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
March 13:
ADAPTIVE RADIATIONS
Ackerly,
Baldwin, B. G., and Sanderson, M. J. (1998).
“Age and rate of diversification of the Hawaiian silversword alliance (Compositae).”
Proceedings of the
Barrett, S. C. H., and
Graham, S. W. (1997).
“Adaptive radiation in the aquatic plant family Pontederiaceae:
Insights from phylogenetic analysis.” Molecular evolution and adaptive
radiation; Symposium, Montreal, Quebec, Canada, July 7-8, 1995, T. J. Givnish and K. J. Sytsma, eds.,
Cambridge University Press, Cambridge, England, UK; New York, New York, USA,
225-258.
Becerra,
J. X. 2005. Timing the origin and expansion of the Mexican
tropical dry forest. Proceedings of the
Berenbaum, M. R., Favret, C., and Schuler, M. A. (1996). “On defining "Key
innovations" in an adaptive radiation: Cytochrome
P450S and Papilionidae.” American
Naturalist, 148(SUPPL), S139-S155.
Bond, J. E., and Opell, B. D. (1998). “Testing adaptive radiation and key
innovation hypotheses in spiders.” Evolution, 52(2), 403-414.
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.
Bruce, R. C. (1996). “Life-history
perspective of adaptive radiation in desmognathine
salamanders.” Copeia, 1996(4), 783-790.
Cameron, R. A. D., Cook, L. M., and
Hallows, J. D. (1996). “Land snails on Porto Santo: Adaptive
and non-adaptive radiation.” Philosophical Transactions of the Royal
Society of
Craddock, E. M., and Kambysellis, M. P. (1997). “Adaptive radiation in the Hawaiian
Drosophila (Diptera: Drosophilidae):
Ecological and reproductive character analyses.” Pacific Science, 51(4),
475-489.
Desutter-Grandcolas, L. (1997). “Studies in cave life
evolution: A rationale for future theoretical developments using phylogenetic
inference.” Journal of Zoological Systematics and
Evolutionary Research, 35(1), 23-32.
Farrell, B. D. (1998). “"Inordinate
fondness": Explained: Why are there so many beetles?” Science (
Foote, M. (1993). “Discordance and Concordance Between Morphological and Taxonomic Diversity.” Paleobiology, 19(2), 185-204.
Francisco-Ortega, J.,
Jansen, R. K., and Santos-Guerra, A. (1996). “Chloroplast DNA evidence of
colonization, adaptive radiation, and hybridization in the evolution of the macaronesian flora.” Proceedings of the
Givnish, T. J. (1997). “Adaptive radiation and
molecular systematics: Issuses
and approaches.” Molecular evolution and adaptive radiation; Symposium,
Montreal, Quebec, Canada, July 7-8, 1995, T. J. Givnish
and K. J. Sytsma, eds., Cambridge University Press,
Cambridge, England, UK; New York, New York, USA, 1-54.
Givnish, T. J., Sytsma,
K. J., Smith, J. F., Hahn, W. J., Benzing, D. H., and
Burkhardt, E. M. (1997). “Molecular evolution and
adaptive radiation in Brocchinia (Bromeliaceae:
Pitcairnioideae) atop tepuis
of the Guayana Shield.” Molecular evolution and
adaptive radiation; Symposium, Montreal, Quebec, Canada, July 7-8, 1995, T. J. Givnish and K. J. Sytsma, eds.,
Cambridge University Press, Cambridge, England, UK; New York, New York, USA,
259-311.
Glor, R. E., J. J. Kolbe, R. Powell, A.
Larson, and J. B. Losos. 2003. Phylogenetic analysis
of ecological and morphological diversification in Hispaniolan
trunk-ground anoles (anolis cybotes
group). Evolution 57:2383-2397.
Grant, P. R. (1998). “Radiations,
communities, and biogeography.” Evolution on islands, P. R. Grant, ed.,
Oxford University Press, New York, New York, USA; Oxford, England, UK, 196-209.
Guyer, C. and J. B. Slowinski. 1993.
Adaptive radiation and the topology of large phylogenies. Evol. 47: 253-263.
Harry, M., Solignac, M., and Lachaise, D.
(1996). “Adaptive radiation in the Afrotropical
region of the Paleotropical genus Lissocephala
(Drosophilidae) on the pantropical
genus Ficus (Moraceae).”
Journal of Biogeography, 23(4), 543-552.
Harvey, P. H., and A. Rambaut.
2000. Comparative analyses for adaptive radiations. PhilTransRoySocLondSerB
355:1599-1605.
Hill, R. S., and Dettmann, M. E. (1996). “Origin and
diversification of the genus Nothofagus.” The
ecology and biogeography of Nothofagus forests, T. T.
R. S. H. Veblen and J. Read, eds., Yale University
Press, New Haven, Connecticut, USA; London, England, UK, 11-24.
Hodges,
S. 1995. Spurring plant diversification: Are floral nectar spurs a key
innovation? Proc. Roy. Soc. London Ser. B 262:343-348.
Hodges,
S. 1997. Floral nectar spurs and diversification. Int. J. Plant Sci. 158:S81-S88.
Johnson, S. D., Linder,
H. P., and Steiner, K. E. (1998).
“Phylogeny and radiation of pollination systems in Disa (Orchidaceae).”
American Journal of Botany, 85(3), 402-411.
Landmann, A., and Winding, N.
(1995). “Adaptive radiation and resource partitioning in Himalayan
high-altitude finches.” Zoology (
Losos, J.
1992. The evolution of convergent structure in
Losos,
J. B., and D. B. Miles. 2002. Testing the hypothesis that a clade has adaptively
radiated: iguanid lizard clades as a case study. Amer. Nat. 160:147-157.
