1
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Cusack DF, Christoffersen B, Smith-Martin CM, Andersen KM, Cordeiro AL, Fleischer K, Wright SJ, Guerrero-Ramírez NR, Lugli LF, McCulloch LA, Sanchez-Julia M, Batterman SA, Dallstream C, Fortunel C, Toro L, Fuchslueger L, Wong MY, Yaffar D, Fisher JB, Arnaud M, Dietterich LH, Addo-Danso SD, Valverde-Barrantes OJ, Weemstra M, Ng JC, Norby RJ. Toward a coordinated understanding of hydro-biogeochemical root functions in tropical forests for application in vegetation models. THE NEW PHYTOLOGIST 2024; 242:351-371. [PMID: 38416367 DOI: 10.1111/nph.19561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 01/10/2024] [Indexed: 02/29/2024]
Abstract
Tropical forest root characteristics and resource acquisition strategies are underrepresented in vegetation and global models, hampering the prediction of forest-climate feedbacks for these carbon-rich ecosystems. Lowland tropical forests often have globally unique combinations of high taxonomic and functional biodiversity, rainfall seasonality, and strongly weathered infertile soils, giving rise to distinct patterns in root traits and functions compared with higher latitude ecosystems. We provide a roadmap for integrating recent advances in our understanding of tropical forest belowground function into vegetation models, focusing on water and nutrient acquisition. We offer comparisons of recent advances in empirical and model understanding of root characteristics that represent important functional processes in tropical forests. We focus on: (1) fine-root strategies for soil resource exploration, (2) coupling and trade-offs in fine-root water vs nutrient acquisition, and (3) aboveground-belowground linkages in plant resource acquisition and use. We suggest avenues for representing these extremely diverse plant communities in computationally manageable and ecologically meaningful groups in models for linked aboveground-belowground hydro-nutrient functions. Tropical forests are undergoing warming, shifting rainfall regimes, and exacerbation of soil nutrient scarcity caused by elevated atmospheric CO2. The accurate model representation of tropical forest functions is crucial for understanding the interactions of this biome with the climate.
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Affiliation(s)
- Daniela F Cusack
- Department of Ecosystem Science and Sustainability, Warner College of Natural Resources, Colorado State University, 1231 Libbie Coy Way, A104, Fort Collins, CO, 80523-1476, USA
- Smithsonian Tropical Research Institute, Apartado, Balboa, 0843-03092, Panama
| | - Bradley Christoffersen
- School of Integrative Biological and Chemical Sciences, The University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | - Chris M Smith-Martin
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, 55108, USA
| | | | - Amanda L Cordeiro
- Department of Ecosystem Science and Sustainability, Warner College of Natural Resources, Colorado State University, 1231 Libbie Coy Way, A104, Fort Collins, CO, 80523-1476, USA
- Smithsonian Tropical Research Institute, Apartado, Balboa, 0843-03092, Panama
| | - Katrin Fleischer
- Department Biogeochemical Signals, Max-Planck-Institute for Biogeochemistry, Hans-Knöll-Straße 10, Jena, 07745, Germany
| | - S Joseph Wright
- Smithsonian Tropical Research Institute, Apartado, Balboa, 0843-03092, Panama
| | - Nathaly R Guerrero-Ramírez
- Silviculture and Forest Ecology of Temperate Zones, Faculty of Forest Sciences and Forest Ecology, University of Göttingen, Gottingen, 37077, Germany
- Centre of Biodiversity and Sustainable Land Use (CBL), University of Göttingen, Gottingen, 37077, Germany
| | - Laynara F Lugli
- School of Life Sciences, Technical University of Munich, Freising, 85354, Germany
| | - Lindsay A McCulloch
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
- National Center for Atmospheric Research, National Oceanographic and Atmospheric Agency, 1850 Table Mesa Dr., Boulder, CO, 80305, USA
| | - Mareli Sanchez-Julia
- Department of Ecology and Evolutionary Biology, Tulane University, New Orleans, LA, 70118, USA
| | - Sarah A Batterman
- Smithsonian Tropical Research Institute, Apartado, Balboa, 0843-03092, Panama
- Cary Institute of Ecosystem Studies, Millbrook, NY, 12545, USA
- School of Geography, University of Leeds, Leeds, LS2 9JT, UK
| | - Caroline Dallstream
- Department of Biology, McGill University, 1205 Av. du Docteur-Penfield, Montreal, QC, H3A 1B1, Canada
| | - Claire Fortunel
- AMAP (Botanique et Modélisation de l'Architecture des Plantes et des Végétations), Université de Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, 34398, France
| | - Laura Toro
- Yale Applied Science Synthesis Program, The Forest School at the Yale School of the Environment, Yale University, New Haven, CT, 06511, USA
| | - Lucia Fuchslueger
- Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, 1030, Austria
| | - Michelle Y Wong
- Cary Institute of Ecosystem Studies, Millbrook, NY, 12545, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, 06511, USA
| | - Daniela Yaffar
- Functional Forest Ecology, Universität Hamburg, Barsbüttel, 22885, Germany
| | - Joshua B Fisher
- Schmid College of Science and Technology, Chapman University, 1 University Drive, Orange, CA, 92866, USA
| | - Marie Arnaud
- Institute of Ecology and Environmental Sciences (IEES), UMR 7618, CNRS-Sorbonne University-INRAE-UPEC-IRD, Paris, 75005, France
- School of Geography, Earth and Environmental Sciences & BIFOR, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Lee H Dietterich
- Department of Ecosystem Science and Sustainability, Warner College of Natural Resources, Colorado State University, 1231 Libbie Coy Way, A104, Fort Collins, CO, 80523-1476, USA
- U.S. Army Engineer Research and Development Center, Environmental Laboratory, Vicksburg, MS, 39180, USA
- Department of Biology, Haverford College, Haverford, PA, 19003, USA
| | - Shalom D Addo-Danso
- Forests and Climate Change Division, CSIR-Forestry Research Institute of Ghana, P.O Box UP 63 KNUST, Kumasi, Ghana
| | - Oscar J Valverde-Barrantes
- Department of Biological Sciences, International Center for Tropical Biodiversity, Florida International University, Miami, FL, 33199, USA
| | - Monique Weemstra
- Department of Biological Sciences, International Center for Tropical Biodiversity, Florida International University, Miami, FL, 33199, USA
| | - Jing Cheng Ng
- Nanyang Technological University, Singapore, 639798, Singapore
| | - Richard J Norby
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, 37996, USA
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2
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You Y, Tian H, Pan S, Shi H, Lu C, Batchelor WD, Cheng B, Hui D, Kicklighter D, Liang XZ, Li X, Melillo J, Pan N, Prior SA, Reilly J. Net greenhouse gas balance in U.S. croplands: How can soils be part of the climate solution? GLOBAL CHANGE BIOLOGY 2024; 30:e17109. [PMID: 38273550 DOI: 10.1111/gcb.17109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Revised: 11/22/2023] [Accepted: 12/01/2023] [Indexed: 01/27/2024]
Abstract
Agricultural soils play a dual role in regulating the Earth's climate by releasing or sequestering carbon dioxide (CO2 ) in soil organic carbon (SOC) and emitting non-CO2 greenhouse gases (GHGs) such as nitrous oxide (N2 O) and methane (CH4 ). To understand how agricultural soils can play a role in climate solutions requires a comprehensive assessment of net soil GHG balance (i.e., sum of SOC-sequestered CO2 and non-CO2 GHG emissions) and the underlying controls. Herein, we used a model-data integration approach to understand and quantify how natural and anthropogenic factors have affected the magnitude and spatiotemporal variations of the net soil GHG balance in U.S. croplands during 1960-2018. Specifically, we used the dynamic land ecosystem model for regional simulations and used field observations of SOC sequestration rates and N2 O and CH4 emissions to calibrate, validate, and corroborate model simulations. Results show that U.S. agricultural soils sequestered13.2 ± 1.16 $$ 13.2\pm 1.16 $$ Tg CO2 -C year-1 in SOC (at a depth of 3.5 m) during 1960-2018 and emitted0.39 ± 0.02 $$ 0.39\pm 0.02 $$ Tg N2 O-N year-1 and0.21 ± 0.01 $$ 0.21\pm 0.01 $$ Tg CH4 -C year-1 , respectively. Based on the GWP100 metric (global warming potential on a 100-year time horizon), the estimated national net GHG emission rate from agricultural soils was122.3 ± 11.46 $$ 122.3\pm 11.46 $$ Tg CO2 -eq year-1 , with the largest contribution from N2 O emissions. The sequestered SOC offset ~28% of the climate-warming effects resulting from non-CO2 GHG emissions, and this offsetting effect increased over time. Increased nitrogen fertilizer use was the dominant factor contributing to the increase in net GHG emissions during 1960-2018, explaining ~47% of total changes. In contrast, reduced cropland area, the adoption of agricultural conservation practices (e.g., reduced tillage), and rising atmospheric CO2 levels attenuated net GHG emissions from U.S. croplands. Improving management practices to mitigate N2 O emissions represents the biggest opportunity for achieving net-zero emissions in U.S. croplands. Our study highlights the importance of concurrently quantifying SOC-sequestered CO2 and non-CO2 GHG emissions for developing effective agricultural climate change mitigation measures.
