Relevant References
To facilitate collaboration and aid in proper attribution of work, please consult this list of references relevant to FATES and its components. Additions, updates and corrections to this list are welcomed. Also, please do not consider this list exhaustive and perform due diligence in attribution of work using FATES.
Users should also consult referencing guides from respective host land models (HLM).
Core References
Fisher, R. A., Muszala, S., Verteinstein, M., Lawrence, P., Xu, C., McDowell, N. G., Knox, R. G., Koven, C., Holm, J., Rogers, B. M., Spessa, A., Lawrence, D., and Bonan, G.: Taking off the training wheels: the properties of a dynamic vegetation model without climate envelopes, CLM4.5(ED), Geosci. Model Dev., 8, 3593-3619, https://doi.org/10.5194/gmd-8-3593-2015, 2015.
Koven, C. D., Knox, R. G., Fisher, R. A., Chambers, J. Q., Christoffersen, B. O., Davies, S. J., Detto, M., Dietze, M. C., Faybishenko, B., Holm, J., Huang, M., Kovenock, M., Kueppers, L. M., Lemieux, G., Massoud, E., McDowell, N. G., Muller-Landau, H. C., Needham, J. F., Norby, R. J., Powell, T., Rogers, A., Serbin, S. P., Shuman, J. K., Swann, A. L. S., Varadharajan, C., Walker, A. P., Wright, S. J., and Xu, C.: Benchmarking and parameter sensitivity of physiological and vegetation dynamics using the Functionally Assembled Terrestrial Ecosystem Simulator (FATES) at Barro Colorado Island, Panama, Biogeosciences, 17, 3017–3044, https://doi.org/10.5194/bg-17-3017-2020, 2020.
Foundation References
ED Patch and Cohort approach: Moorcroft, P.R., G.C. Hurtt, and S.W. Pacala, 2001. A method for scaling vegetation dynamics: the ecosystem demography model ED. Ecological monographs 71.4, pp. 557-586.
Perfect Plasticity Approximation: Purves, D.W. et al., 2008. Predicting and understanding forest dynamics using a simple tractable model. Proceedings of the National Academy of Sciences 105.44, pp. 17018-17022.
Fire
We recommend reaching out to Rosie Fisher and Adrianna Foster if planning to investigate fire modeling.
Fire Model (SPITFIRE): Thonicke, K., Spessa, A., Prentice, I. C., Harrison, S. P., Dong, L., and Carmona-Moreno, C.: The influence of vegetation, fire spread and fire behaviour on biomass burning and trace gas emissions: results from a process-based model, Biogeosciences, 7, 1991-2011, https://doi.org/10.5194/bg-7-1991-2010, 2010.
Logging
Please reference the following if using the logging module.
Huang, M., Xu, Y., Longo, M., Keller, M., Knox, R. G., Koven, C. D., and Fisher, R. A.: Assessing impacts of selective logging on water, energy, and carbon budgets and ecosystem dynamics in Amazon forests using the Functionally Assembled Terrestrial Ecosystem Simulator, Biogeosciences, 17, 4999–5023, https://doi.org/10.5194/bg-17-4999-2020, 2020.
Crown Damage
Please reference the following if using the crown damage module. We recommend reaching out to Jessica Needham if interested in reseearch with crown damage.
Needham, J. F., Arellano, G., Davies, S. J., Fisher, R. A., Hammer, V., Knox, R. G., Mitre, D., Muller-Landau, H. C., Zuleta, D., & Koven, C. D. (2022). Tree crown damage and its effects on forest carbon cycling in a tropical forest. Global Change Biology, 28, 5560–5574. https://doi.org/10.1111/gcb.16318
Recruitment
Please reach out to Adam Hanbury-Brown if performing research or publishing with TRS recruitment dynamics.
Hanbury-Brown, A.R., Powell, T.L., Muller-Landau, H.C., Wright, S.J. and Kueppers, L.M. (2022), Simulating environmentally-sensitive tree recruitment in vegetation demographic models. New Phytologist, 235: 78-93. https://doi.org/10.1111/nph.18059
FATES-Hydro
We recommend reaching out to Brad Christoffersen, Chonggang Xu, Yilin Fang or Junyan Ding if interested in research with FATES-Hydro. Please cite the following (when relevant) :
Foundational:
Xu, C., Christoffersen, B., Robbins, Z., Knox, R., Fisher, R. A., Chitra-Tarak, R., Slot, M., Solander, K., Kueppers, L., Koven, C., and McDowell, N.: Quantification of hydraulic trait control on plant hydrodynamics and risk of hydraulic failure within a demographic structured vegetation model in a tropical forest (FATES-HYDRO V1.0), EGUsphere, https://doi.org/10.5194/egusphere-2023-278, 2023.
