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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

Feb. 1-6: QUALITATIVE CHARACTER EVOLUTION:

Ballard, H. E., and K. J. Sytsma. Evolution and biogeography of the woody Hawaiian Violets (Viola Violaceae): artic origins, herbaceous ancestry, and bird dispersal. Evolution 54: 1521-1532.

Bargelloni, L., S. Marcato, L. Zane, and T. Patarnello. 2000. Mitochondrial phylogeny of notothenioids: A molecular approach to Antarctic fish evolution and biogeography. Systematic Biology 49: 114-129.

Bininda-Emonds, O. and J. L. Gittleman. 2000. Are pinnipeds functionally different from fissiped carnivores? The importance of phylogenetic comparative analyses. Evolution 54: 1011-1023.

Brooks, D.R., & D. McLennan. 1991. Phylogeny, Ecology, and Behavior. University of Chicago Press.

Brown, J. M., M. A. McPeek, and M. L. May. 2000. A phylogenetic perspective on habitat shifts and diversity in the North American Enallagma damselflies. Systematic biology 49: 697-712.

Cruickshank, R. H., and R. H. Thomas. 1999. Evolution of haplodiploidy in Dermanssine mites (Acari: Mesostigmata). Evolution 53: 1796-1803.

D’Hasse, C. 2000. Is psammophily an evolutionary dead end? A phylogenetic test in the genus Willemia (Collembola: Hypogatruridae). Cladistics 16: 255-273.

Dobson, F.S. 1985. The use of phylogeny in behavior and ecology. Evolution 39:1384-1388.

Dodd, M. E, J. Silvertown, and M. W. Chase. 1999. Phylogenetic analysis of trait evolution and species diversity variation among angiosperm families. Evolution 53: 732-744.

** Donoghue, M.J. 1989. Phylogenies and analysis of evolutionary sequences, with examples from seed plants. Evolution 43:1137-1156. (maddison’s test application)

Eggleton, P. and R. I. Vane-Wright (ed.). 1994. Phylogenetics and Ecology. Academic Press, London.

Funk, V.A. and D.R. Brooks. 1990. Phylogenetic systematics as the basis of comparative biology. Smithsonian Institution Press.

Goodwillie, C. 1999. Multiple origins of self-compatibility in Lianthus section Leptosiphon (Polemoniaceae): phylogenetic evidence from internal-transcribed-spacer sequence data. Evolution 53: 1387-1395.

Harvey, P.H. and M.D. Pagel. 1991. The comparative method in evolutionary biology. Oxford University Press.

Henry, C. S., M. L. M. Wells, and C. M. Simon. 1999. Convergent evolution of courtship songs among crytpic species of the Carnea group of green lacewings (Neuroptera: Chrysopidae: Chrysoperla). Evolution 53: 1165-1179.

Hrbek, T. and A. Larson. 1999. The evolution of diapause in Killifish family Rivulidae (Atherinomorpha, Cyprinodontiformes): a molecular phylogenetic and biogeographic perspective. Evolution 53: 122-1216.

Hunt, J. H. 1999. Trait mapping and salience in the evolution of eusocial wasps. Evolution 53: 225-237.

Johnson, S. G. and Bragg, E. 1999. Age and polyphyletic origins of hybrid and spontaneous parthenogenetic Campeloma (Gastropoda: Viviparidae) from the southeastern United States. Evolution 53: 1769-1781.

Lorch, P. D. and J. McA. Eadie. 1999. Power of the concentrated changes test for correlated evolution. Systematic Biology 48: 170-191.

**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.

McMillan, W. O., L. A. Weigt, and S. R. Palumbi. 1999. Color pattern evolution, assortative mating, and genetic differentiation in brightly colored butterfly fishes (Chaetodontidae). Evolution 53: 247-260.

McCracken, K. G., J. Harshman, D. A. McClellan, A. D. Afton. 1999. Data set incongruence and correlated character evolution: an example of functional convergence in the hind-limbs of stifftail diving ducks. Systematic Biology 48: 683-714.

Oakley, T. H. and C. W. Cunningham. 2000. Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phjylogeny. Evolution 54: 397-405.

Omland, K. E. and S. M. Lanyon. Reconstructing plumage evolution in orioles (Icterus): repeated convergence and reversal in patterns. Evolution 54: 2119-2133.

Page, R.D.M. 1994. Parallel phylogenies - reconstructing the history of host-parasite assemblages. Cladistics 10(2): 155-173.

*Pagel M. (1994) Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc. R. Soc. Lond. B, 255, 37-45

*Pagel M. (1999) The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Syst. Biol., 48, 612-622

Pearse, D. E. and G. H. Pogson. 2000. Parallel evolution of the melanic form of the California legless lizard, Anniella pulchra, inferred from mitochondrial DNA sequence variation. Evolution 54: 1041-1046.

Pitnick, S., T. Markow, and G. S. Spicer. 1999. Evolution of multiple kinds of female sperm-storage organs in Drosophila. Evolution 53: 1804-1822.

Schulze, S. R., S. A. Rice, J. L. Simon, and S. A. Karl. Evolution of poecilogony and the biogeography of North American populations of the polychaete Streblospio. Evolution 54: 147-1259.

Schwenk, K. 2000. Functional units and their evolution. Pp.165-198 in G. P. Wagner (ed.), The Character Concept in Evolutionary Biology. San Diego, Academic Press.

Schluter D., Price T., Mooers A. & Ludwig D. (1997) Likelihood of ancestor states in adaptive radiation. Evolution, 51, 1699-1711

Vermeij, G. J. and D. R. Lindberg. 2000. Delayed herbivory and the assembly of marine benthic ecosystems. Paleobiology 26: 419-430.

Weibel, A. C., T. E. Dowling, anf B. J. Turner. 1999. Evidence that an outcrossing population is a derived lineage in a hermaphroditic fish (Rivulus marmoratus). Evolution 53: 1271-1225.

Weller, S. G. and A. K. Sakai. 1999. USING PHYLOGENETIC APPROACHES FOR THE ANALYSIS OF PLANT BREEDING SYSTEM EVOLUTION. Annu. Rev. Ecol. Syst. Vol. 30: 167-199.

Werdelin, L. and B. S. Tullberg. 1995. A comparison of two methods to study correlated discrete characters on phylogenetic trees. Cladistics 11: 265-277.

Wiens, J.J., T. W. Reeder and A. N. Montes de Oca. 1999. Molecular phylogenetics and evolution of sexual dichromatism among populations of the Yarrow’s spiny lizard (Sceloporus jarrovii). Evolution 53: 1884-1897.

Wilson, J. A. and M. T. Carrano. 1999. Titanosaurs and the origin of “wide-gauge” trackways: a biomechanical and systematic perspective on sauropod locomotion. Paleobiology 25: 252-267.