1. Covariation & estimation of pars intro to practical part of DEB course 2011 Bas Kooijman Dept theoretical biology Vrije Universiteit Amsterdam Bas@bio.vu.nl http://www.bio.vu.nl/thbhttp://www.bio.vu.nl/thb/ Lisbon, 2011/04/04

2. Scales of life 8a Life span 10 log a Volume 10 log m 3 earth whale bacterium water molecule life on earth whale bacterium ATP molecule 30 20 10 0 -10 -20 -30

3. Primary DEB parameters 2.8a time-length-energy time-length-mass

4. Compound vs primary parameters 8.2.1c

5. Primary scaling relationships 8.2.1 Kooijman 1986 J. Theor. Biol. 121: 269-282

6. Inter-species zoom factor 8.2.1a

7. Body weight 8.2.2 Body weight has contribution from structure and reserve if reproduction buffer is excluded

8. Body composition 3.2a

9. Ash-Free-Dry/Wet Weight 3.2b Relevance for energetics: dry mass ↔ wet volume

10. Feeding rate 8.2.2f slope = 1 poikilothermic tetrapods Data: Farlow 1976 Inter-species: J Xm  V Intra-species: J Xm  V 2/3 Mytilus edulis Data: Winter 1973 Length, cm Filtration rate, l/h

11. Scaling of respiration 8.2.2d Respiration: contributions from growth and maintenance Weight: contributions from structure and reserve Kooijman 1986 J Theor Biol 121: 269-282

12. Metabolic rate 8.2.2e Log weight, g Log metabolic rate, w endotherms ectotherms unicellulars slope = 1 slope = 2/3 Length, cm O 2 consumption,  l/h Inter-species Intra-species 0.0226 L 2 + 0.0185 L 3 0.0516 L 2.44 2 curves fitted: (Daphnia pulex) Data: Hemmingson 1969; curve fitted from DEB theoryData: Richman 1958; curve fitted from DEB theory

13. 25 °C T A = 7 kK 10 log ultimate length, mm 10 log von Bert growth rate, a -1 ↑ ↑ 0 Von Bertalanffy growth rate 8.2.2i

14. One-sample case 2.8d

15. Two-sample case: D. magna 20°C 2.8e Optimality of life history parameters?

16. measured quantities  primary pars 2.8f Standard DEB model (isomorph, 1 reserve, 1 structure) reserve & maturity: hidden variables measured for 2 food levels primary parameters

17. DEBtool/animal/get_pars 2.8g Functions get_pars_* obtain compound DEB parameters from easy-to-observe quantities and the functions iget_pars_* do the reverse, which can be used for checking. The routines are organized as follows: get_pars iget_pars food level one several one several Constraint kJ = kM kJ != kM kJ = kM kJ = kM kJ != kM kJ = kM growth get_pars_g get_pars_h get_pars_i iget_pars_g iget_pars_h iget_pars_iget_pars_gget_pars_hget_pars_iiget_pars_giget_pars_higet_pars_i growth & reprod get_pars_r get_pars_s get_pars_t iget_pars_r iget_pars_s iget_pars_tget_pars_rget_pars_sget_pars_tiget_pars_riget_pars_siget_pars_t Functions for several food levels do not use age at birth data. If one food level is available, we have to make use of the assumption of stage transitions at fixed amounts of structure (k_M = k_J). If several food levels are available, we no longer need to make this assumption, but it does simplify matters considerably. Functions elas_pars_g and elas_pars_r give elasticity coefficients.elas_pars_gelas_pars_r Function get_pars_u converts compound parametersget_pars_u into unscaled primary parameters at abundant food. Kooijman at al 2008 Biol Rev 83: 533-525

18. DEBtool/animal/get_pars 2.8h g get_pars_  iget_pars_  r s h u s h r g red quantities depend on food level, green do not Kooijman at al 2008 Biol Rev 83: 533-525

19. Add_my_pet: Phyton_regius 2.8i weight, g time since birth, d Data by Bart Laarhoven