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Affiliation(s)
- Yongfa You
- Center for Earth System Science and Global Sustainability (CES3), Schiller Institute for Integrated Science and Society, Boston College, Chestnut Hill, Massachusetts, USA
- Department of Earth and Environmental Sciences, Boston College, Chestnut Hill, Massachusetts, USA
- College of Forestry, Wildlife and Environment, Auburn University, Auburn, Alabama, USA
| | - Hanqin Tian
- Center for Earth System Science and Global Sustainability (CES3), Schiller Institute for Integrated Science and Society, Boston College, Chestnut Hill, Massachusetts, USA
- Department of Earth and Environmental Sciences, Boston College, Chestnut Hill, Massachusetts, USA
| | - Shufen Pan
- Center for Earth System Science and Global Sustainability (CES3), Schiller Institute for Integrated Science and Society, Boston College, Chestnut Hill, Massachusetts, USA
- College of Forestry, Wildlife and Environment, Auburn University, Auburn, Alabama, USA
- Department of Engineering, Boston College, Chestnut Hill, Massachusetts, USA
| | - Hao Shi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Chaoqun Lu
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, Iowa, USA
| | | | - Bo Cheng
- Biosystems Engineering Department, Auburn University, Auburn, Alabama, USA
| | - Dafeng Hui
- Department of Biological Sciences, Tennessee State University, Nashville, Tennessee, USA
| | - David Kicklighter
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Xin-Zhong Liang
- Department of Atmospheric and Oceanic Science and Earth System Science Interdisciplinary Center, University of Maryland, College Park, Maryland, USA
| | - Xiaoyong Li
- Center for Earth System Science and Global Sustainability (CES3), Schiller Institute for Integrated Science and Society, Boston College, Chestnut Hill, Massachusetts, USA
- Department of Earth and Environmental Sciences, Boston College, Chestnut Hill, Massachusetts, USA
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jerry Melillo
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Naiqing Pan
- Center for Earth System Science and Global Sustainability (CES3), Schiller Institute for Integrated Science and Society, Boston College, Chestnut Hill, Massachusetts, USA
- Department of Earth and Environmental Sciences, Boston College, Chestnut Hill, Massachusetts, USA
| | - Stephen A Prior
- USDA-ARS National Soil Dynamics Laboratory, Auburn, Alabama, USA
| | - John Reilly
- Joint Program on the Science and Policy of Global Change, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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3
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de Koning K, Broekhuijsen J, Kühn I, Ovaskainen O, Taubert F, Endresen D, Schigel D, Grimm V. Digital twins: dynamic model-data fusion for ecology. Trends Ecol Evol 2023; 38:916-926. [PMID: 37208222 DOI: 10.1016/j.tree.2023.04.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 05/21/2023]
Abstract
Digital twins (DTs) are an emerging phenomenon in the public and private sectors as a new tool to monitor and understand systems and processes. DTs have the potential to change the status quo in ecology as part of its digital transformation. However, it is important to avoid misguided developments by managing expectations about DTs. We stress that DTs are not just big models of everything, containing big data and machine learning. Rather, the strength of DTs is in combining data, models, and domain knowledge, and their continuous alignment with the real world. We suggest that researchers and stakeholders exercise caution in DT development, keeping in mind that many of the strengths and challenges of computational modelling in ecology also apply to DTs.
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Affiliation(s)
- Koen de Koning
- Wageningen University and Research, Environmental Systems Analysis Group, P.O. Box 47, 6700, AA, Wageningen, The Netherlands
| | - Jeroen Broekhuijsen
- Nederlandse organisatie voor toegepast natuurwetenschappenlijk onderzoek - TNO, Department of Monitoring & Control Services, Eemsgolaan 3, 9727 DW Groningen, The Netherlands
| | - Ingolf Kühn
- Helmholtz Centre for Environmental Research - UFZ, Department of Community Ecology, Theodor-Lieser-Strasse, 4, 06120 Halle, Germany; Martin Luther University Halle-Wittenberg, Institute for Biology/Geobotany & Botanical Garden, Große Steinstraße 79/80, 06108 Halle, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany
| | - Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35 (Survontie 9C), FI-40014 Jyväskylä, Finland; Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, Helsinki 00014, Finland; Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim N-7491, Norway
| | - Franziska Taubert
- Helmholtz Centre for Environmental Research - UFZ, Department of Ecological Modelling, Permoserstr. 15, 04318 Leipzig, Germany
| | - Dag Endresen
- University of Oslo, Natural History Museum, Sars gate 1, NO-0562 Oslo, Norway.
| | - Dmitry Schigel
- Global Biodiversity Information Facility - GBIF Secreteriat, Universitetsparken 15, DK-2100 Copenhagen Ø, Denmark
| | - Volker Grimm
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstrasse 4, 04103 Leipzig, Germany; Helmholtz Centre for Environmental Research - UFZ, Department of Ecological Modelling, Permoserstr. 15, 04318 Leipzig, Germany; University of Potsdam, Plant Ecology and Nature Conservation, Am Mühlenberg 3, 14476 Potsdam, Germany
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4
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Keetz LT, Lieungh E, Karimi-Asli K, Geange SR, Gelati E, Tang H, Yilmaz YA, Aas KS, Althuizen IHJ, Bryn A, Falk S, Fisher R, Fouilloux A, Horvath P, Indrehus S, Lee H, Lombardozzi D, Parmentier FJW, Pirk N, Vandvik V, Vollsnes AV, Skarpaas O, Stordal F, Tallaksen LM. Climate-ecosystem modelling made easy: The Land Sites Platform. GLOBAL CHANGE BIOLOGY 2023; 29:4440-4452. [PMID: 37303068 DOI: 10.1111/gcb.16808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 05/03/2023] [Indexed: 06/13/2023]
Abstract
Dynamic Global Vegetation Models (DGVMs) provide a state-of-the-art process-based approach to study the complex interplay between vegetation and its physical environment. For example, they help to predict how terrestrial plants interact with climate, soils, disturbance and competition for resources. We argue that there is untapped potential for the use of DGVMs in ecological and ecophysiological research. One fundamental barrier to realize this potential is that many researchers with relevant expertize (ecology, plant physiology, soil science, etc.) lack access to the technical resources or awareness of the research potential of DGVMs. Here we present the Land Sites Platform (LSP): new software that facilitates single-site simulations with the Functionally Assembled Terrestrial Ecosystem Simulator, an advanced DGVM coupled with the Community Land Model. The LSP includes a Graphical User Interface and an Application Programming Interface, which improve the user experience and lower the technical thresholds for installing these model architectures and setting up model experiments. The software is distributed via version-controlled containers; researchers and students can run simulations directly on their personal computers or servers, with relatively low hardware requirements, and on different operating systems. Version 1.0 of the LSP supports site-level simulations. We provide input data for 20 established geo-ecological observation sites in Norway and workflows to add generic sites from public global datasets. The LSP makes standard model experiments with default data easily achievable (e.g., for educational or introductory purposes) while retaining flexibility for more advanced scientific uses. We further provide tools to visualize the model input and output, including simple examples to relate predictions to local observations. The LSP improves access to land surface and DGVM modelling as a building block of community cyberinfrastructure that may inspire new avenues for mechanistic ecosystem research across disciplines.
