy of phylogenetic
inferences about sampling and diversity.
Systematic Biology 49: 65-86.
Wagner, P. J. and C. A.
Sidor. 2000.
Age rank/clade rank metrics – sampling, taxonomy, and the meaning of “stratigraphic consistency.”
Systematic Biology 49: 463-479.
Wills, M. A. 1999.
Congruence between phylogeny and stratigraphy:
randomization tests and the Gap Excess Ratio.
Systematic Biology 48: 559-580.