EECB 703 Readings/Calendar

The course calendar is also available as a Google Calendar: link

Discussion groups can be found here. The person first in each list will be the discussion group leader. The second person in each list will be the designated note-taker (responsible for updating the study guide). All group members are expected to participate every week.

For the official list of readings and questions, click here

Aug 29

Course overview, syllabus, etc.

Sep 5

Behavioral Ecology, Dr. Vladimir Pravosudov

Trivers, R. L. (1974). Parent-offspring conflict. American zoologist, 14(1), 249-264.

Zahavi, A. (1975). Mate selection—a selection for a handicap. Journal of theoretical Biology, 53(1), 205-214.

Davis, J. M., & Stamps, J. A. (2004). The effect of natal experience on habitat preferences. Trends in Ecology & Evolution, 19(8), 411-416.

Diversity and Neutral Models, Dr. Lee Dyer

Chave, J. (2004). Neutral theory and community ecology. Ecology letters, 7(3), 241-253.

Kraft, N.J., Comita, L.S., Chase, J.M., Sanders, N.J., Swenson, N.G., Crist, T.O., Stegen, J.C., Vellend, M., Boyle, B., Anderson, M.J. and Cornell, H.V., 2011. Disentangling the drivers of β diversity along latitudinal and elevational gradients. Science, 333(6050), pp.1755-1758.

Sep 12

Diseases of wild populations, Dr. Jamie Voyles

Keesing, F., Holt, R. D., & Ostfeld, R. S. (2006). Effects of species diversity on disease risk. Ecology Letters, 9(4), 485-498

Young, H. S., Dirzo, R., Helgen, K. M., McCauley, D. J., Billeter, S. A., Kosoy, M. Y., … & Dittmar, K. (2014). Declines in large wildlife increase landscape-level prevalence of rodent-borne disease in Africa. Proceedings of the National Academy of Sciences, 111(19), 7036-7041

Specialization & niche dynamics, Dr. Matt Forister

Leiby, N., & Marx, C. J. 2014. Metabolic erosion primarily through mutation accumulation, and not tradeoffs, drives limited evolution of substrate specificity in Escherichia coli. PLoS biology, 12(2), e1001789

Poisot, T., Bever, J. D., Nemri, A., Thrall, P. H., & Hochberg, M. E. 2011. A conceptual framework for the evolution of ecological specialisation. Ecology Letters, 14, 841-851

Konuma, J., Sota, T., & Chiba, S. (2013). A maladaptive intermediate form: a strong trade‐off revealed by hybrids between two forms of a snail‐feeding beetle. Ecology, 94(11), 2638-2644

Sep 19

Population ecology, Dr. Kevin Shoemaker

Turchin, P. (2001). Does population ecology have general laws?. Oikos, 94(1), 17-26

Hanski, I. (1998). Metapopulation dynamics. Nature, 396(6706), 41-49

Recommended but not required:

Sibly, R. M., Barker, D., Denham, M. C., Hone, J., & Pagel, M. (2005). On the regulation of populations of mammals, birds, fish, and insects. Science, 309(5734), 607-610

Griffith, A. B., Salguero‐Gómez, R., Merow, C., & McMahon, S. (2016). Demography beyond the population. Journal of Ecology, 104(2), 271-280

Population genetics, Dr. Marjorie Matocq

Wang, I. J., & Bradburd, G. S. (2014). Isolation by environment. Molecular Ecology, 23(23), 5649-5662

Marko, P. B., & Hart, M. W. (2011). The complex analytical landscape of gene flow inference. Trends in ecology & evolution, 26(9), 448-456

Sep 26

Mathematical models for EECB, Dr. Paul Hurtado

Ellner, S. P., & Guckenheimer, J. (2011). Dynamic models in biology. Princeton University Press. Chapter 1 (Ch. 9 also recommended but not required).

Waddington, C. H. (1968). Towards a theoretical biology. Nature, 218(5141), 525-527.

