Material and Content Theoretical Ecology Course 2015

Utrecht, Friday 30 January 2015

• T.J. Case (2000) An Illustrated Guide to Theoretical Ecology
  Oxford UP, ISBN1-800-334-4249

Please consult your library, book shop or other sources to obtain a copy.

Guidance for finding the location: To reach the Buys Ballot building (Room 106), Princetonplein 5, Utrecht, take Bus 12 or 12S (stop: Padualaan) from Utrecht Central Station.

Amsterdam, Monday 2 February 2015

• Kooijman, S. A. L. M. (2010) Summary of concepts of Dynamic Energy Budget Theory for metabolic organisation. .
  This summary skips all mathematics and empirical evidence. A complete description can be found in Kooijman (2010). The book is used in this course as background material. You can order the DEB book for 36 euro via Karin Uyldert. Please do not forget to indicate the details of address and name of recipient to which the book must be sent.
• Sousa, T., Domingos,T. and Kooijman, S. A. L. M. (2010) Formalised (DEB) theory restores coherence in core biology. Phil. Trans. R. Soc. B, 365: 3413-3428
• Kooijman, S. A. L. M. and Troost, T.(2007) Quantitative steps in the evolution of metabolic organisation as specified by the Dynamic Energy Budget theory. Biol. Rev. 82: 1 - 30
• Kooijman, S. A. L. M. (2011) Energy Budgets. In Hastings, A. and Gross, L. (Eds): Sourcebook in Theoretical Ecology: to appear.
• Lika, K., Augustine, S., Pecquerie, L and Kooijman, S. A. L. M. 2014. The bijection from data to parameter space with the standard DEB model quantifies the supply-demand spectrum. J. Theor, Biol.: 354: 35-47

Before arrival read the Energy Budgets paper which summarizes the standard model of the DEB theory.

Guidance for finding the location: We start at 10:00 in Room T550 Vrije Universiteit, W&N Building, De Boelelaan 1081, 1081 HV Amsterdam
From Central Station Amsterdam

• metro tram 51, direction Amstelveen Westwijk (16 minutes), stop at: De Boelelaan/VU
• tram 5, direction Amstelveen Binnenhof (25 minutes), stop at: De Boelelaan/VU tram 16 or 24, direction VUmc, final stop

From Station Amsterdam Zuid

• express tram 51 (1 minute), direction Amstelveen Westwijk
• tram 5 (1 minute), direction Amstelveen Binnenhof
• it's a 10 minute walk to the VU from Station Amsterdam Zuid

Notice that we are NOT in the main building but in the W&N building de Boelelaan entrance 1081.
Enter the main building at the main intrance. Walk straight and leave the main building at the backside (otherwise ask at the information desk in the main building). Enter the W&N building at de Boelelaan 1081. Take the elevator to level 5, and go for the T-wing to room T550.

Leiden, Monday 9 February 2015

• Metz, J.A.J., Roos, A. M. de & Bosch, F. van den (1988) Population models incorporating physiological structure: a quick survey and an application to size structured population dynamics in waterfleas. In: Eberman, B. & Persson, L. (eds), Size-structured populations: ecology and evolution. Berlin, Springer, 106-124
• Roos, A.M. de, Diekmann, O. & Metz, J. A. J. (1992) Studying the dynamics of structured population models: a versatile technique and its application to Daphnia. Am. Nat. 139: 123-147
• Diekmann, O., Gyllenberg, M. & Metz, J. A. J. (2003) Steady State Analysis of Structured Population Models. Theor Pop Biol 63: 309-338
• Diekmann, O., Gyllenberg,M., Metz, J. A. J., Nakaoka, S. & de Roos, A.M. (2010) Daphnia revisited: local stability and bifurcation theory for physiologically structured population models explained by way of an example. J Math Biol. 61: 277-318 DOI 10.1007/s00285-009-0299-y
• Metz, J.A.J. (2008) Fitness. Pp. 1599-1612 in S.E. Jørgensen & B.D. Fath (Eds) Evolutionary Ecology. Vol. 2 of Encyclopedia of Ecology. Elsevier, Oxford
• Metz, JAJ (2011) Thoughts on the geometry of meso-evolution: collecting mathematical elements for a post-modern synthesis. P.197-234 in F. A. C. C. Chalub and J. F. Rodrigues (eds.), The Mathematics of Darwin's Legacy, Birkhauser, Basel.
• Metz JAJ (2012) Adaptive Dynamics. p 7-17 in Alan Hastings & Louis J. Gross eds. Encyclopedia of Theoretical Ecology. California University Press
• Metz, J.A.J. & de Kovel, C.G.F. (2013) The canonical equation of adaptive dynamics for Mendelian diploids and haplo-diploids. Interface Focus 3: 20130025
• M. Gyllenberg, J. A. J. Metz, and R. Service (2011) When do optimisation arguments make evolutionary sense? P. 235-269. In F. A. C. C. Chalub and J. F. Rodrigues (eds.) The Mathematics of Darwin's Legacy, Birkhauser, Basel.

