Integrative Biology 200B
Spring 1999

"PRINCIPLES OF PHYLOGENETICS:  ECOLOGY AND EVOLUTION"
Reading List # 4

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.

March 30.  Comparing sister clades within a cladogram

Guyer, C. and J.B. Slowinski.  1991.  Comparisons of observed phylogenetic topologies with null expectations among three monophyletic lineages.  Evolution 45:340-50.
Huelsenbeck, J. P. and M. Kirkpatrick.  1996.  Do phylogenetic methods produce trees with different shapes?  Evol. 50: 1418-1424.
** Losos, J. B. and F. R. Adler.  1995.  Stumped by trees? A generalized null model for patterns of organismal diversity.  Am. Nat. 145: 329-342.
Mooers, A. Ø.  1995.  Tree balance and tree completeness.  Evol. 49: 379-384.
Slowinski, J.B. and C. Guyer, 1989.  Testing the stochasticity of patterns of organismal diversity:  an improved null model.  Am.Nat. 134:907-921
Lemen, C.A. and P.W. Freeman.  1989.  Testing macroevolutionary hypotheses with cladistic analysis:  evidence against rectangular evolution.  Evolution 43:1538-1554.

April 1.  Adaptive Radiations.

* Baldwin, B. G., and Sanderson, M. J. (1998). žAge and rate of diversification of the Hawaiian silversword alliance (Compositae).Ó Proceedings of the National Academy of Sciences of the United States of America, 95(16), 9402-9406.
Barrett, S. C. H., and Graham, S. W. (1997). žAdaptive radiation in the aquatic plant family Pontederiaceae: Insights from phylogenetic analysis.Ó 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.
Berenbaum, M. R., Favret, C., and Schuler, M. A. (1996). žOn defining "Key innovations" in an adaptive radiation: Cytochrome P450S and Papilionidae.Ó American Naturalist, 148(SUPPL), S139-S155.
Bond, J. E., and Opell, B. D. (1998). žTesting adaptive radiation and key innovation hypotheses in spiders.Ó 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). žLife-history perspective of adaptive radiation in desmognathine salamanders.Ó Copeia, 1996(4), 783-790.
Cameron, R. A. D., Cook, L. M., and Hallows, J. D. (1996). žLand snails on Porto Santo: Adaptive and non-adaptive radiation.Ó Philosophical Transactions of the Royal Society of London B Biological Sciences, 351(1337), 309-327.
Chiba, S. (1996). žEcological and morphological diversification within single species and character displacement in Mandarina, endemic land snails of the Bonin Islands.Ó Journal of Evolutionary Biology, 9(3), 277-291.
Craddock, E. M., and Kambysellis, M. P. (1997). žAdaptive radiation in the Hawaiian Drosophila (Diptera: Drosophilidae): Ecological and reproductive character analyses.Ó Pacific Science, 51(4), 475-489.
Desutter-Grandcolas, L. (1997). žStudies in cave life evolution: A rationale for future theoretical developments using phylogenetic inference.Ó Journal of Zoological Systematics and Evolutionary Research, 35(1), 23-32.
Farrell, B. D. (1998). ž"Inordinate fondness": Explained: Why are there so many beetles?Ó Science (Washington D C), 281(5376), 555-559.
Foote, M. (1993). žDiscordance and Concordance Between Morphological and Taxonomic Diversity.Ó Paleobiology, 19(2), 185-204.
Francisco-Ortega, J., Jansen, R. K., and Santos-Guerra, A. (1996). žChloroplast DNA evidence of colonization, adaptive radiation, and hybridization in the evolution of the macaronesian flora.Ó Proceedings of the National Academy of Sciences of the United States of America, 93(9), 4085-4090.
Givnish, T. J. (1997). žAdaptive radiation and molecular systematics: Issuses and approaches.Ó 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). žMolecular evolution and adaptive radiation in Brocchinia (Bromeliaceae: Pitcairnioideae) atop tepuis of the Guayana Shield.Ó 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.
Grant, P. R. (1998). žRadiations, communities, and biogeography.Ó 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). žAdaptive radiation in the Afrotropical region of the Paleotropical genus Lissocephala (Drosophilidae) on the pantropical genus Ficus (Moraceae).Ó Journal of Biogeography, 23(4), 543-552.
Hill, R. S., and Dettmann, M. E. (1996). žOrigin and diversification of the genus Nothofagus.Ó 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.
Johnson, S. D., Linder, H. P., and Steiner, K. E. (1998). žPhylogeny and radiation of pollination systems in Disa (Orchidaceae).Ó American Journal of Botany, 85(3), 402-411.
Landmann, A., and Winding, N. (1995). žAdaptive radiation and resource partitioning in Himalayan high-altitude finches.Ó Zoology (Jena), 99(1), 8-20.
