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1. Traits.build: A data model, workflow and R package for building harmonised ecological trait databases

Author

Elizabeth Wenk, Payal Bal, David Coleman, Rachael Gallagher, Sophie Yang, and Daniel Falster

Subjects
Trait database, FAIR data principles, Database model, R package, Trait ecology, Information technology, T58.5-58.64, Ecology, QH540-549.5
Abstract

Trait databases have proliferated over the past decades, facilitating research on the ecology, evolution, and conservation of taxa across the Tree of Life. Typically, teams of independent researchers build these databases, and each must develop their own workflow and output structure. This divests research hours from downstream tasks such as trait-based analysis and interpretation and the resultant datasets are often difficult to integrate due to disparate database structures. Here we introduce the {traits.build} R-package, which offers a generalised workflow for building trait databases. {traits.build} contains bespoke functions for propagating metadata files, extensive tutorials, and sample configuration files, allowing researchers to efficiently build a new trait database using open-source tools. In addition, the {traits.build} output structure is fully documented by a data model, ensuring the meaning of each variable and semantic relationship between variables is transparent and consistent. The data standard links to terms in previously published data standards, drawing strongly on DarwinCore and the Ecological Trait-data Standard, but also includes the ability to fully map location and context properties absent from these vocabularies. It is the first published database-building workflow that adheres to the Extensible Observation Ontology. Simultaneously developing a generalised workflow and publishing a data standard for the workflow provides {traits.build} users a straightforward pathway to build a new trait database that achieves the FAIR principles. The meaning of all variables in a {traits.build} database are already documented, allowing further integration with either other {traits.build} databases or indeed any other database with a documented data model. This follows the vision of the Open Traits Network to build trait databases whose data can be easily integrated for further analysis.

Published
2024
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2. AnimalTraits - a curated animal trait database for body mass, metabolic rate and brain size

Author

Marie E. Herberstein, Donald James McLean, Elizabeth Lowe, Jonas O. Wolff, Md Kawsar Khan, Kaitlyn Smith, Andrew P. Allen, Matthew Bulbert, Bruno A. Buzatto, Mark D. B. Eldridge, Daniel Falster, Laura Fernandez Winzer, Simon C. Griffith, Joshua S. Madin, Ajay Narendra, Mark Westoby, Martin J. Whiting, Ian J. Wright, and Alexandra J. R. Carthey

Subjects
Science
Abstract

Measurement(s) metabolic rate quantification • body mass • brain size Technology Type(s) metabolic rate measurement • body mass quantification • brain mass brain volume

Published
2022
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3. AusTraits, a curated plant trait database for the Australian flora