Recommended but not required:

Chowell, G., Viboud, C., Simonsen, L., Merler, S., & Vespignani, A. (2017). Perspectives on model forecasts of the 2014–2015 Ebola epidemic in West Africa: lessons and the way forward. BMC medicine, 15(1), 42.

Landscape Ecology, Dr. Peter Weisberg

Turner, Monica G. 2005. Landscape ecology: what is the state of the science? Ann. Rev. Ecol. Evol. Syst. 36: 319 – 344.

Serra-Diaz, J.M., R.M. Scheller, A.D. Syphard and J. Franklin. 2015. Disturbance and climate refugia mediate tree range shifts during climate change. Landscape Ecology 30: 1039-1053.

Oct 3

Soil Ecology, Dr. Ben Sullivan

Vitousek, P. M., & Reiners, W. A. (1975). Ecosystem succession and nutrient retention: a hypothesis. BioScience, 25(6), 376-381

McGill, W. B., & Cole, C. V. (1981). Comparative aspects of cycling of organic C, N, S and P through soil organic matter. Geoderma, 26(4), 267-286

Wieder, W. R., Bonan, G. B., & Allison, S. D. (2013). Global soil carbon projections are improved by modelling microbial processes. Nature Climate Change, 3(10), 909-912

Microbial Ecology, Dr. David Vuono

Pace, N. R. (2009). Mapping the tree of life: progress and prospects. Microbiology and Molecular Biology Reviews, 73(4), 565-576.

Thompson, J. R., Pacocha, S., Pharino, C., Klepac-Ceraj, V., Hunt, D. E., Benoit, J., … & Polz, M. F. (2005). Genotypic diversity within a natural coastal bacterioplankton population. Science, 307(5713), 1311-1313.

Recommended but not required:

Pepe-Ranney, C., Campbell, A. N., Koechli, C. N., Berthrong, S., & Buckley, D. H. (2016). Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil. Frontiers in microbiology, 7.

Oct 10

Ecoimmunology, Dr. Angela Smilanich

Schulenburg, H., Kurtz, J., Moret, Y., & Siva-Jothy, M. T. (2009). Introduction. ecological immunology. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 364(1513), 3-14

Pamminger, T., Treanor, D., & Hughes, W. O. (2016, January). Pleiotropic effects of juvenile hormone in ant queens and the escape from the reproduction–immunocompetence trade-off. In Proc. R. Soc. B (Vol. 283, No. 1822, p. 20152409). The Royal Society.

Applied evolution, Dr. Beth Leger

Schoener, T. W. (2011). The newest synthesis: understanding the interplay of evolutionary and ecological dynamics. science, 331(6016), 426-429.

Oduor, A. M. (2013). Evolutionary responses of native plant species to invasive plants: a review. New Phytologist, 200(4), 986-992.

Oct 17

Community ecology, Dr. Beth Pringle

Vellend, M. 2016. Chapter 3: A brief history of ideas in community ecology. pp 20-35 in The Theory of Ecological Communities, Princeton University Press: Princeton.

Gotelli, N. J., G.R. Graves, C. Rahbek. 2010. Macroecological signals of species interactions in the Danish avifauna. PNAS 107: 5030-5035

Physiological ecology, Dr. Jack Hayes

Huey, R. B., Kearney, M. R., Krockenberger, A., Holtum, J. A., Jess, M., & Williams, S. E. (2012). Predicting organismal vulnerability to climate warming: roles of behaviour, physiology and adaptation. Phil. Trans. R. Soc. B, 367(1596), 1665-1679.

Kearney, M., & Porter, W. (2009). Mechanistic niche modelling: combining physiological and spatial data to predict species’ ranges. Ecology letters, 12(4), 334-350.

Oct 24

Phenotypic Plasticity, Dr. Jenny Ouyang

Pigliucci M. 2005. Evolution of phenotypic plasticity: where are we going now? Trends in Ecology & Evolution, 20, 481-486.

Pigliucci M. “Phenotypic Plasticity.” In. Evolution: The Extended Synthesis. Eds. Pigliucci and Mueller. 2010. Massachusetts Institute of Technology Press. pgs 355-378.