Losos, J. B., Jackman, T. R., Larson, A., De Queiroz, K., and Rodriguez-Schettino, L. (1998). žContingency and determinism in replicated adaptive radiations of island lizards.Ó Science (Washington D C), 279(5359), 2115-2118.
Losos, J. B., Warheit, K. I., and Schoener, T. W. (1997). žAdaptive differentiation following experimental island colonization in Anolis lizards.Ó Nature (London), 387(6628), 70-73.
Macleod, N. (1993). žThe Maastrichtian-Danian Radiation of Triserial and Biserial Planktic Foraminifera Testing Phylogenetic and Adaptational Hypotheses in the Microfossil Record.Ó Marine Micropaleontology, 21(1-3), 47-100.
Martin, A. P., and Bermingham, E. (1998). žSystematics and evolution of lower Central American cichlids inferred from analysis of cytochrome b gene sequences.Ó Molecular Phylogenetics and Evolution, 9(2), 192-203.
Mindell, D. P. (1996). žPositive selection and rates of evolution in immunodeficiency viruses from humans and chimpanzees.Ó Proceedings of the National Academy of Sciences of the United States of America, 93(8), 3284-3288.
Mooers, A. O., and Heard, S. B. (1997). žInferring evolutionary process from phylogenetic tree shape.Ó Quarterly Review of Biology, 72(1), 31-54.
Norris, R.D.  1991.  Biased extinction and evolutionary trends.  Paleobiology 17:388-99.
Paradis, E. (1998). žDetecting shifts in diversification rates without fossils.Ó American Naturalist, 152(2), 176-187.
Price, P. W., and Roininen, H. (1993). žAdaptive Radiation in Gall Induction.Ó 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). žCorrelated evolution and independent contrasts.Ó Philosophical Transactions of the Royal Society of London B Biological Sciences, 352(1352), 519-529.
Radtkey, R. R., and Case, T. J. (1996). žAdaptive radiation of day geckos (Phelsuma).Ó Bulletin of the Ecological Society of America, 77(3 SUPPL. PART 2), 365.
Reinthal, P. N., and Meyer, A. (1997). žMolecular phylogenetic tests of speciation models in Lake Malawi cichlid fishes.Ó 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, 375-390.
Sanderson, M. J. (1997). žA nonparametric approach to estimating divergence times in the absence of rate constancy.Ó Molecular Biology and Evolution, 14(12), 1218-1231.
** Sanderson, M. J., and Donoghue, M. J. (1994). žShifts in diversification rate with the origin of angiosperms.Ó Science (Washington D C), 264(5165), 1590-1593.
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). žDiversification rates in a temperate legume clade: Are there "so many species" of Astragalus (Fabaceae)?Ó American Journal of Botany, 83(11), 1488-1502.
Schluter, D. (1994). žExperimental evidence that competition promotes divergence in adaptive radiation.Ó Science (Washington D C), 266(5186), 798-801.
Schulter, D., Price, T., Mooers, A. O., and Ludwig, D. (1997). žLikelihood of ancestor states in adaptive radiation.Ó Evolution, 51(6), 1699-1711.
Snorrason, S. S., Skulason, S., Jonsson, B., Malmquist, H. J., Jonasson, P. M., Sandlund, O. T., and Lindem, T. (1994). žTrophic specialization in Arctic charr Salvelinus alpinus (Pisces; Salmonidae): Morphological divergence and ontogenetic niche shifts.Ó Biological Journal of the Linnean Society, 52(1), 1-18.
Stoch, F. (1995). žThe ecological and historical determinants of crustacean diversity in groundwaters, or: Why are there so many species?Ó Memoires de Biospeologie, 22, 139-160.
Veith, M., Steinfartz, S., Zardoya, R., Seitz, A., and Meyer, A. (1998). žA molecular phylogeny of 'true' salamanders (family Salamandridae) and the evolution of terrestriality of reproductive modes.Ó Journal of Zoological Systematics and Evolutionary Research, 36(1-2), 7-16.
Verheyen, E., Ruber, L., Snoeks, J., and Meyer, A. (1996). žMitochondrial phylogeography of rock-dwelling cichlid fishes reveals evolutionary influence of historical lake level fluctuations of Lake Tanganyika, Africa.Ó Philosophical Transactions of the Royal Society of London B Biological Sciences, 351(1341), 797-805.
Winemiller, K. O., Kelso-Winemiller, L. C., and Brenkert, A. L. (1995). žEcomorphological diversification and convergence on fluvial cichlid fishes.Ó Environmental Biology of Fishes, 44(1-3), 235-261.
Zink, R. M., and Slowinski, J. B. (1995). žEvidence from molecular systematics for decreased avian diversification in the Pleistocene Epoch.Ó Proceedings of the National Academy of Sciences of the United States of America, 92(13), 5832-5835.