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Affiliation(s)
- Lasse T Keetz
- Department of Geosciences, University of Oslo, Oslo, Norway
| | - Eva Lieungh
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Sonya R Geange
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | | | - Hui Tang
- Department of Geosciences, University of Oslo, Oslo, Norway
- Natural History Museum, University of Oslo, Oslo, Norway
- Finnish Meteorological Institute, Climate System Research, Helsinki, Finland
| | - Yeliz A Yilmaz
- Department of Geosciences, University of Oslo, Oslo, Norway
- Centre for Biogeochemistry in the Anthropocene, University of Oslo, Oslo, Norway
| | - Kjetil S Aas
- Department of Geosciences, University of Oslo, Oslo, Norway
- CICERO Center for International Climate Research, Oslo, Norway
| | - Inge H J Althuizen
- Division of Climate and Environment, NORCE Norwegian Research Centre, Bergen, Norway
| | - Anders Bryn
- Natural History Museum, University of Oslo, Oslo, Norway
- Centre for Biogeochemistry in the Anthropocene, University of Oslo, Oslo, Norway
| | - Stefanie Falk
- Department of Geography, Ludwig Maximilian University of Munich, Munich, Germany
| | - Rosie Fisher
- CICERO Center for International Climate Research, Oslo, Norway
- Climate and Global Dynamics Laboratory, National Center for Atmospheric Research, Boulder, Colorado, USA
| | | | - Peter Horvath
- Natural History Museum, University of Oslo, Oslo, Norway
| | | | - Hanna Lee
- Division of Climate and Environment, NORCE Norwegian Research Centre, Bergen, Norway
- Department of Biology, Norwegian University of Science and Technology NTNU, Trondheim, Norway
| | - Danica Lombardozzi
- Climate and Global Dynamics Laboratory, National Center for Atmospheric Research, Boulder, Colorado, USA
| | - Frans-Jan W Parmentier
- Department of Geosciences, University of Oslo, Oslo, Norway
- Centre for Biogeochemistry in the Anthropocene, University of Oslo, Oslo, Norway
- Department of Physical Geography and Ecosystem Science, Lund University, Lund, Sweden
| | - Norbert Pirk
- Department of Geosciences, University of Oslo, Oslo, Norway
| | - Vigdis Vandvik
- Department of Biological Sciences, University of Bergen, Bergen, Norway
- Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway
| | - Ane V Vollsnes
- Centre for Biogeochemistry in the Anthropocene, University of Oslo, Oslo, Norway
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Olav Skarpaas
- Natural History Museum, University of Oslo, Oslo, Norway
| | - Frode Stordal
- Department of Geosciences, University of Oslo, Oslo, Norway
- Centre for Biogeochemistry in the Anthropocene, University of Oslo, Oslo, Norway
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5
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Lofton ME, Howard DW, Thomas RQ, Carey CC. Progress and opportunities in advancing near-term forecasting of freshwater quality. GLOBAL CHANGE BIOLOGY 2023; 29:1691-1714. [PMID: 36622168 DOI: 10.1111/gcb.16590] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/23/2022] [Indexed: 05/28/2023]
Abstract
Near-term freshwater forecasts, defined as sub-daily to decadal future predictions of a freshwater variable with quantified uncertainty, are urgently needed to improve water quality management as freshwater ecosystems exhibit greater variability due to global change. Shifting baselines in freshwater ecosystems due to land use and climate change prevent managers from relying on historical averages for predicting future conditions, necessitating near-term forecasts to mitigate freshwater risks to human health and safety (e.g., flash floods, harmful algal blooms) and ecosystem services (e.g., water-related recreation and tourism). To assess the current state of freshwater forecasting and identify opportunities for future progress, we synthesized freshwater forecasting papers published in the past 5 years. We found that freshwater forecasting is currently dominated by near-term forecasts of water quantity and that near-term water quality forecasts are fewer in number and in the early stages of development (i.e., non-operational) despite their potential as important preemptive decision support tools. We contend that more freshwater quality forecasts are critically needed and that near-term water quality forecasting is poised to make substantial advances based on examples of recent progress in forecasting methodology, workflows, and end-user engagement. For example, current water quality forecasting systems can predict water temperature, dissolved oxygen, and algal bloom/toxin events 5 days ahead with reasonable accuracy. Continued progress in freshwater quality forecasting will be greatly accelerated by adapting tools and approaches from freshwater quantity forecasting (e.g., machine learning modeling methods). In addition, future development of effective operational freshwater quality forecasts will require substantive engagement of end users throughout the forecast process, funding, and training opportunities. Looking ahead, near-term forecasting provides a hopeful future for freshwater management in the face of increased variability and risk due to global change, and we encourage the freshwater scientific community to incorporate forecasting approaches in water quality research and management.
