Integrative Biology 200B     Spring 1999

"PRINCIPLES OF PHYLOGENETICS:  ECOLOGY AND EVOLUTION"
Reading List # 3

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.

Feb. 25 & March 2.  QUALITATIVE CHARACTER EVOLUTION:

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

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, London.

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

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

**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.

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

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

March 4th. ADAPTATION:

Armbruster, W. S. (1994). ěEarly evolution of Dalechampia (Euphorbiaceae): Insights from phylogeny, biogeography, and comparative ecology.î Annals of the Missouri Botanical Garden, 81(2), 302-316.

Armbruster, W. S. (1997). ěExaptations link evolution of plant-herbivore and plant-pollinator interactions: A phylogenetic inquiry.î Ecology (Washington D C), 78(6), 1661-1672.

Brandon, R. N. 1990. Adaptation and Environment. Princeton University Press, Princeton, NJ.

Coddington, J. 1988. Cladistic tests of adaptational hypotheses. Cladistics 4:3-22.

Craddock, E. M., and Kambysellis, M. P. (1997). ěAdaptive radiation in the Hawaiian Drosophila (Diptera: Drosophilidae): Ecological and reproductive character analyses.î Pacific Science, 51(4), 475-489.

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.

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.

Gould, S.J. and E.S. Vrba 1982.  Exaptation--a missing term in the science of form.  Paleobiology 8:4-15.

* Gould, S.J. and R. Lewontin 1979.  The spandrels of San Marco and the Panglossian Paradigm: a critique of the adaptationist programme.  Pp. 147-164 in: The evolution of adaptation by natural selection (J. Maynard Smith & R. Holliday, eds.).  Roy. Soc. London.

Guyer, C. and J.B. Slowinski.  1991.  Comparisons of observed phylogenetic topologies with null expectations among three monophyletic lineages.  Evolution 45:340-50.

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. Cambridge University Press, New York.

Kappeler, P. M., and Heymann, E. W. (1996). ěNonconvergence in the evolution of primate life history and socio-ecology.î Biological Journal of the Linnean Society, 59(3), 297-326.

Kiltie, R.A. 1985.  Evolution and function of horns and hornlike organs in female ungulates.  Biol. J. Linn. Soc. 24:299-320.

Lauder, G.V. 1981.  Form and function: structural analysis in evolutionary morphology.  Paleobiology 7:430-442.

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.

Mishler, B.D. 1988. Reproductive ecology of bryophytes. Pp. 285-306 in J. Lovett Doust and L. Lovett Doust (eds.), Plant Reproductive Ecology. Oxford University Press.

Mitter, C., B. Farrell, and B. Wiegmann. 1988. The phylogenetic study of adaptive zones: Has phytophagy promoted insect diversification? Amer. Nat. 132:107-128.

Price, P. W. (1994). ěPhylogenetic constraints, adaptive syndromes, and emergent properties: From individuals to population dynamics.î Researches on Population Ecology (Kyoto), 36(1), 3-14.

Ridley, M. 1983. The explanation of organic diversity: the comparative method and adaptations formating. Oxford University Press.

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.

Wagner, W L. Hawaiian biogeography: Evolution on a hot spot archipelago. Wagner, W. L. and V. A. Funk (Ed.). Hawaiian biogeography: Evolution on a hot spot archipelago. xvii+467p. Smithsonian Institution Press: Washington, DC, USA; London, England, UK. 1995.

**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.

March 9th.  BEHAVIORAL DATA

Andersen, N. M. (1994). ěThe evolution of sexual size dimorphism and mating systems in water striders (Hemiptera: Gerridae): A phylogenetic approach.î Ecoscience, 1(3), 208-214.

Chan, L. K. W. (1996). ěPhylogenetic interpretations of primate socioecology: With special reference to social and ecological diversity in Macaca.î Phylogenies and the comparative method in animal behavior, E. P. Martins, ed., Oxford University Press, Inc., New York, New York, USA; Oxford, England, UK, 324-360.

Crespi, B. J., and Choe, J. C. (1997). ěExplanation and evolution of social systems.î The evolution of social behavior in insects and arachnids, J. C. Choe and B. J. Crespi, eds., Cambridge University Press, Cambridge, England, UK; New York, New York, USA, 499-524.

Driskell, A. C. (1997). ěMorphological and behavioral evolution in the honeyeaters (Passeriformes: Meliphagidae).î American Zoologist, 37(5), 198A.

