Advanced Organismal Biology

Bioe 200B

Ecology and Evolutionary Biology

Fall 2013








Notes & Papers

Last modified: 25 November 2013

LECTURE NOTES: from lectures w all info filled in


2-3_Interactions & Interaction Strengths pdf

4 Top-Down v Bottom-up

4b....finish TD v BU (I may not get to this)

5 Diversity/stability 1

6 Diversity/stability 2


FOX Readings: I've changed the paper for November 14. Some of the others may change, too, but not the topics

Nov 14: These two papers are about the same system. We will discuss them together.

Callaway et al 2011. Escape from competition: Neighbors reduce Centaurea stoebe performance at home but not away [effect on Centaurea]

Sun et al. 2013. Dissecting impact of plant invaders: Do invaders behave differently in the new range? [effect of Centaurea]

Nov 19: Levine. 2000. Species diversity, biotic invasions, and scale issues

Nov 21: Schmitz. 2008. Effects of predator hunting mode on ecosystem function

Nov 26: Zavaleta 2010. Multiple ecosystem functions and species diversity [NOTE I have already switched the dates. we do Zavaleta first and then Ling after T-day.]

Dec 3: Ling.2009. Overfishing, resilience of kelp beds, and climate-driven phase shifts.

Dec 5: Siepielski et al. 2010. Experimental evidence for neutral community dynamics

...This paper is longer than our usual. I chose it because it is an experimental test of neutral vs. niche dynamics, and has a particularly interesting and readable discussion of the issues. Since most of you have probably not been exposed to neutral theory before this class, this discussion should be very useful, particularly as it clarifies predictions of neutral vs. niche explanations. You may ignore the models on pages 848, 849, and 854.

For another takeon neutral theory (and the most common types of tests) I have also included a recent paper testing neutral theory and the heated set of comments that are generated. See Ricklefs & Renner 2012: Tropical tree species richness and abundance reject neutrality.

NOTES on: leading a discussion

Checklist for critiquing a research article


Readings Costa Section

Tuesday Oct 1- Physiological Constraint and Life History Tradeoffs

Sibly, R. M. and J. H. Brown. 2007. Effects of body size and lifestyle on evolution of mammal life histories. Proceedings of the National Academy of Sciences:0707725104.

Sibly, R. M., C. C. Witt, N. A. Wright, C. Venditti, W. Jetz, and J. H. Brown. 2012. Energetics, lifestyle, and reproduction in birds. Proceedings of the National Academy of Sciences 109:10937-10941.pdf files/Sibly-2012-Energetics, lifestyl.pdf

Thursday Oct 3- Ecological Implications of Body Size

Goldbogen, J. A., J. Calambokidis, D. A. Croll, M. F. McKenna, E. Oleson, J. Potvin, N. D. Pyenson, G. Schorr, R. E. Shadwick, and B. R. Tershy. 2012. Scaling of lunge-feeding performance in rorqual whales: mass-specific energy expenditure increases with body size and progressively limits diving capacity. Functional Ecology 26:216-226.

Clauset, A. 2013. How Large Should Whales Be? PLoS ONE 8:e53967.

Tuesday Oct 8- Temperature Adaptation 1

Peckham, H. S., D. Maldonado-Diaz, Y. Tremblay, R. Ochoa, J. Polovina, G. Balazs, P. H. Dutton, and W. J. Nichols. 2011. Demographic implications of alternative foraging strategies in juvenile loggerhead turtles Caretta caretta of the North Pacific Ocean. Marine Ecology-Progress Series 425:269-280.pdf files/Peckham_Etal_MEPS_2011.pdf

Thursday Oct 10- Temperature Adaptation 2

Gilbert, C., S. Blanc, Y. Le Maho, and A. Ancel. 2008. Energy saving processes in huddling emperor penguins: from experiments to theory. Journal of Experimental Biology 211:1-8Gi

Hetem, R. S., W. M. Strauss, L. G. Fick, S. K. Maloney, L. C. R. Meyer, M. Shobrak, A. Fuller, and D. Mitchell. 2010. Variation in the daily rhythm of body temperature of free-living Arabian oryx (Oryx leucoryx): does water limitation drive heterothermy? Journal of Comparative Physiology B-Biochemical Systemic and Environmental Physiology 180 :1111-1119.

Tuesday Oct 15- Linking Proximate to Ultimate

Saraux, C., C. Le Bohec, J. M. Durant, V. A. Viblanc, M. Gauthier-Clerc, D. Beaune, Y. H. Park, N. G. Yoccoz, N. C. Stenseth, and Y. Le Maho. 2011. Reliability of flipper-banded penguins as indicators of climate change. Nature 469:203-206

Steven J. Cooke, Daniel T. Blumstein, Richard Buchholz, Tim Caro, Esteban Fernández-Juricic, Craig E. Franklin, Julian Metcalfe, Constance M. O’Connor, Colleen Cassady St. Clair, William J. Sutherland and Martin Wikelski. 2013. Physiology, Behavior, and Conservation. Physiological and Biochemical Zoology

Additional Readings (the first three are must read).