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Affiliation(s)
- Mary E Lofton
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - Dexter W Howard
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
| | - R Quinn Thomas
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
- Department of Forest Resources and Environmental Conservation, Virginia Tech, Blacksburg, Virginia, USA
| | - Cayelan C Carey
- Department of Biological Sciences, Virginia Tech, Blacksburg, Virginia, USA
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6
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Slingsby JA, Wilson AM, Maitner B, Moncrieff GR. Regional ecological forecasting across scales: A manifesto for a biodiversity hotspot. Methods Ecol Evol 2023. [DOI: 10.1111/2041-210x.14046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jasper A. Slingsby
- Department of Biological Sciences and Centre for Statistics in Ecology, Environment and Conservation University of Cape Town Cape Town South Africa
- Fynbos Node, South African Environmental Observation Network, Centre for Biodiversity Conservation Cape Town South Africa
| | - Adam M. Wilson
- Department of Geography, Department of Environment and Sustainability University at Buffalo Buffalo New York USA
| | - Brian Maitner
- Department of Geography, Department of Environment and Sustainability University at Buffalo Buffalo New York USA
| | - Glenn R. Moncrieff
- Fynbos Node, South African Environmental Observation Network, Centre for Biodiversity Conservation Cape Town South Africa
- Centre for Statistics in Ecology, Environment and Conservation, Department of Statistical Sciences University of Cape Town Cape Town South Africa
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7
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Halpern BS, Boettiger C, Dietze MC, Gephart JA, Gonzalez P, Grimm NB, Groffman PM, Gurevitch J, Hobbie SE, Komatsu KJ, Kroeker KJ, Lahr HJ, Lodge DM, Lortie CJ, Lowndes JSS, Micheli F, Possingham HP, Ruckelshaus MH, Scarborough C, Wood CL, Wu GC, Aoyama L, Arroyo EE, Bahlai CA, Beller EE, Blake RE, Bork KS, Branch TA, Brown NEM, Brun J, Bruna EM, Buckley LB, Burnett JL, Castorani MCN, Cheng SH, Cohen SC, Couture JL, Crowder LB, Dee LE, Dias AS, Diaz‐Maroto IJ, Downs MR, Dudney JC, Ellis EC, Emery KA, Eurich JG, Ferriss BE, Fredston A, Furukawa H, Gagné SA, Garlick SR, Garroway CJ, Gaynor KM, González AL, Grames EM, Guy‐Haim T, Hackett E, Hallett LM, Harms TK, Haulsee DE, Haynes KJ, Hazen EL, Jarvis RM, Jones K, Kandlikar GS, Kincaid DW, Knope ML, Koirala A, Kolasa J, Kominoski JS, Koricheva J, Lancaster LT, Lawlor JA, Lowman HE, Muller‐Karger FE, Norman KEA, Nourn N, O'Hara CC, Ou SX, Padilla‐Gamino JL, Pappalardo P, Peek RA, Pelletier D, Plont S, Ponisio LC, Portales‐Reyes C, Provete DB, Raes EJ, Ramirez‐Reyes C, Ramos I, Record S, Richardson AJ, Salguero‐Gómez R, Satterthwaite EV, Schmidt C, Schwartz AJ, See CR, Shea BD, Smith RS, Sokol ER, Solomon CT, Spanbauer T, Stefanoudis PV, Sterner BW, Sudbrack V, Tonkin JD, Townes AR, Valle M, Walter JA, Wheeler KI, Wieder WR, Williams DR, Winter M, Winterova B, Woodall LC, Wymore AS, Youngflesh C. Priorities for synthesis research in ecology and environmental science. Ecosphere 2023. [DOI: 10.1002/ecs2.4342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Benjamin S. Halpern
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
- Bren School of Environmental Science and Management University of California Santa Barbara California USA
| | - Carl Boettiger
- Department of Environmental Science, Policy, and Management University of California Berkeley California USA
| | - Michael C. Dietze
- Department of Earth & Environment Boston University Boston Massachusetts USA
| | - Jessica A. Gephart
- Department of Environmental Science American University Washington District of Columbia USA
| | - Patrick Gonzalez
- Department of Environmental Science, Policy, and Management University of California Berkeley California USA
- Institute for Parks, People, and Biodiversity University of California Berkeley California USA
| | - Nancy B. Grimm
- School of Life Sciences Arizona State University Tempe Arizona USA
| | - Peter M. Groffman
- City University of New York Advanced Science Research Center at the Graduate Center New York New York USA
- Cary Institute of Ecosystem Studies Millbrook New York USA
| | - Jessica Gurevitch
- Department of Ecology and Evolution Stony Brook University Stony Brook New York USA
| | - Sarah E. Hobbie
- Department of Ecology, Evolution and Behavior University of Minnesota St. Paul Minnesota USA
| | | | - Kristy J. Kroeker
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz California USA
| | - Heather J. Lahr
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
| | - David M. Lodge
- Cornell Atkinson Center for Sustainability Cornell University Ithaca New York USA
- Department of Ecology and Evolutionary Biology Cornell University Ithaca New York USA
| | - Christopher J. Lortie
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
- Department of Biology York University Toronto Ontario Canada
| | - Julie S. S. Lowndes
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
| | - Fiorenza Micheli
- Hopkins Marine Station, Oceans Department Stanford University Pacific Grove California USA
- Stanford Center for Ocean Solutions Pacific Grove California USA
| | - Hugh P. Possingham
- Centre for Biodiversity and Conservation Science (CBCS) The University of Queensland Brisbane Queensland Australia
| | | | - Courtney Scarborough
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
| | - Chelsea L. Wood
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Grace C. Wu
- Environmental Studies University of California Santa Barbara California USA
| | - Lina Aoyama
- Environmental Studies Program and Department of Biology University of Oregon Eugene Oregon USA
| | - Eva E. Arroyo
- Department of Ecology Evolution and Environmental Biology New York New York USA
| | | | - Erin E. Beller
- Real Estate and Workplace Services Sustainability Team Google Inc. Mountain View California USA
| | | | | | - Trevor A. Branch
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Norah E. M. Brown
- Department of Biology University of Victoria Victoria British Columbia Canada
| | - Julien Brun
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
| | - Emilio M. Bruna
- Department of Wildlife Ecology & Conservation University of Florida Gainesville Florida USA
| | - Lauren B. Buckley
- Department of Biology University of Washington Seattle Washington USA
| | - Jessica L. Burnett
- Core Science Systems Science Analytics and Synthesis U.S. Geological Survey, 8th and Kipling, Denver Federal Center Lakewood Colorado USA
| | - Max C. N. Castorani
- Department of Environmental Sciences University of Virginia Charlottesville Virginia USA
| | - Samantha H. Cheng
- Center for Biodiversity and Conservation American Museum of Natural History New York New York USA
| | - Sarah C. Cohen
- Estuary and Ocean Science Center, Biology Department San Francisco State University San Francisco California USA
| | | | - Larry B. Crowder
- Hopkins Marine Station, Oceans Department Stanford University Pacific Grove California USA
| | - Laura E. Dee
- Department of Ecology and Evolutionary Biology University of Colorado Boulder Colorado USA
| | - Arildo S. Dias
- Department of Physical Geography (IPG) Goethe‐Universität Frankfurt (Campus Riedberg) Frankfurt am Main Germany
| | | | - Martha R. Downs
- National Center for Ecological Analysis and Synthesis University of California Santa Barbara California USA
| | - Joan C. Dudney
- Department of Plant Sciences UC Davis Davis California USA
| | - Erle C. Ellis
- Geography & Environmental Systems University of Maryland Baltimore Maryland USA
| | - Kyle A. Emery
- Department of Geography UC Los Angeles Los Angeles California USA
| | | | - Bridget E. Ferriss
- Resource Ecology and Fisheries Management Division Alaska Fisheries Science Center, National Marine Fisheries Service, NOAA Seattle Washington USA
| | - Alexa Fredston
- Department of Ocean Sciences University of California Santa Cruz California USA
| | - Hikaru Furukawa
- School of Earth and Space Exploration Arizona State University Tempe Arizona USA
| | - Sara A. Gagné
- Department of Geography and Earth Sciences University of North Carolina at Charlotte Charlotte North Carolina USA
| | | | - Colin J. Garroway
- Department of Biological Sciences University of Manitoba Winnipeg Manitoba Canada
| | - Kaitlyn M. Gaynor
- Departments of Zoology and Botany University of British Columbia Vancouver British Columbia Canada
| | - Angélica L. González
- Department of Biology & Center for Computational and Integrative Biology Rutgers University Camden New Jersey USA
| | - Eliza M. Grames
- Department of Biology University of Nevada, Reno Reno Nevada USA
| | - Tamar Guy‐Haim
- National Institute of Oceanography Israel Oceanographic and Limnological Research (IOLR) Haifa Israel
| | - Ed Hackett
- School of Human Evolution & Social Change Arizona State University Tempe Arizona USA
| | - Lauren M. Hallett
- Environmental Studies Program and Department of Biology University of Oregon Eugene Oregon USA
| | - Tamara K. Harms
- Institute of Arctic Biology and Department of Biology & Wildlife University of Alaska Fairbanks Fairbanks Alaska USA
| | - Danielle E. Haulsee
- Hopkins Marine Station, Oceans Department Stanford University Pacific Grove California USA
| | - Kyle J. Haynes
- Blandy Experimental Farm University of Virginia Boyce Virginia USA