Gillespie, R. G., Croom, H. B., and Palumbo, S. R. (1994). ěMultiple origins of a spider radiation in Hawaii.î Proceedings of the National Academy of Sciences of the United States of America, 91(6), 2290-2294.

Gwynne, D. T. (1995). ěVariation in bushcricket nuptial gifts may be due to common ancestry rather than ecology as taxonomy and diet are almost perfectly confounded.î Behavioral Ecology, 6(4), 458.

Hardy, I. C. W., and Mayhew, P. J. (1998). ěSex ratio, sexual dimorphism and mating structure in bethylid wasps.î Behavioral Ecology and Sociobiology, 42(6), 383-395.

Harrison, R. G., and Bogdanowicz, S. M. (1995). ěMitochondrial DNA phylogeny of North American field crickets: Perspectives on the evolution of life cycles, songs, and habitat associations.î Journal of Evolutionary Biology, 8(2), 209-232.

Houle, A. (1997). ěThe role of phylogeny and behavioral competition in the evolution of coexistence among primates.î Canadian Journal of Zoology, 75(6), 827-846.

**Martins, E. P. (1996). ěPhylogenies and the comparative method in animal behavior.î Phylogenies and the comparative method in animal behavior, E. P. Martins, ed., Oxford University Press, Inc., New York, New York, USA; Oxford, England, UK.

McCracken, K. G., and Sheldon, F. H. (1997). ěAvian vocalizations and phylogenetic signal.î Proceedings of the National Academy of Sciences of the United States of America, 94(8), 3833-3836.

McKitrick, M. C. (1993). ěTrends in the evolution of hindlimb musculature in aerial-foraging birds.î Auk, 110(2), 189-206.

Perry, G. (1996). ěThe evolution of sexual dimorphism in the lizard Anolis polylepis (Iguania): Evidence from intraspecific variation in foraging behavior and diet.î Canadian Journal of Zoology, 74(7), 1238-1245.

Sheldon, F. H., and Whittingham, L. A. (1997). ěPhylogeny in studies of bird ecology, behavior, and morphology.î Avian molecular evolution and systematics, D. P. Mindell, ed., Academic Press, Inc., San Diego, California, USA; London, England, UK, 279-299.

Westneat, M. W. (1995). ěFeeding, function, and phylogeny: Analysis of historical biomechanics in labrid fishes using comparative methods.î Systematic Biology, 44(3), 361-383.

Westneat, M. W. (1995). ěPhylogenetic systematics and biomechanics in ecomorphology.î Environmental Biology of Fishes, 44(1-3), 263-283.

March 11th. HETEROCHRONY:

Cunningham, C W; Buss, L W.  Molecular Evidence for Multiple Episodes of
Paedomorphosis in the Family Hydractiniidae Biochemical Systematics and Ecology, v.21,
n.1, 1993:57-69

Dommergues, J-L; David, B; Marchand, D.  Ontogeny and phylogeny:
Paleontological applications. Geobios (Lyon), v.19, n.3, 1986:335-356

Grande, T.  Phylogeny and paedomorphosis in an African family of
freshwater fishes (Gonorynchiformes: Kneriidae). Fieldiana Zoology, n.78, 1994:I-III,
1-20

Kellogg, E A.  Ontogenetic studies of florets in Poa (Gramineae): Allometry and heterochrony. Evolution, v.44, n.8,:1978-1989

Klingenberg, C P.  Heterochrony and allometry: The analysis of evolutionary change in
ontogeny. Biological Reviews of the Cambridge Philosophical Society, v.73, n.1, 1998:79-123

**Kluge, A G.  Ontogeny and phylogenetic systematics. Cladistics, v.1, n.1,1985:13-27

Lammers, T G.  Sequential Pedomorphosis Among the Endemic Hawaiian Lobelioideae Campanulaceae Taxon, v.39, n.2, 1990:206-211

Long, J A.  Heterochrony and the origin of tetrapods. Lethaia, v.23, n.2,
1990:157-166

Masuyama, S.  Progenesis as an adaptive strategy in the annual fern
Ceratopteris thalictroides in Japan. Plant Species Biology, v.11, n.2-3, 1996:225-232

Mcnamara, K J.  A Guide To the Nomenclature of Heterochrony. Journal of Paleontology,
v.60, n.1, 1986:4-13

Mcnamara, K J.  The Role of Heterochrony in the Evolution of Cambrian Trilobites
Biological Reviews of the Cambridge Philosophical Society, v.61, n.2, 1986:121-156

Mishler, B.D.   1986. Ontogeny and phylogeny in Tortula (Musci: Pottiaceae).  Systematic Botany 11: 189-208.

