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
17. COEVOLUTION:
Barrett, P.M. and K.J. Willis. 2001. Did dinosaurs invent flowers?
Dinosaur-angiosper coevolution
revisited. Biological Reviews. 76(3):411-447.
Brandon, R. N. 1990. Adaptation
and Environment.
Brooks, D. R. 1981. Hennig’s
parasitoligical method: A proposed solution. Syst. Zool. 30: 229-249.
Brooks, D. R. 1990. Parsimony analyisis in historical biogeography and coevolution: Methodological and theoretical update. Syst. Zool. 39: 14-30.
Brooks, D.R., & D. McLennan.
1991. Phylogeny, Ecology, and Behavior.
Coddington, J. 1988. Cladistic
tests of adaptational hypotheses. Cladistics
4:3-22.
de Queiroz, K.
1996. Including the characters of interest during tree
reconstruction and the problems of circularity and bias in studies of character
evolution. Am. Nat. 148: 700-708.
Dobson, F.S. 1985. The
use of phylogeny in behavior and ecology. Evolution 39:1384-1388.
Donoghue, M.J. 1989. Phylogenies
and analysis of evolutionary sequences, with examples from seed plants.
Evolution 43:1137-1156.
Eggleton, P. and R. I. Vane-Wright (ed.). 1994. Phylogenetics and
Ecology. Academic Press,
Friday, A. 1987. Models
of evolutionary change and the estimation of evolutionary trees. OxfordSurveys Evol. Biol.
4:61-88.
Frumhoff, P. C. and H. K.
Reeve. 1994. Using
phylogenies to test hypotheses of adaptation: a critique of some current
approaches. Evol. 48: 172-180.
Funk, V.A. and
Grafen, A. 1989. The phylogenetic regression.
Phil. Trans. Royal Soc.
Hafner, M. S., and R. D. M. Page.
1995. Molecular Phylogenies and Host-Parasite Cospeciation
- Gophers and Lice as a Model System. Philosophical
Transactions of the Royal Society of
Hafner, M. S., and S. A. Nadler.
1988. Phylogenetic Trees Support the Coevolution of
Parasites and Their Hosts. Nature 332:258-259.
Hansen, T. F. and E. P.
Martins. 1996.
Translating between micorevolutionary process and macroevolutionary patterns: the correlation structure of interspecific data. Evol. 50: 1404-1417.
Huelsenbeck, J P; Rannala, B; Yang, Z. 1997. Statistical tests of host-parasite cospeciation. Evolution, v.51, n.2, (1997): 410-419.
Huelsenbeck, J. P., B. Rannala, and B. Larget. 2000. A Bayesian framework
for the analysis of cospeciation. Evolution
54:352-364.
Huey, R.B. and A.F.
Bennett. 1987. Phylogenetic
studies of co-adaptation: preferred temperature versus optimal performance
temperatures of lizards. Evolution 41: 1098-115.
Huey, R.B. 1987. Phylogeny, history,
and the comparative method. Pp. 76-101 in Feder,
M.E., A.F. Bennett, W.W. Burggren, R.B. Huey (eds). New
Directions in Ecological Physiology.
Losos, J. B. 1996. Phylogenies and comparative
biology, Stage II: Testing causal hypotheses derived from phylogenies with data
from extant taxa. Syst. Biol. 45: 259-260. [Maddison, W.P. 1990. A method for testing the correlated
evolution of two binary characters: are gains and losses concentrated on
certain branches of a phylogenetic tree? Evolution 44: 539-557.
Martins, E. P. 1996. Phylogenies, spatial autoregression,
and the comparative method: a computer simulation test. Evol. 50: 1750-1765.
Martins, E.P. and T.
Garland, Jr. 1991.
Phylogenetic analyses of the correlated evolution of continuous characters: a
simulation study. Evolution 45: 534-557.
Miles, D. B. and A. E.
Dunham. 1993.
Historical perspectives in ecology and evolutionary biology: the use of
phylogenetic comparative analyses. Ann. Rev. Ecol. Syst.
24: 587-619.
Mishler, B.D. 1988. Reproductive
ecology of bryophytes. Pp. 285-306 in J. Lovett Doust and L. Lovett Doust (eds.),
Plant Reproductive Ecology.
Mitter, C., B. Farrell, and
B. Wiegmann. 1988. The phylogenetic study of adaptive zones: Has phytophagy promoted insect diversification? Amer. Nat.
132:107-128.
Page, R. D. M., and M. A. Charleston.
1998. Trees within trees: phylogeny and historical associations. Trends in
Ecology & Evolution 13:356-359.
Page, R. D. M. 1996. Temporal congruence
revisited: Comparison of mitochondrial DNA sequence divergence in cospeciating pocket gophers and their chewing lice. Systematic Biology 45:151- 167.
Page, R., editor. 2003. Tangled trees:
phylogeny, cospeciation, and coevolution.
Percy, D. M., R. D. M. Page, and Q. C. B. Cronk. 2004. Plant-insect interactions:
Double-dating associated insect and plant lineages reveals asynchronous
radiations. Systematic Biology 53:120-127.
Ridley, M. 1983. The explanation of
organic diversity: the comparative method and adaptations formating.
Siddall, M. E. 1996. Phylogenetic covariance
probability: confidence and historical associations. Syst.
Biol. 45: 48-66.
Sillin-Tullberg, B. 1988. Evolution of gregariousness in aposematic butterfly larvae: a phylogenetic analysis.
Evolution 42: 293-305.
Wanntorp, H. 1983. Historical constraints in
adaptation theory: traits and non-traits. Oikos
41:157-159.
Wanntorp, H. et al. 1990. Phylogenetic approaches
in ecology. Oikos 57: 119-132.
Weiblen, G. D., and G. L. Bush.
2002. Speciation in fig pollinators and parasites. Molecular Ecology
11:1573-1578.
Werdelin, L. and B. S. Tullberg.
1995. A comparison of two methods to study correlated discrete characters on
phylogenetic trees. Cladistics 11: 265-277.
Westneat, M.W. 1995. Feeding, function, and phylogeny:
an analysis of historical biomechanics in labrid
fishes using comparative methods. Syst. Biol. 44:3:
361-383.