| | - Elliott L. Hazen
- Department of Ecology and Evolutionary Biology University of California Santa Cruz Santa Cruz California USA
| | - Rebecca M. Jarvis
- School of Science Auckland University of Technology Auckland New Zealand
| | | | - Gaurav S. Kandlikar
- Division of Biological Sciences & Division of Plant Sciences University of Missouri Columbia Missouri USA
| | - Dustin W. Kincaid
- Vermont EPSCoR and Gund Institute for Environment University of Vermont Burlington Vermont USA
| | - Matthew L. Knope
- Department of Biology University of Hawai'i at Hilo Hilo Hawaii USA
| | - Anil Koirala
- Warnell School of Forestry and Natural Resources University of Georgia Athens Georgia USA
| | - Jurek Kolasa
- Department of Biology McMaster University Hamilton Ontario Canada
| | - John S. Kominoski
- Institute of Environment Florida International University Miami Florida USA
| | - Julia Koricheva
- Department of Biological Sciences Royal Holloway University of London Surrey UK
| | | | - Jake A. Lawlor
- Department of Biology McGill University Montreal Quebec Canada
| | - Heili E. Lowman
- Department of Natural Resources and Environmental Science University of Nevada, Reno Reno Nevada USA
| | | | - Kari E. A. Norman
- Département de sciences biologiques Université de Montréal Montréal Québec Canada
| | - Nan Nourn
- Department of Fisheries and Wildlife Michigan State University East Lansing Michigan USA
| | - Casey C. O'Hara
- Bren School of Environmental Science and Management University of California Santa Barbara California USA
| | - Suzanne X. Ou
- Department of Biology Stanford University Stanford California USA
| | | | - Paula Pappalardo
- Marine Invasions Laboratory Smithsonian Environmental Research Center Tiburon California USA
| | - Ryan A. Peek
- Center for Watershed Sciences University of California Davis California USA
| | - Dominique Pelletier
- UMR DECOD, HALGO, Département Ressources Biologiques et Environnement Institut Français de Recherche pour l'Exploitation de la Mer Lorient France
| | - Stephen Plont
- Department of Biological Sciences Virginia Polytechnic Institute and State University Blacksburg Virginia USA
| | - Lauren C. Ponisio
- Institute of Ecology and Evolution, Department of Biology University of Oregon Eugene Oregon USA
| | | | - Diogo B. Provete
- Instituto de Biociências Universidade Federal de Mato Grosso do Sul Campo Grande Brazil
| | - Eric J. Raes
- Minderoo Foundation, Flourishing Oceans Nedlands Western Australia Australia
| | | | - Irene Ramos
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO) Mexico City Mexico
| | - Sydne Record
- Department of Wildlife, Fisheries, and Conservation Biology University of Maine Orono Maine USA
| | - Anthony J. Richardson
- School of Mathematics and Physics University of Queensland St Lucia Queensland Australia
| | | | - Erin V. Satterthwaite
- California Sea Grant Scripps Institution of Oceanography, University of California, San Diego La Jolla California USA
| | - Chloé Schmidt
- Department of Biological Sciences University of Manitoba Winnipeg Manitoba Canada
| | - Aaron J. Schwartz
- Department of Ecology and Evolutionary Biology University of Colorado Boulder Colorado USA
| | - Craig R. See
- Center for Ecosystem Science and Society Northern Arizona University Flagstaff Arizona USA
| | - Brendan D. Shea
- Department of Fish and Wildlife Conservation Virginia Tech Blacksburg Virginia USA
| | - Rachel S. Smith
- Department of Environmental Sciences University of Virginia Charlottesville Virginia USA
| | - Eric R. Sokol
- Battelle, National Ecological Observatory Network (NEON) Boulder Colorado USA
| | | | - Trisha Spanbauer
- Department of Environmental Sciences/Lake Erie Center University of Toledo Toledo Ohio USA
| | | | | | - Vitor Sudbrack
- Department of Ecology and Evolution University of Lausanne Lausanne Switzerland
| | - Jonathan D. Tonkin
- School of Biological Sciences University of Canterbury Christchurch New Zealand
| | - Ashley R. Townes
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Mireia Valle
- AZTI, Marine Research, Basque Research and Technology Alliance (BRTA) Sukarrieta Spain
| | - Jonathan A. Walter
- Center for Watershed Sciences University of California Davis California USA
| | - Kathryn I. Wheeler
- Department of Earth & Environment Boston University Boston Massachusetts USA
| | - William R. Wieder
- Climate and Global Dynamics Laboratory, Terrestrial Sciences Section National Center for Atmospheric Research Boulder Colorado USA
| | - David R. Williams
- Sustainability Research Institute, School of Earth and Environment University of Leeds Leeds UK
| | - Marten Winter
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐Leipzig Leipzig Germany
| | - Barbora Winterova
- Department of Botany and Zoology, Faculty of Science Masaryk University Brno Czech Republic
| | - Lucy C. Woodall
- School of Aquatic and Fishery Sciences University of Washington Seattle Washington USA
| | - Adam S. Wymore
- Department of Natural Resources and the Environment University of New Hampshire Durham New Hampshire USA
| | - Casey Youngflesh
- Ecology, Evolution, and Behavior Program Michigan State University East Lansing Michigan USA
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8
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Barros C, Luo Y, Chubaty AM, Eddy IMS, Micheletti T, Boisvenue C, Andison DW, Cumming SG, McIntire EJB. Empowering ecological modellers with a
PERFICT
workflow: Seamlessly linking data, parameterisation, prediction, validation and visualisation. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.14034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ceres Barros
- Faculty of Forestry University of British Columbia Vancouver British Columbia Canada
| | - Yong Luo
- Faculty of Forestry University of British Columbia Vancouver British Columbia Canada
- Canadian Forest Service (Pacific Forestry Centre) Natural Resources Canada Victoria British Columbia Canada
- Forest Analysis and Inventory Branch, BC Ministry of Forests, Lands Natural Resource Operations and Rural Development Victoria British Columbia Canada
| | | | - Ian M. S. Eddy
- Canadian Forest Service (Pacific Forestry Centre) Natural Resources Canada Victoria British Columbia Canada
| | - Tatiane Micheletti
- Faculty of Forestry University of British Columbia Vancouver British Columbia Canada
| | - Céline Boisvenue
- Faculty of Forestry University of British Columbia Vancouver British Columbia Canada
- Canadian Forest Service (Pacific Forestry Centre) Natural Resources Canada Victoria British Columbia Canada
| | - David W. Andison
- Bandaloop Landscape‐Ecosystem Services Ltd. Nelson British Columbia Canada
| | - Steven G. Cumming
- Faculté de Foresterie, de Géographie et de Géomatique, Département des Sciences du Bois et de la Forêt, Pavillon Abitibi‐Price Université Laval Québec Canada
| | - Eliot J. B. McIntire
- Faculty of Forestry University of British Columbia Vancouver British Columbia Canada
- Canadian Forest Service (Pacific Forestry Centre) Natural Resources Canada Victoria British Columbia Canada
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9
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Kivi MS, Blakely B, Masters M, Bernacchi CJ, Miguez FE, Dokoohaki H. Development of a data-assimilation system to forecast agricultural systems: A case study of constraining soil water and soil nitrogen dynamics in the APSIM model. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153192. [PMID: 35063525 DOI: 10.1016/j.scitotenv.2022.153192] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
As we face today's large-scale agricultural issues, the need for robust methods of agricultural forecasting has never been clearer. Yet, the accuracy and precision of our forecasts remains limited by current tools and methods. To overcome the limitations of process-based models and observed data, we iteratively designed and tested a generalizable and robust data-assimilation system that systematically constrains state variables in the APSIM model to improve forecast accuracy and precision. Our final novel system utilizes the Ensemble Kalman Filter to constrain model states and update model parameters at observed time steps and incorporates an algorithm that improves system performance through the joint estimation of system error matrices. We tested this system at the Energy Farm, a well-monitored research site in central Illinois, where we assimilated observed in situ soil moisture at daily time steps for two years and evaluated how assimilation impacted model forecasts of soil moisture, yield, leaf area index, tile flow, and nitrate leaching by comparing estimates with in situ observations. The system improved the accuracy and precision of soil moisture estimates for the assimilation layers by an average of 42% and 48%, respectively, when compared to the free model. Such improvements led to changes in the model's soil water and nitrogen processes and, on average, increased accuracy in forecasts of annual tile flow by 43% and annual nitrate loads by 10%. Forecasts of aboveground measures did not dramatically change with assimilation, a fact which highlights the limited potential of soil moisture as a constraint for a site with no water stress. Extending the scope of previous work, our results demonstrate the power of data assimilation to constrain important model estimates beyond the assimilated state variable, such as nitrate leaching. Replication of this study is necessary to further define the limitations and opportunities of the developed system.