Mishler, B.D.   1988.   Relationships between ontogeny and phylogeny, with reference to bryophytes.  In C. J. Humphries (ed.),   Ontogeny and Systematics, pp. 117-136.  Columbia University Press.

McKinney, M. L.  1988.  Heterochrony in evolution: a multidisciplinary approach.  Plenum Press, New York.

Meier, R.  A test and review of the empirical performance of the
ontogenetic criterion. Systematic Biology, v.46, n.4, 1997:699-721

Wake, D B; Hanken, J.  Direct development in the lungless salamanders: What are
the consequences for developmental biology, evolution and phylogenesis?
International Journal of Developmental Biology, v.40, n.4, 1996:859-869

Wiltshire, R J E; Murfet, I C; Reid, J B.  The genetic control of heterochrony:
Evidence from developmental mutants of Pisum sativum L. Journal of Evolutionary
Biology, v.7, n.4, 1994:447-465

Zelditch, M. L. and W. L. Fink.  1996.  Heterochrony and heterotopy: stability and innovation in the evolution of form.  Paleobiol. 22: 241-254.

Zopfi, H. J. (1995). ěLife history variation and infraspecific heterochrony in Rhinanthus glacialis (Scrophulariaceae).î Plant Systematics and Evolution, 198(3-4), 209-233.

March 16th. TRENDS, EVOLUTIONARY RATES:

Baverstock, P. R., and M. Adams.  1987.  Comparative rates of molecular, chromosomal, and morphological evolution in some Australian vertebrates.  Pages 175-188 in K. S. W. Campbell and M. F. Day, eds.  Rates of evolution.  Allen & Unwin, London.

Bookstein, F. L.  1987.  Random walk and the existence of evolutionary rates.  Paleobiology   11:258-271.

Bookstein, F. L.  1989.  Comment on a rate test.  Evolution   43:1569-1570.

Cavalli-Sforza, L., and A. Piazza.  1975.  Analysis of evolution:  Evolutionary rates, independence, and treeness.  Theoret.  Popul.  Biol.  8:127-165.

Campbell, K. S. W., and M. F. Day.  1987.  Rates of evolution.  Allen & Unwin, London.

Cheetham, A H; Jackson, J B C; Hayek, L-A C.  1993.  Quantitative genetics of bryozoan phenotypic evolution. I. Rate tests for random change versus selection in differentiation of living species.  Evolution, v.47, n.5, 1526-1538.

Cracraft, J.  1984.  Conceptual and methodological aspects of the study of evolutionary rates, with some comments on bradytely in birds.  In:  Living Fossils (Ed. by N. Eldredge, and S. Stanley), pp. 95-104.  New York:  Springer-Verlag.

Eldredge, N.  1982.  Phenomenological levels and evolutionary rates.  Syst.  Zool.  31:338-347.

Fenster, E. J., and U. Sorhannus.  1991.  On the measurement of morphological rates of evolution.  A review.  Evol.  Biol., 25, 375-410.

Garland, T., Jr.  1992.  Rate tests for phenotypic evolution using phylogenetically independant contrasts.  Am.  Nat.  140:509-519.

Gingerich, P. D.  1983.  Rates of evolution:  Effects of time and temporal scaling.  Science, 222, 159-161.

Gingerich, P. D.  1993.  Quantification and comparison of evolutionary rates.  Am. J. Sci., 293-A, 453-478.

Gittleman, J. L.,Anderson, C. G., Kot, M., and Luh, H.-K.  1996.  Comparing behavioral and morphological evolution:  using molecular phylogenies to measure phylogeny, plasticity, and rates.  In Phylogenies and the comparative method in animal behavior, (ed. E.P. Martins), pp.  167-206.  Oxford University Press.

Gittleman, J. L.,Anderson, C. G., Kot, M., and Luh, H.-K.  1996.  Comparative tests of evolutionary lability and rates using molecular phylogenies.  In New Uses for New Phylogeneies , (ed. Paul H. Harvey et al.), pp.  289-307. Oxford University Press.

Hackett, S. J., and Rosenberg, K. V.  1990.  Comparison of phenotypic and genetic differentiation in South American antwrens (Formicariidae).  The Auk  107:473-489.

Haldane, J. B. S.  1949.  Suggestions as to quantitative measurement of rates of evolution.  Evolution, 3, 51-56.