Chamberlin, T. C. 1965. The method of multiple working hypotheses. Science 148:754-759.

Gould, S. J. and R. C. Lewontin. 1979. The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptationist programme. Proc R Soc Lond B Biol Sci 205:581-598.

Platt, J. R. 1964. Strong Inference. Science 146:347-353.

Brown, J. H. and P. F. Nicoletto. 1991. Spatial Scaling of Species Composition: Body Masses of North American Land Mammals. The American Naturalist 138 :1478-1512.

Calder, W. A. 2001. Ecological Consequences of Body Size. eLS. John Wiley & Sons, Ltd.

Cooke, S. J., L. Sack, C. E. Franklin, A. P. Farrell, J. Beardall, M. Wikelski, and S. L. Chown. 2013. What is conservation physiology? Perspectives on an increasingly integrated and essential science. Conservation Physiology 1.

Costa, D. P. and B. Sinervo. 2004. Field physiology: physiological insights from animals in nature. Annual Review of Physiology 66:209-238.

Costa, D. P., G. A. Breed, and P. W. Robinson. 2012. New Insights into Pelagic Migrations: Implications for Ecology and Conservation. Annual Review of Ecology, Evolution, and Systematics 43:73-96.

Gauthier-Clerc, M., J. P. Gendner, C. A. Ribic, W. R. Fraser, E. J. Woehler, S. Descamps, C. Gilly, C. Le Bohec, and Y. Le Maho. 2004. Long-term effects of flipper bands on penguins. Proceedings of the Royal Society of London Series B-Biological Sciences 271:S423-S426.

Wikelski, M. 2005. Evolution of body size in Galapagos marine iguanas. Proceedings of the Royal Society B-Biological Sciences 272:1985-1993.

Lenski, R. E. and A. F. Bennett. 1993. Evolutionary Response of Escherichia coli to Thermal Stress. The American Naturalist 142:S47-S64.

Wikelski, M. and S. J. Cooke. 2006. Conservation physiology. Trends Ecol. Evol. 21:38-46.

Readings Kilpatrick Section

Thursday October 17th
Salinas, S. and S. B. Munch. 2012. Thermal legacies: transgenerational effects of temperature on growth in a vertebrate. Ecology Letters 15:159-163.

Blount, Z. D., C. Z. Borland, and R. E. Lenski. 2008. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 105:7899-7906

Tuesday October 22st
Hairston, N. G., S. P. Ellner, M. A. Geber, T. Yoshida, and J. A. Fox. 2005. Rapid evolution and the convergence of ecological and evolutionary time. Ecology Letters 8:1114-1127.
Grant, P. R. and B. R. Grant. 2002. Unpredictable evolution in a 30-year study of Darwin's finches. Science 296:707-711.

Thursday October 24th
Gavrilets, S. and J. B. Losos. 2009. Adaptive Radiation: Contrasting Theory with Data. Science 323:732-737.
Smith, J. M. and G. R. Price. 1973. The logic of animal conflict. Nature 246:15-18.

Tuesday October 29th
Currie, D. J., G. G. Mittelbach, H. V. Cornell, R. Field, J. F. Guegan, B. A. Hawkins, D. M. Kaufman, J. T. Kerr, T. Oberdorff, E. O'Brien, and J. R. G. Turner. 2004. Predictions and tests of climate-based hypotheses of broad-scale variation in taxonomic richness. Ecology Letters 7:1121-1134.
He, F. L. and S. P. Hubbell. 2011. Species-area relationships always overestimate extinction rates from habitat loss. Nature 473:368-371.

Thursday October 31st
Read, A. F., T. Day, and S. Huijben. 2011. The evolution of drug resistance and the curious orthodoxy of aggressive chemotherapy. Proceedings of the National Academy of Sciences of the United States of America 108:10871-10877.
Read, A. F., P. A. Lynch, and M. B. Thomas. 2009. How to Make Evolution-Proof Insecticides for Malaria Control. Plos Biology 7:e1000058.

Tuesday November 5th
Gomulkiewicz, R. and R. D. Holt. 1995. When does evolution by natural-selection prevent extinction? Evolution 49:201-207.
Kilpatrick, A. M. 2006. Facilitating the evolution of resistance to avian malaria in Hawaiian birds. Biological Conservation 128:475-485.

Thursday November 7th
Felsenstein, J. 1985. Phylogenies and the Comparative Method. American Naturalist 125:1-15.
Blomberg, S. P., T. Garland, and A. R. Ives. 2003. Testing for phylogenetic signal in comparative data: Behavioral traits are more labile. Evolution 57:717-745.




Back to Top






Notes & Papers