Charmantier A, Mccleery RH, Cole LR, Perrins C, Kruuk LEB, Sheldon BC (2008) Adaptive phenotypic plasticity in response to climate change in a wild bird population. Science, 320, 800-803.

Chemical Ecology, Dr. Lora Robinson

Salazar, D., Jaramillo, A. & Marquis, R. J. 2016. The impact of plant chemical diversity on plant–herbivore interactions at the community level. Oecologia 181, 1199-1208

Raguso, R. A. et al. The raison d’être of chemical ecology. 2015. Ecology 96, 617-630

Oct 31

Species & speciation, Dr. Matt Forister

Orr, H. A., & Presgraves, D. C. (2000). Speciation by postzygotic isolation: forces, genes and molecules. BioEssays, 22(12), 1085-1094.

Rabosky, D.L. (2016). Reproductive isolation and the causes of speciation rate variation in nature. Biological Journal of the Linnean Society, 118(1), pp.13-25.

Recommended but not required:

Mallet, J. (2008). Hybridization, ecological races and the nature of species: empirical evidence for the ease of speciation. Philosophical Transactions of the Royal Society of London B: Biological Sciences, 363(1506), 2971-2986.

Feder, J. L., Flaxman, S. M., Egan, S. P., Comeault, A. A., & Nosil, P. (2013). Geographic mode of speciation and genomic divergence. Annual Review of Ecology, Evolution, and Systematics, 44, 73-97.

Paleoecology, Dr. Scott Mensing and Dr. Adam Csank

Mensing, S. A., Tunno, I., Sagnotti, L., Florindo, F., Noble, P., Archer, C., … & Piovesan, G. (2015). 2700 years of Mediterranean environmental change in central Italy: a synthesis of sedimentary and cultural records to interpret past impacts of climate on society. Quaternary Science Reviews, 116, 72-94.

Roberts, N. (2013). The Holocene: an environmental history. John Wiley & Sons. Ch. 2.

Recommended but not required:

Flower, Aquila; Gavin, Daniel G.; Heyerdahl, Emily K.; Parsons, Russell A.; and Cohn, Gregory M., “Western Spruce Budworm Outbreaks Did Not Increase Fire Risk over the Last Three Centuries: A Dendrochronological Analysis of Inter-Disturbance Synergism” (2014). Environmental Studies. 26. http://cedar.wwu.edu/envs_facpubs/26

Nov 7

Philosophy of Biology, Dr. Carlos Mariscal

What is a Species?
Ereshefsky, M. (1992). Eliminative pluralism. Philosophy of Science, 59(4), 671-690. Optional: Mishler, B. D., & Brandon, R. N. (1987). Individuality, pluralism, and the phylogenetic species concept. Biology and Philosophy, 2(4), 397-414.

The Extended Evolutionary Synthesis
Laland, K., Wray, G. A., & Hoekstra, H. E. (2014). Does evolutionary theory need a rethink?. Nature, 514(7521), 161. Optional: Laland, K. N., Uller, T., Feldman, M. W., Sterelny, K., Müller, G. B., Moczek, A., … & Odling-Smee, J. (2015, August). The extended evolutionary synthesis: its structure, assumptions and predictions. In Proc. R. Soc. B (Vol. 282, No. 1813, p. 20151019). The Royal Society. Optional: Booth, A., Mariscal, C., & Doolittle, W. F. (2016). The modern synthesis in the light of microbial genomics. Annual review of microbiology, 70, 279-297.

Understanding Function in DNA
Graur, D., Zheng, Y., Price, N., Azevedo, R. B., Zufall, R. A., & Elhaik, E. (2013). On the immortality of television sets:“function” in the human genome according to the evolution-free gospel of ENCODE. Genome biology and evolution, 5(3), 578-590. Optional: Doolittle, W. F., Brunet, T. D., Linquist, S., & Gregory, T. R. (2014). Distinguishing between “function” and “effect” in genome biology. Genome biology and evolution, 6(5), 1234-1237. Optional: Graur, D., Zheng, Y., & Azevedo, R. B. (2015). An evolutionary classification of genomic function. Genome biology and evolution, 7(3), 642-645.