Must read articles are indicated above in bold, other papers provide additional information and are optional.

Guidance for finding the location: Walking from the station to the Sylvius lab takes about 20 minutes. Leave Leiden Central Station in the direction LUMC-Oegstgeest. Cross the small parking lot, and then a little to the left take the road diagonally crossing the lawn (Bontuspad) to end up at a parking garage. Follow the foot and bike path left of that garage (Hippocratespad). After crossing an open area, with quaint little bridges on your left followed by an ugly small pub on your right, you reach a bigger road (Darwinweg). Go right till the roundabout. There take the road to the left (first clockwise, Zernikedreef). After a small bit of walking take the first road to the right (Endegeesterwatering; closed of with a movable barrier for cars). When you have come to a parking lot on your right you can cross the water to the left, to end up in front of the Sylvius building. An alternative is not to take the rather gloomy Endegeesterwatering, but to go right only after the TNO laboratory, over a little bridge, where you already can see the lab, and follow the bike path to the right. The lecture theatre (15.03) is on the first floor, at the right hand side of the corridor behind the first door to the right when you come from the stairs.

Groningen,  Monday 16 February 2015

• C.A. Botero, F.J. Weissing, J. Wright & D.R. Rubenstein (2015): Evolutionary tipping points in the capacity to adapt to environmental change. Proc. Natl. Acad. Sci. USA 112:184-189, doi:10.1073/pnas.1408589111
• I. Pen, T. Uller, B. Feldmeyer, A. Harts, G.M. While & E. Wapstra (2010): Climate driven population divergence in sex-determining systems. Nature 468, 436-439.
• G.S. van Doorn & M. Kirkpatrick (2007): Turnover of sex chromosomes induced by sexual conflict Nature 449, 909-912.
  
  

Guidance for finding the location: Linnaeusborg, Zernike Complex, Groningen; see website. Take the elevator next to the reception desk at the main entrance to the building up to the 8th floor. Turn right out of the elevator and turn right again. You'll see Room 08.80 right in front of you.

Utrecht, Friday 20 February 2015

• Crombach, A. & Hogeweg, P. (2009) Evolution of resource cycling in ecosystems and individuals. BMC Evol. Biol. 9:122 doi: 10.1186/1471-2148-9-122
• Hogeweg, P. (2012) Toward a theory of multilevel evolution: long-term information integration shapes the mutational landscape and enhances evolvability. Adv Exp Med Biol. 751:195-224 doi: 10.1007/978-1-4614-3567-9_10
• Pagie, L. W. P. & Hogeweg, P. (2000) Individual- and population-based diversity in restriction-modification systems. Bull. Math. Biol., 62: 759-774
• Savill, N.J., Rohani, P. & Hogeweg, P. (1997) Self-reinforcing spatial patterns enslave evolution in a host parasitoid system.J. theor. Biol., 188: 11-20

• Takeuchi N. & Hogeweg, P. (2012) Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life. Phys Life Rev., 9(3): 219-263 doi: 10.1016/j.plrev.2012.06.001
• Ten Tusscher, K.H. & Hogeweg, P. (2009) The role of genome and gene regulatory network canalization in the evolution of multi-trait polymorphisms and sympatric speciation. BMC Evol. Biol. 9:15 9 doi: 10.1186/1471-2148-9-159
• Van de Laan, J. D. and Hogeweg, P. (1995) Predator-prey coevolution: interactions among different time scales. Proc. Royal Soc. London B 259: 35-42

Guidance for finding the location: see above; in the morning Room 307 of the Kruyt (Oost) Building, Padualaan 8, de Uithof; in the afternoon Room 112 of the Buys Ballot building, Princetonplein 5, de Uithof, Utrecht (bus 12 or 12S from centraal station Utrecht).