Losos,
J. B., M. Leal, R. E. Glor, K. de Queiroz,
P. E. Hertz, L. R. Schettino, A. C. Lara, T. R. Jackman, and A. Larson. 2003.
Niche lability in the evolution of a
Losos, J. B., Warheit, K. I., and Schoener, T.
W. (1997). “Adaptive differentiation following experimental island
colonization in Anolis lizards.” Nature (
Macleod, N. (1993). “The
Maastrichtian-Danian Radiation of Triserial
and Biserial Planktic
Foraminifera Testing Phylogenetic and Adaptational
Hypotheses in the Microfossil Record.” Marine Micropaleontology,
21(1-3), 47-100.
Marks, C. O., and M. J. Lechowicz.
2006. Alternative designs and the evolution of functional diversity. American
Naturalist 167:55-66.
Martin, A. P., and Bermingham, E. (1998). “Systematics and evolution of
lower Central American cichlids inferred from analysis of cytochrome
b gene sequences.” Molecular Phylogenetics and
Evolution, 9(2), 192-203.
Mindell, D. P. (1996). “Positive selection
and rates of evolution in immunodeficiency viruses from humans and
chimpanzees.” Proceedings of the
Mooers, A. O., and Heard, S.
B. (1997). “Inferring evolutionary process from phylogenetic tree shape.”
Quarterly Review of Biology, 72(1), 31-54.
Norris, R.D. 1991.
Biased extinction and evolutionary trends. Paleobiology
17:388-99.
Paradis, E. (1998). “Detecting shifts in diversification
rates without fossils.” American Naturalist, 152(2), 176-187.
Price, P. W., and Roininen, H. (1993). “Adaptive Radiation in Gall Induction.”
Sawfly Life History Adaptations to Woody Plants, M. R. Wagner and R. K. F,
eds., Academic Press, Inc., San Diego, California, Usa;
London, England, Uk, 229-257.
Price, T. (1997). “Correlated evolution
and independent contrasts.” Philosophical Transactions of the Royal Society of
Radtkey, R. R., and Case, T.
J. (1996). “Adaptive radiation of day geckos (Phelsuma).”
Bulletin of the Ecological Society of
Reinthal, P. N., and Meyer, A.
(1997). “Molecular phylogenetic tests of speciation models in
Richardson, J. E., R. T. Pennington, T. D. Pennington, and
P. M. Hollingsworth. 2001. Rapid diversification of a
species-rich genus of Neotropical rain forest trees.
Science 293:2242-2245.
Richardson,
J., F. Weitz, M. Fay, Q. Cronk,
H. Linder, G. Reeves, and M. Chase. 2001. Rapid and recent origin of species
richness in the
Sanderson, M. J. (1997). “A nonparametric
approach to estimating divergence times in the absence of rate constancy.”
Molecular Biology and Evolution, 14(12), 1218-1231
Sanderson,
M. 1998. Reappraising adaptive radiation. AmerJBot.
85:1650-1655.
Sanderson, M. J., and Donoghue, M.
J. (1994). “Shifts in diversification rate with the
origin of angiosperms.” Science (
Sanderson, M. J. and M. J. Donoghue. 1996.
Reconstructing shifts in diversification rates on phylogenetic
trees. Trends Ecol. Evol. 11: 15-20.
Sanderson, M. J., and Wojciechowski, M. F. (1996). “Diversification rates in a temperate
legume clade: Are there "so many species" of Astragalus
(Fabaceae)?” American Journal of Botany, 83(11),
1488-1502.
Schluter, D. (1994). “Experimental
evidence that competition promotes divergence in adaptive radiation.”
Science (
Schluter, D. 2000. The ecology of adaptive radiations.
Schulter, D., Price, T., Mooers, A. O., and Ludwig, D. (1997). “Likelihood of
ancestor states in adaptive radiation.” Evolution, 51(6), 1699-1711.
SILVERTOWN, J., J. FRANCISCO-ORTEGA, and M. CARINE.
2005. The monophyly of island radiations: an
evaluation of niche pre-emption and some alternative explanations. Journal of
Ecology 93:653-657.
Snorrason, S. S., Skulason,
S., Jonsson, B., Malmquist,
H. J., Jonasson, P. M., Sandlund,
O. T., and Lindem, T. (1994). “Trophic
specialization in Arctic charr Salvelinus
alpinus (Pisces; Salmonidae):
Morphological divergence and ontogenetic niche shifts.” Biological Journal of
the Linnean Society, 52(1), 1-18.
Stoch, F. (1995). “The ecological and historical
determinants of crustacean diversity in groundwaters,
or: Why are there so many species?” Memoires de Biospeologie, 22, 139-160.
Veith, M., Steinfartz, S., Zardoya, R.,
Seitz, A., and Meyer, A. (1998).
“A molecular phylogeny of 'true' salamanders (family Salamandridae) and the evolution of terrestriality
of reproductive modes.” Journal of Zoological Systematics
and Evolutionary Research, 36(1-2), 7-16.
Verheyen, E., Ruber, L., Snoeks, J., and Meyer,
A. (1996).
“Mitochondrial phylogeography of rock-dwelling
cichlid fishes reveals evolutionary influence of historical lake level
fluctuations of
Winemiller, K. O., Kelso-Winemiller, L. C., and Brenkert,
A. L. (1995). “Ecomorphological diversification and
convergence on fluvial cichlid fishes.” Environmental Biology of Fishes,
44(1-3), 235-261.
Zink, R. M., and Slowinski, J. B. (1995). “Evidence from
molecular systematics for decreased avian
diversification in the Pleistocene Epoch.” Proceedings of the