Genomic variation & architecture, Dr. Tom Parchman

Ellegren, H., Smeds, L., Burri, R., Olason, P. I., Backström, N., Kawakami, T., … & Uebbing, S. (2012). The genomic landscape of species divergence in Ficedula flycatchers. Nature, 491(7426), 756-760.

Chapter 2 from: Lynch, M. (2007). The origins of genome architecture (Vol. 98). Sunderland: Sinauer Associates.

Nov 14

Comparative genomics & gene evolution, Dr. David Alvarez-Ponce

Cork, J. M., & Purugganan, M. D. (2004). The evolution of molecular genetic pathways and networks. Bioessays, 26(5), 479-484.

Alvarez-Ponce, D., & McInerney, J. O. (2011). The human genome retains relics of its prokaryotic ancestry: human genes of archaebacterial and eubacterial origin exhibit remarkable differences. Genome biology and evolution, 3, 782-790.

Ecological & evolutionary epigenetics, Dr. David Zeh

Bonilla MM, Zeh JA, Zeh DW. 2016. An epigenetic resolution of the lek paradox. BioEssays 38, 355-366.

Zeh DW, Zeh JA, Ishida Y. 2009. Transposable elements and an epigenetic basis for punctuated equilibria. Bioessays, 31, 715-726.

Nov 21

Conservation Biology and Ecosystem Management, Dr. Sudeep Chandra

Strongly recommended:

Biodiversity, Scientists, and Religious Communities: Conservation Through Collaboration (AAAS news article)

Schaefer, J. (2017). New Hope for the Oceans: Engaging Faith-Based Communities in Marine Conservation. Frontiers in Marine Science, 4, 62.

Bhagwat, S., & Palmer, M. (2009). Conservation: the world’s religions can help. Nature, 461(7260), 37-37.

Additional recommended reading:

Rolston III, H. (2010). Saving Creation: Faith Shaping Environmental Policy. Harv. L. & Pol’y Rev., 4, 121.

Phylogenetics, Dr. Guy Hoelzer

Degnan, J. H., & Rosenberg, N. A. 2009. Gene tree discordance, phylogenetic inference and the multispecies coalescent. Trends in ecology & evolution, 24(6), 332-340

Felsenstein, J. 1988. Phylogenies from molecular sequences: inference and reliability. Annual review of genetics, 22(1), 521-565

Optional: Huelsenbeck, J. P., & Rannala, B. 1997. Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science, 276(5310), 227-232

Nov 28

Global Change and Conservation, Dr. Ken Nussear

Araújo, M. B., & New, M. (2007). Ensemble forecasting of species distributions. Trends in ecology & evolution, 22(1), 42-47.

Kearney, M. (2006). Habitat, environment and niche: what are we modelling?. Oikos, 115(1), 186-191.

Buckley, L. B., Urban, M. C., Angilletta, M. J., Crozier, L. G., Rissler, L. J., & Sears, M. W. (2010). Can mechanism inform species’ distribution models?. Ecology letters, 13(8), 1041-1054.

Dec 5

Final Study Session

Dec 12

Final exam

noon-3pm, MS 227

Closed book (except for one note-sheet); 8 short essays, ~300 words each (max 600 words), with questions chosen from a pool constructed as follows: from each of the 25 topics, I will pick 1-2 questions (so you’ll see a list of ca. 40 questions); I’ll divide that list roughly into three parts (beginning, middle and end of the semester), and you’ll have to pick 3 questions from the first, 3 questions from the middle and 2 questions from the end.

In other words, you have a ton of choice, but you also can’t completely ignore some section of the course!

Although the exam is “closed book” and closed-internet, you can bring one sheet (8.5 x 11) of written notes, with writing on front and back.

I will email you the exam via webcampus at the start of the exam period. Please type your answers directly underneath the questions that you have chosen, and (when you’re all finished) please delete the questions that you have not answered.