Christoffersen, B.O., Gloor, M., Fauset, S., Fyllas, N. M., Galbraith, D. R., Baker, T. R., Kruijt, B., Rowland, L., Fisher, R. A., Binks, O. J., Sevanto, S., Xu, C., Jansen, S., Choat, B., Mencuccini, M., McDowell, N. G., Meir, P. Linking hydraulic traits to tropical forest function in a size-structured and trait-driven model (TFS~v.1-Hydro). Geoscientific Model Development, 9(11), 2016, pp: 4227-4255, https://www.geosci-model-dev.net/9/4227/2016/, DOI = 10.5194/gmd-9-4227-2016.
Matrix Solvers:
Fang Y., L. Leung, R. Knox, C.D. Koven, and B. Bond-Lamberty. 2022. “Impact of the numerical solution approach of a plant hydrodynamic model (v0.1) on vegetation dynamics.” Geoscientific Model Development 15, no. 16:6385-6398. PNNL-SA-172156. doi:10.5194/gmd-15-6385-2022
Advanced Rooting Depth Controls:
Pre-print (update): Ding, J., Buotte, P., Bales, R., Christoffersen, B., Fisher, R. A., Goulden, M., Knox, R., Kueppers, L., Shuman, J., Xu, C., and Koven, C. D.: Coordination of rooting, xylem, and stoma strategies explains the response of conifer forest stands to multi-year drought in the Southern Sierra Nevada of California, Biogeosciences Discuss. [preprint], https://doi.org/10.5194/bg-2023-16, in review, 2023.
Nutrient Model
Please cite the following if using nitrogen or phosphorus limitations with FATES. We recommend reaching out to Ryan Knox, Charles Koven, Anthony Walker, Rosie Fisher and Jennifer Holm if interested in nutrient limitations with FATES.
Pre-print (update): Ryan G Knox, Charles D. Koven, William J. Riley, et al. Nutrient Dynamics in a Coupled Terrestrial Biosphere and Land Model (ELM-FATES). ESS Open Archive . March 06, 2023. DOI: 10.22541/essoar.167810418.80767445/v1
LAI
If you enable variable SLA with crown depth, activated when parameters fates_leaf_slamax != fates_leaf_slatop, please cite the following reference. We recommend reaching out to Marlies Kovenock, Abigail Swann, Charles Koven, Rosie Fisher and Ryan Knox if interested in learning more.
Kovenock, M., Koven, C. D., Knox, R. G., Fisher, R. A., & Swann, A. L. S. (2021). Leaf trait plasticity alters competitive ability and functioning of simulated tropical trees in response to elevated carbon dioxide. Global Biogeochemical Cycles, 35, e2020GB006807. https://doi.org/10.1029/2020GB006807
Allometry
Used when fates_allom_amode = 1, fates_allom_lmode = 1, and provides parameters (if used):
Saldarriaga, J. G., West, D. C., Tharp, M. L., & Uhl, C. (1988). Long-term chronosequence of forest succession in the upper Rio Negro of Colombia and Venezuela. Journal of Ecology, 76(4), 938-958. DOI: 10.2307/2260625
Used when fates_allom_amode = 4, fates_allom_hmode = 4, and provides parameters (if used):
Chave, J. , Réjou‐Méchain, M. , Búrquez, A. , Chidumayo, E. , Colgan, M. S., Delitti, W. B., Duque, A. , Eid, T. , Fearnside, P. M., Goodman, R. C., Henry, M. , Martínez‐Yrízar, A. , Mugasha, W. A., Muller‐Landau, H. C., Mencuccini, M. , Nelson, B. W., Ngomanda, A. , Nogueira, E. M., Ortiz‐Malavassi, E. , Pélissier, R. , Ploton, P. , Ryan, C. M., Saldarriaga, J. G. and Vieilledent, G. (2014), Improved allometric models to estimate the aboveground biomass of tropical trees. Glob Change Biol, 20: 3177-3190. doi:10.1111/gcb.12629
Used when fates_allom_hmode = 3, and provides parameters (if used):
Poorter L, L Bongers and F Bongers. Architecture of 54 moist-forest tree species: traits, trade-offs, and functional groups. Ecology 87(5), 2006.
Used when fates_allom_hmode = 5, and provides parameters (if used):
Martinez Cano, I. and Muller-Landau, H. C. and Wright, S. J. and Bohlman, S. A. and Pacala, S. W. Tropical tree height and crown allometries for the Barro Colorado Nature Monument, Panama: a comparison of alternative hierarchical models incorporating interspecific variation in relation to life history traits, Biogeosciences, 16(4), pp. 847–862, 2019.