Author

Daniel Falster, Rachael Gallagher, Elizabeth H. Wenk, Ian J. Wright, Dony Indiarto, Samuel C. Andrew, Caitlan Baxter, James Lawson, Stuart Allen, Anne Fuchs, Anna Monro, Fonti Kar, Mark A. Adams, Collin W. Ahrens, Matthew Alfonzetti, Tara Angevin, Deborah M. G. Apgaua, Stefan Arndt, Owen K. Atkin, Joe Atkinson, Tony Auld, Andrew Baker, Maria von Balthazar, Anthony Bean, Chris J. Blackman, Keith Bloomfield, David M. J. S. Bowman, Jason Bragg, Timothy J. Brodribb, Genevieve Buckton, Geoff Burrows, Elizabeth Caldwell, James Camac, Raymond Carpenter, Jane A. Catford, Gregory R. Cawthray, Lucas A. Cernusak, Gregory Chandler, Alex R. Chapman, David Cheal, Alexander W. Cheesman, Si-Chong Chen, Brendan Choat, Brook Clinton, Peta L. Clode, Helen Coleman, William K. Cornwell, Meredith Cosgrove, Michael Crisp, Erika Cross, Kristine Y. Crous, Saul Cunningham, Timothy Curran, Ellen Curtis, Matthew I. Daws, Jane L. DeGabriel, Matthew D. Denton, Ning Dong, Pengzhen Du, Honglang Duan, David H. Duncan, Richard P. Duncan, Marco Duretto, John M. Dwyer, Cheryl Edwards, Manuel Esperon-Rodriguez, John R. Evans, Susan E. Everingham, Claire Farrell, Jennifer Firn, Carlos Roberto Fonseca, Ben J. French, Doug Frood, Jennifer L. Funk, Sonya R. Geange, Oula Ghannoum, Sean M. Gleason, Carl R. Gosper, Emma Gray, Philip K. Groom, Saskia Grootemaat, Caroline Gross, Greg Guerin, Lydia Guja, Amy K. Hahs, Matthew Tom Harrison, Patrick E. Hayes, Martin Henery, Dieter Hochuli, Jocelyn Howell, Guomin Huang, Lesley Hughes, John Huisman, Jugoslav Ilic, Ashika Jagdish, Daniel Jin, Gregory Jordan, Enrique Jurado, John Kanowski, Sabine Kasel, Jürgen Kellermann, Belinda Kenny, Michele Kohout, Robert M. Kooyman, Martyna M. Kotowska, Hao Ran Lai, Etienne Laliberté, Hans Lambers, Byron B. Lamont, Robert Lanfear, Frank van Langevelde, Daniel C. Laughlin, Bree-Anne Laugier-Kitchener, Susan Laurance, Caroline E. R. Lehmann, Andrea Leigh, Michelle R. Leishman, Tanja Lenz, Brendan Lepschi, James D. Lewis, Felix Lim, Udayangani Liu, Janice Lord, Christopher H. Lusk, Cate Macinnis-Ng, Hannah McPherson, Susana Magallón, Anthony Manea, Andrea López-Martinez, Margaret Mayfield, James K. McCarthy, Trevor Meers, Marlien van der Merwe, Daniel J. Metcalfe, Per Milberg, Karel Mokany, Angela T. Moles, Ben D. Moore, Nicholas Moore, John W. Morgan, William Morris, Annette Muir, Samantha Munroe, Áine Nicholson, Dean Nicolle, Adrienne B. Nicotra, Ülo Niinemets, Tom North, Andrew O’Reilly-Nugent, Odhran S. O’Sullivan, Brad Oberle, Yusuke Onoda, Mark K. J. Ooi, Colin P. Osborne, Grazyna Paczkowska, Burak Pekin, Caio Guilherme Pereira, Catherine Pickering, Melinda Pickup, Laura J. Pollock, Pieter Poot, Jeff R. Powell, Sally A. Power, Iain Colin Prentice, Lynda Prior, Suzanne M. Prober, Jennifer Read, Victoria Reynolds, Anna E. Richards, Ben Richardson, Michael L. Roderick, Julieta A. Rosell, Maurizio Rossetto, Barbara Rye, Paul D. Rymer, Michael A. Sams, Gordon Sanson, Hervé Sauquet, Susanne Schmidt, Jürg Schönenberger, Ernst-Detlef Schulze, Kerrie Sendall, Steve Sinclair, Benjamin Smith, Renee Smith, Fiona Soper, Ben Sparrow, Rachel J. Standish, Timothy L. Staples, Ruby Stephens, Christopher Szota, Guy Taseski, Elizabeth Tasker, Freya Thomas, David T. Tissue, Mark G. Tjoelker, David Yue Phin Tng, Félix de Tombeur, Kyle Tomlinson, Neil C. Turner, Erik J. Veneklaas, Susanna Venn, Peter Vesk, Carolyn Vlasveld, Maria S. Vorontsova, Charles A. Warren, Nigel Warwick, Lasantha K. Weerasinghe, Jessie Wells, Mark Westoby, Matthew White, Nicholas S. G. Williams, Jarrah Wills, Peter G. Wilson, Colin Yates, Amy E. Zanne, Graham Zemunik, and Kasia Ziemińska

Subjects
Science
Abstract

Measurement(s) plant trait Technology Type(s) digital curation Sample Characteristic - Organism Viridiplantae Sample Characteristic - Location Australia Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.14545755

Published
2021
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6. Ten (mostly) simple rules to future-proof trait data in ecological and evolutionary sciences

Author

Alexander Keller, Markus Ankenbrand, Helge Bruelheide, Stefanie Dekeyzer, Brian J Enquist, Mohammad Bagher Erfanian, Daniel Falster, Rachael V Gallagher, Jen Hammock, Jens Kattge, Sara D Leonhardt, Joshua Madin, Brian Maitner, Margot Neyret, Renske E Onstein, William D Pearse, Jorrit H Poelen, Roberto Salguero-Gomez, Florian D Schneider, Anikó B Tóth, and Caterina Penone