Hecht, M. K.  1965.  The role of natural selection and evolutionary rates in the origin of higher levels of organization.  Syst. Zool., 14, 301-317.

Legendre, P.  1993.  Spatial autocorrelation:  Trouble or new paradigm?  Ecology, 74, 1659-1673.

Lynch, M.  1990.  The rate of morphological evolution in mammals from the standpoint of the neutral expectation.  Am. Nat., 136, 727-741.

Maddison, W. P., and Slatkin, M.  1991.  Null models for the number of evolutionary steps in a character on a phylogenetic tree.  Evolution  45:1184-1197.

**Martins, E. P.  1994.  Estimating the rate of phenotypic evolution from comparative data.  Am. Nat., 144, 193-209.

Milligan, B G.  Estimating evolutionary rates for discrete characters.  Scotland, R. W., D. J. Siebert and D. M. Williams (Ed.). Systematics Association Special Volume, Vol. 52.  Models in phylogeny reconstruction;  Meeting, Oxford, England, UK, August 1993. xi+360p. Oxford University  Press: Oxford, England, UK; New York, New York, USA.  ISBN 0-19-854824-9. p. 299-311.

Nee, S. et al. 1992. Tempo and mode of evolution revealed from molecular phylogenies. Proc. Natl. Acad. Sci. USA 89:8322-8326.
Nee, S. et al. 1994. Extinction rates can be estimated from molecular phylogenies. Philos. Trans. R. Soc. London Ser. B 344: 305-311.

Novacek, M. J., and Norell, M. A.  1982.  Fossils, phylogeny, and taxonomic rates of evolution.  Syst.  Zool.  31:366-375.

Parsons, P. A.  1987.  Evolutionary rates under environmental stress.  Evol. Biol.  21:311-348.
Parsons, P. A.  1991.  Evolutionary rates:  stress and species boundaries.  Ann. Rev. Ecol. and Syst.  22:1-18.

Patterson, B.  1949.  Rates of evolution in taeniodonts, pp.  243-278.  In:  Jepsen, G. L., Mayr, E., Simpson, G. G.  (eds.), Genetics, paleontology, and evolution.  Princeton:  Princeton U. Press.

Raup, D. M., and Marshall, L. G.  1980.  Variation between groups in evolutionary rates:  a statistical test of significance.  Paleobiology  6:9-23.

Rosenzweig, M. L., J. S. Brown, and T. L. Vincent.  1987.  Red queens and ESS:  the coevolution of evolutionary rates.  Evolutionary Ecology 1:59-94.

Simpson, G. G.  1944.  Tempo and Mode in Evolution.  New York:  Columbia University Press.

Slatkin, M., and Arter, A. E.  1991.  Spatial autocorrelation methods in population genetics.  Am. Nat.  138:499-517.

Spicer, G. S.  1993.  Morphological evolution of the Drosophila virilis species group as assessed by rate tests for natural selection on quantitative characters.  Evolution, 47(4), pp.  1240-1254.

Stanley, S. M.  1985.  Rates of evolution.  Paleobiology  11:13-26.

Turelli, M., J. H. Giellespie, and R. Lande.  1988.  Rate tests for selection on quantitative characters during macroevolution and microevolution.  Evolution 42:1085-1089.

March 18th. PHYLOGENETICS IN RELATION TO CONSERVATION:

Faith, D. P.  1992a.  Conservation evaluation and phylogenetic diversity.  Biological Conservation 61:1-10.

Faith, D. P.  1992b.  Systematics and conservation: on predicting the feature diversity of subsets of taxa.  Cladistics 8:361-373.

**Forey, P.L.,  C. J. Humphries and P. H. Williams.  1994.  Systematics and conservation evaluation,  Systematics Association Special Volume No. 50.  Clarendon Press, Oxford.

Mishler, B.D. 1995.  Plant systematics and conservation: science and society.  Madroño 42: 103-113.

Polhemus, D. A. (1997). ěPhylogenetic analysis of the Hawaiian damselfly genus Megalagrion (Odonata: Coenagrionidae): Implications for biogeography, ecology, and conservation biology.î Pacific Science, 51(4), 395-412.

Tyler, H. A., Brown, K. S., Jr., and Wilson, K. H. (1994). ěSwallowtail butterflies of the Americas: A study in biological dynamics, ecological diversity, biosystematics, and conservation.î

Vane-Wright, R. I., C. J. Humphries and P. H. Williams.  1991.  What to protect? -- Systematics and the agony of choice.  Biological Conservation 55:235-254.