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Affiliation(s)
- Marissa S Kivi
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Turner Hall AW-101, 1102 S Goodwin Ave, Urbana, IL 61801, USA.
| | - Bethany Blakely
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Morrill Hall, 505 S. Goodwin Ave, Urbana, IL 61801, USA; Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801, USA.
| | - Michael Masters
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Morrill Hall, 505 S. Goodwin Ave, Urbana, IL 61801, USA; Institute for Sustainability, Energy and Environment, University of Illinois at Urbana-Champaign, 1101 W. Peabody, Suite 350, Urbana, IL 61801, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL 61801, USA.
| | - Carl J Bernacchi
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Turner Hall AW-101, 1102 S Goodwin Ave, Urbana, IL 61801, USA; Department of Plant Biology, University of Illinois at Urbana-Champaign, Morrill Hall, 505 S. Goodwin Ave, Urbana, IL 61801, USA; Global Change and Photosynthesis Research, USDA-ARS, Urbana, IL 61801, USA.
| | - Fernando E Miguez
- Department of Agronomy, Iowa State University, Agronomy Hall 1206, 716 Farm House Ln, Ames, IA 50011, USA.
| | - Hamze Dokoohaki
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Turner Hall AW-101, 1102 S Goodwin Ave, Urbana, IL 61801, USA.
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10
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McIntire EJB, Chubaty AM, Cumming SG, Andison D, Barros C, Boisvenue C, Haché S, Luo Y, Micheletti T, Stewart FEC. PERFICT: A Re-imagined foundation for predictive ecology. Ecol Lett 2022; 25:1345-1351. [PMID: 35315961 PMCID: PMC9310704 DOI: 10.1111/ele.13994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/02/2022]
Abstract
Making predictions from ecological models—and comparing them to data—offers a coherent approach to evaluate model quality, regardless of model complexity or modelling paradigm. To date, our ability to use predictions for developing, validating, updating, integrating and applying models across scientific disciplines while influencing management decisions, policies, and the public has been hampered by disparate perspectives on prediction and inadequately integrated approaches. We present an updated foundation for Predictive Ecology based on seven principles applied to ecological modelling: make frequent Predictions, Evaluate models, make models Reusable, Freely accessible and Interoperable, built within Continuous workflows that are routinely Tested (PERFICT). We outline some benefits of working with these principles: accelerating science; linking with data science; and improving science‐policy integration.
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Affiliation(s)
- Eliot J B McIntire
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia, Canada.,Faculty of Forestry, Forest Resources Management, The University of British Columbia, Vancouver, British Columbia, Canada.,Département des sciences du bois et de la forêt, Pavillon Abitibi-Price, 2405, rue de la Terrasse, Université Laval, Québec City, Québec, Canada
| | - Alex M Chubaty
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia, Canada.,Département des sciences du bois et de la forêt, Pavillon Abitibi-Price, 2405, rue de la Terrasse, Université Laval, Québec City, Québec, Canada.,FOR-CAST Research & Analytics, Calgary, Alberta, Canada
| | - Steven G Cumming
- Département des sciences du bois et de la forêt, Pavillon Abitibi-Price, 2405, rue de la Terrasse, Université Laval, Québec City, Québec, Canada
| | - Dave Andison
- Faculty of Forestry, Forest Resources Management, The University of British Columbia, Vancouver, British Columbia, Canada.,Bandaloop Landscape-Ecosystem Services Ltd., Nelson, British Columbia, Canada
| | - Ceres Barros
- Faculty of Forestry, Forest Resources Management, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Céline Boisvenue
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia, Canada.,Faculty of Forestry, Forest Resources Management, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Samuel Haché
- Canadian Wildlife Service, Environment and Climate Change Canada, Yellowknife, Northwest Territories, Canada
| | - Yong Luo
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia, Canada.,Forest Analysis and Inventory Branch, BC Ministry of Forests, Victoria, British Columbia, Canada
| | - Tatiane Micheletti
- Faculty of Forestry, Forest Resources Management, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Frances E C Stewart
- Pacific Forestry Centre, Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia, Canada.,University of Victoria, School of Environmental Studies, Victoria, British Columbia, Canada.,Department of Biology, Wilfrid Laurier University, Waterloo, Ontario, Canada
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11
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Guidelines for Publicly Archiving Terrestrial Model Data to Enhance Usability, Intercomparison, and Synthesis. DATA SCIENCE JOURNAL 2022. [DOI: 10.5334/dsj-2022-003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
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12
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Fisher JB, Sikka M, Block GL, Schwalm CR, Parazoo NC, Kolus HR, Sok M, Wang A, Gagne‐Landmann A, Lawal S, Guillaume A, Poletti A, Schaefer KM, El Masri B, Levy PE, Wei Y, Dietze MC, Huntzinger DN. The Terrestrial Biosphere Model Farm. JOURNAL OF ADVANCES IN MODELING EARTH SYSTEMS 2022; 14:e2021MS002676. [PMID: 35860620 PMCID: PMC9285607 DOI: 10.1029/2021ms002676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 06/15/2023]
Abstract
Model Intercomparison Projects (MIPs) are fundamental to our understanding of how the land surface responds to changes in climate. However, MIPs are challenging to conduct, requiring the organization of multiple, decentralized modeling teams throughout the world running common protocols. We explored centralizing these models on a single supercomputing system. We ran nine offline terrestrial biosphere models through the Terrestrial Biosphere Model Farm: CABLE, CENTURY, HyLand, ISAM, JULES, LPJ-GUESS, ORCHIDEE, SiB-3, and SiB-CASA. All models were wrapped in a software framework driven with common forcing data, spin-up, and run protocols specified by the Multi-scale Synthesis and Terrestrial Model Intercomparison Project (MsTMIP) for years 1901-2100. We ran more than a dozen model experiments. We identify three major benefits and three major challenges. The benefits include: (a) processing multiple models through a MIP is relatively straightforward, (b) MIP protocols are run consistently across models, which may reduce some model output variability, and (c) unique multimodel experiments can provide novel output for analysis. The challenges are: (a) technological demand is large, particularly for data and output storage and transfer; (b) model versions lag those from the core model development teams; and (c) there is still a need for intellectual input from the core model development teams for insight into model results. A merger with the open-source, cloud-based Predictive Ecosystem Analyzer (PEcAn) ecoinformatics system may be a path forward to overcoming these challenges.
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Affiliation(s)
- Joshua B. Fisher
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
- Schmid College of Science and TechnologyChapman UniversityOrangeCAUSA
| | - Munish Sikka
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | - Gary L. Block
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | | | | | - Hannah R. Kolus
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | - Malen Sok
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | - Audrey Wang
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | | | - Shakirudeen Lawal
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | | | - Alyssa Poletti
- Jet Propulsion LaboratoryCalifornia Institute of TechnologyPasadenaCAUSA
| | - Kevin M. Schaefer
- National Snow and Ice Data CenterCooperative Institute for Research in Environmental SciencesUniversity of ColoradoBoulderCOUSA
| | - Bassil El Masri
- Department of Earth and Environmental SciencesMurray State UniversityMurrayKYUSA
| | | | - Yaxing Wei
- Environmental Sciences DivisionOak Ridge National LaboratoryClimate Change Science InstituteOak RidgeTNUSA
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13
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Kyker‐Snowman E, Lombardozzi DL, Bonan GB, Cheng SJ, Dukes JS, Frey SD, Jacobs EM, McNellis R, Rady JM, Smith NG, Thomas RQ, Wieder WR, Grandy AS. Increasing the spatial and temporal impact of ecological research: A roadmap for integrating a novel terrestrial process into an Earth system model. GLOBAL CHANGE BIOLOGY 2022; 28:665-684. [PMID: 34543495 PMCID: PMC9293342 DOI: 10.1111/gcb.15894] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/17/2021] [Indexed: 06/13/2023]
Abstract
Terrestrial ecosystems regulate Earth's climate through water, energy, and biogeochemical transformations. Despite a key role in regulating the Earth system, terrestrial ecology has historically been underrepresented in the Earth system models (ESMs) that are used to understand and project global environmental change. Ecology and Earth system modeling must be integrated for scientists to fully comprehend the role of ecological systems in driving and responding to global change. Ecological insights can improve ESM realism and reduce process uncertainty, while ESMs offer ecologists an opportunity to broadly test ecological theory and increase the impact of their work by scaling concepts through time and space. Despite this mutualism, meaningfully integrating the two remains a persistent challenge, in part because of logistical obstacles in translating processes into mathematical formulas and identifying ways to integrate new theories and code into large, complex model structures. To help overcome this interdisciplinary challenge, we present a framework consisting of a series of interconnected stages for integrating a new ecological process or insight into an ESM. First, we highlight the multiple ways that ecological observations and modeling iteratively strengthen one another, dispelling the illusion that the ecologist's role ends with initial provision of data. Second, we show that many valuable insights, products, and theoretical developments are produced through sustained interdisciplinary collaborations between empiricists and modelers, regardless of eventual inclusion of a process in an ESM. Finally, we provide concrete actions and resources to facilitate learning and collaboration at every stage of data-model integration. This framework will create synergies that will transform our understanding of ecology within the Earth system, ultimately improving our understanding of global environmental change, and broadening the impact of ecological research.
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Affiliation(s)
- Emily Kyker‐Snowman
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew HampshireUSA
| | - Danica L. Lombardozzi
- Climate and Global Dynamics LaboratoryNational Center for Atmospheric ResearchBoulderColoradoUSA
| | - Gordon B. Bonan
- Climate and Global Dynamics LaboratoryNational Center for Atmospheric ResearchBoulderColoradoUSA
| | - Susan J. Cheng
- Department of Ecology and Evolutionary Biology and Center for Research on Learning and TeachingUniversity of MichiganAnn ArborMichiganUSA
| | - Jeffrey S. Dukes
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteIndianaUSA
- Department of Biological SciencesPurdue UniversityWest LafayetteIndianaUSA
| | - Serita D. Frey
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew HampshireUSA
| | - Elin M. Jacobs
- Department of Forestry and Natural ResourcesPurdue UniversityWest LafayetteIndianaUSA
| | - Risa McNellis
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
| | - Joshua M. Rady
- Department of Forest Resources and Environmental ConservationVirginia TechBlacksburgVirginiaUSA
| | - Nicholas G. Smith
- Department of Biological SciencesTexas Tech UniversityLubbockTexasUSA
| | - R. Quinn Thomas
- Department of Forest Resources and Environmental ConservationVirginia TechBlacksburgVirginiaUSA
| | - William R. Wieder
- Climate and Global Dynamics LaboratoryNational Center for Atmospheric ResearchBoulderColoradoUSA
- Institute of Arctic and Alpine ResearchUniversity of ColoradoBoulderColoradoUSA
| | - A. Stuart Grandy
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew HampshireUSA
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14
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Bodner K, Rauen Firkowski C, Bennett JR, Brookson C, Dietze M, Green S, Hughes J, Kerr J, Kunegel‐Lion M, Leroux SJ, McIntire E, Molnár PK, Simpkins C, Tekwa E, Watts A, Fortin M. Bridging the divide between ecological forecasts and environmental decision making. Ecosphere 2021. [DOI: 10.1002/ecs2.3869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Korryn Bodner
- Department of Ecology and Evolution University of Toronto Toronto Ontario Canada
- Department of Biological Sciences University of Toronto Scarborough Toronto Ontario Canada
| | - Carina Rauen Firkowski
- Department of Ecology and Evolution University of Toronto Toronto Ontario Canada
- Department of Biology McGill University Montreal Quebec Canada
| | | | - Cole Brookson
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Michael Dietze
- Department of Earth & Environment Boston University Boston Massachusetts USA
| | - Stephanie Green
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Josie Hughes
- National Wildlife Research Centre Environment and Climate Change Canada Ottawa Ontario Canada
| | - Jeremy Kerr
- Department of Biology University of Ottawa Ottawa Ontario Canada
| | - Mélodie Kunegel‐Lion
- Canadian Forest Service Northern Forestry Centre Natural Resources Canada Edmonton Alberta Canada
| | - Shawn J. Leroux
- Department of Biology Memorial University of Newfoundland St. John’s Newfoundland Canada
| | - Eliot McIntire
- Canadian Forest Service Pacific Forestry Centre Natural Resources Canada Victoria British Columbia Canada
- Faculty of Forestry Forest Resources Management University of British Columbia Vancouver British Columbia Canada
| | - Péter K. Molnár
- Department of Ecology and Evolution University of Toronto Toronto Ontario Canada
- Department of Biological Sciences University of Toronto Scarborough Toronto Ontario Canada
| | - Craig Simpkins
- School of Environment University of Auckland Auckland New Zealand
- Department of Biology Wilfrid Laurier University Waterloo Ontario Canada
- Department of Ecological Modelling Georg‐August University of Goettingen Goettingen Germany
| | - Edward Tekwa
- Department of Zoology University of British Columbia Vancouver British Columbia Canada
| | | | - Marie‐Josée Fortin
- Department of Ecology and Evolution University of Toronto Toronto Ontario Canada
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15
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Raiho AM, Nicklen EF, Foster AC, Roland CA, Hooten MB. Bridging implementation gaps to connect large ecological datasets and complex models. Ecol Evol 2021; 11:18271-18287. [PMID: 35003672 PMCID: PMC8717344 DOI: 10.1002/ece3.8420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/12/2021] [Accepted: 11/16/2021] [Indexed: 11/09/2022] Open
Abstract
Merging robust statistical methods with complex simulation models is a frontier for improving ecological inference and forecasting. However, bringing these tools together is not always straightforward. Matching data with model output, determining starting conditions, and addressing high dimensionality are some of the complexities that arise when attempting to incorporate ecological field data with mechanistic models directly using sophisticated statistical methods. To illustrate these complexities and pragmatic paths forward, we present an analysis using tree-ring basal area reconstructions in Denali National Park (DNPP) to constrain successional trajectories of two spruce species (Picea mariana and Picea glauca) simulated by a forest gap model, University of Virginia Forest Model Enhanced-UVAFME. Through this process, we provide preliminary ecological inference about the long-term competitive dynamics between slow-growing P. mariana and relatively faster-growing P. glauca. Incorporating tree-ring data into UVAFME allowed us to estimate a bias correction for stand age with improved parameter estimates. We found that higher parameter values for P. mariana minimum growth under stress and P. glauca maximum growth rate were key to improving simulations of coexistence, agreeing with recent research that faster-growing P. glauca may outcompete P. mariana under climate change scenarios. The implementation challenges we highlight are a crucial part of the conversation for how to bring models together with data to improve ecological inference and forecasting.
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Affiliation(s)
- Ann M. Raiho
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
| | - E. Fleur Nicklen
- Denali National Park and PreserveNational Park ServiceFairbanksAlaskaUSA
| | - Adrianna C. Foster
- School of Informatics, Computing, and Cyber SystemsNorthern Arizona UniversityFlagstaffArizonaUSA
| | - Carl A. Roland
- Denali National Park and PreserveNational Park ServiceFairbanksAlaskaUSA
| | - Mevin B. Hooten
- Department of Fish, Wildlife, and Conservation BiologyColorado State UniversityFort CollinsColoradoUSA
- Department of StatisticsColorado State UniversityFort CollinsColoradoUSA
- Colorado Cooperative Fish and Wildlife Research UnitU.S. Geological SurveyFort CollinsColoradoUSA
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16
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Wang Z, Gong H, Huang M, Gu F, Wei J, Guo Q, Song W. A multimodel random forest ensemble method for an improved assessment of Chinese terrestrial vegetation carbon density. Methods Ecol Evol 2021. [DOI: 10.1111/2041-210x.13729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Zhaosheng Wang
- National Ecosystem Science Data Center Key Laboratory of Ecosystem Network Observation and Modeling Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences Beijing China
| | - He Gong
- National Ecosystem Science Data Center Key Laboratory of Ecosystem Network Observation and Modeling Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences Beijing China
| | - Mei Huang
- National Ecosystem Science Data Center Key Laboratory of Ecosystem Network Observation and Modeling Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences Beijing China
| | - Fengxue Gu
- Key Laboratory of Dryland Agriculture Ministry of Agriculture Institute of Environment and Sustainable Development in Agriculture Chinese Academy of Agricultural Sciences Beijing China
| | - Jie Wei
- National Ecosystem Science Data Center Key Laboratory of Ecosystem Network Observation and Modeling Institute of Geographic Sciences and Natural Resources Research Chinese Academy of Sciences Beijing China
| | - Qingchun Guo
- School of Environment and Planning Liaocheng University Liaocheng China
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17
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Urban MC, Travis JMJ, Zurell D, Thompson PL, Synes NW, Scarpa A, Peres-Neto PR, Malchow AK, James PMA, Gravel D, De Meester L, Brown C, Bocedi G, Albert CH, Gonzalez A, Hendry AP. Coding for Life: Designing a Platform for Projecting and Protecting Global Biodiversity. Bioscience 2021. [DOI: 10.1093/biosci/biab099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Time is running out to limit further devastating losses of biodiversity and nature's contributions to humans. Addressing this crisis requires accurate predictions about which species and ecosystems are most at risk to ensure efficient use of limited conservation and management resources. We review existing biodiversity projection models and discover problematic gaps. Current models usually cannot easily be reconfigured for other species or systems, omit key biological processes, and cannot accommodate feedbacks with Earth system dynamics. To fill these gaps, we envision an adaptable, accessible, and universal biodiversity modeling platform that can project essential biodiversity variables, explore the implications of divergent socioeconomic scenarios, and compare conservation and management strategies. We design a roadmap for implementing this vision and demonstrate that building this biodiversity forecasting platform is possible and practical.
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Affiliation(s)
- Mark C Urban
- University of Connecticut, Storrs, Connecticut, United States
| | | | | | | | | | - Alice Scarpa
- University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | | | | | | | | | - Luc De Meester
- Laboratory of Aquatic Ecology, Evolution, and Conservation, KU Leuven, Leuven, Belgium, with the Leibniz-Institut für Gewässerökologie und Binnenfischerei, Berlin, Germany, and with the Institute of Biology, Freie Universität Berlin, Berlin, Germany
| | - Calum Brown
- IMK-IFU, Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany
| | - Greta Bocedi
- University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Cécile H Albert
- Aix Marseille Univ, CNRS, Univ Avignon, IRD, IMBE, Marseille, France
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18
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Banbury Morgan R, Herrmann V, Kunert N, Bond-Lamberty B, Muller-Landau HC, Anderson-Teixeira KJ. Global patterns of forest autotrophic carbon fluxes. GLOBAL CHANGE BIOLOGY 2021; 27:2840-2855. [PMID: 33651480 DOI: 10.1111/gcb.15574] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
Carbon (C) fixation, allocation, and metabolism by trees set the basis for energy and material flows in forest ecosystems and define their interactions with Earth's changing climate. However, while many studies have considered variation in productivity with latitude and climate, we lack a cohesive synthesis on how forest carbon fluxes vary globally with respect to climate and one another. Here, we draw upon 1,319 records from the Global Forest Carbon Database, representing all major forest types and the nine most significant autotrophic carbon fluxes, to comprehensively review how annual C cycling in mature, undisturbed forests varies with latitude and climate on a global scale. Across all flux variables analyzed, rates of C cycling decreased continuously with absolute latitude-a finding that confirms multiple previous studies and contradicts the idea that net primary productivity of temperate forests rivals that of tropical forests. C flux variables generally displayed similar trends across latitude and multiple climate variables, with no differences in allocation detected at this global scale. Temperature variables in general, and mean annual temperature or temperature seasonality in particular, were the best single predictors of C flux, explaining 19%-71% of variation in the C fluxes analyzed. The effects of temperature were modified by moisture availability, with C flux reduced under hot and dry conditions and sometimes under very high precipitation. Annual C fluxes increased with growing season length and were also influenced by growing season climate. These findings clarify how forest C flux varies with latitude and climate on a global scale. In an era when forests will play a critical yet uncertain role in shaping Earth's rapidly changing climate, our synthesis provides a foundation for understanding global patterns in forest C cycling.
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Affiliation(s)
- Rebecca Banbury Morgan
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
- School of Geography, University of Leeds, Leeds, UK
| | - Valentine Herrmann
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
| | - Norbert Kunert
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama, Republic of Panama
- Institute of Botany, University of Natural Resources and Applied Life Sciences, Vienna, Austria
| | - Ben Bond-Lamberty
- Joint Global Change Research Institute, Pacific Northwest National Laboratory, College Park, MD, USA
| | - Helene C Muller-Landau
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama, Republic of Panama
| | - Kristina J Anderson-Teixeira
- Conservation Ecology Center, Smithsonian Conservation Biology Institute, Front Royal, VA, USA
- Forest Global Earth Observatory, Smithsonian Tropical Research Institute, Panama, Republic of Panama
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