Published
2022

7. Tallo-a global tree allometry and crown architecture database

Author

Tommaso Jucker, Fabian Jörg Fischer, Jérôme Chave, David A. Coomes, John Caspersen, Arshad Ali, Grace Jopaul Loubota Panzou, Ted R. Feldpausch, Daniel Falster, Vladimir A. Usoltsev, Stephen Adu‐Bredu, Luciana F. Alves, Mohammad Aminpour, Ilondea B. Angoboy, Niels P. R. Anten, Cécile Antin, Yousef Askari, Rodrigo Muñoz, Narayanan Ayyappan, Patricia Balvanera, Lindsay Banin, Nicolas Barbier, John J. Battles, Hans Beeckman, Yannick E. Bocko, Ben Bond‐Lamberty, Frans Bongers, Samuel Bowers, Thomas Brade, Michiel van Breugel, Arthur Chantrain, Rajeev Chaudhary, Jingyu Dai, Michele Dalponte, Kangbéni Dimobe, Jean‐Christophe Domec, Jean‐Louis Doucet, Remko A. Duursma, Moisés Enríquez, Karin Y. van Ewijk, William Farfán‐Rios, Adeline Fayolle, Eric Forni, David I. Forrester, Hammad Gilani, John L. Godlee, Sylvie Gourlet‐Fleury, Matthias Haeni, Jefferson S. Hall, Jie‐Kun He, Andreas Hemp, José L. Hernández‐Stefanoni, Steven I. Higgins, Robert J. Holdaway, Kiramat Hussain, Lindsay B. Hutley, Tomoaki Ichie, Yoshiko Iida, Hai‐sheng Jiang, Puspa Raj Joshi, Hasan Kaboli, Maryam Kazempour Larsary, Tanaka Kenzo, Brian D. Kloeppel, Takashi Kohyama, Suwash Kunwar, Shem Kuyah, Jakub Kvasnica, Siliang Lin, Emily R. Lines, Hongyan Liu, Craig Lorimer, Jean‐Joël Loumeto, Yadvinder Malhi, Peter L. Marshall, Eskil Mattsson, Radim Matula, Jorge A. Meave, Sylvanus Mensah, Xiangcheng Mi, Stéphane Momo, Glenn R. Moncrieff, Francisco Mora, Sarath P. Nissanka, Kevin L. O'Hara, Steven Pearce, Raphaël Pelissier, Pablo L. Peri, Pierre Ploton, Lourens Poorter, Mohsen Javanmiri Pour, Hassan Pourbabaei, Juan Manuel Dupuy‐Rada, Sabina C. Ribeiro, Casey Ryan, Anvar Sanaei, Jennifer Sanger, Michael Schlund, Giacomo Sellan, Alexander Shenkin, Bonaventure Sonké, Frank J. Sterck, Martin Svátek, Kentaro Takagi, Anna T. Trugman, Farman Ullah, Matthew A. Vadeboncoeur, Ahmad Valipour, Mark C. Vanderwel, Alejandra G. Vovides, Weiwei Wang, Li‐Qiu Wang, Christian Wirth, Murray Woods, Wenhua Xiang, Fabiano de Aquino Ximenes, Yaozhan Xu, Toshihiro Yamada, Miguel A. Zavala, Jucker, Tommaso [0000-0002-0751-6312], Chave, Jérôme [0000-0002-7766-1347], Coomes, David [0000-0002-8261-2582], Ali, Arshad [0000-0001-9966-2917], Apollo - University of Cambridge Repository, Coomes, David A [0000-0002-8261-2582], Department of Natural Resources, UT-I-ITC-FORAGES, and Faculty of Geo-Information Science and Earth Observation

Subjects
Forest Ecology, Cubierta de Copas, Altura del Arbol, Bases de Datos, Forests, Carbon Cycle, Trees, ITC-HYBRID, Remote Sensing, Databases, remote sensing, Taxonomic Coverage, Cobertura Geográfica, Settore BIO/07 - ECOLOGIA, Ecología Forestal, Teledetección, Existencias de Biomasa Forestal, Environmental Chemistry, Radio de la Copa, Bosecologie en Bosbeheer, Biomass, stem diameter, forest ecology, Ecosystem, forest biomass stocks, General Environmental Science, Global and Planetary Change, Stem Diameter, tree height, Ecology, Allometric Scaling, Canopy, Crown Radius, Forest Biomass Stocks, Trabajo Global, PE&RC, Carbon, Forest Ecology and Forest Management, Tree Height, Escala Alométrica, ITC-ISI-JOURNAL-ARTICLE, Global Work, Diámetro de Tallo, Centre for Crop Systems Analysis, Geographical Coverage, Cobertura Taxonómica, allometric scaling, crown radius
Abstract

Funder: Agua Salud Project, Funder: U.S. Department of Energy; Id: http://dx.doi.org/10.13039/100000015, Funder: CAPES; Id: http://dx.doi.org/10.13039/501100002322, Data capturing multiple axes of tree size and shape, such as a tree's stem diameter, height and crown size, underpin a wide range of ecological research-from developing and testing theory on forest structure and dynamics, to estimating forest carbon stocks and their uncertainties, and integrating remote sensing imagery into forest monitoring programmes. However, these data can be surprisingly hard to come by, particularly for certain regions of the world and for specific taxonomic groups, posing a real barrier to progress in these fields. To overcome this challenge, we developed the Tallo database, a collection of 498,838 georeferenced and taxonomically standardized records of individual trees for which stem diameter, height and/or crown radius have been measured. These data were collected at 61,856 globally distributed sites, spanning all major forested and non-forested biomes. The majority of trees in the database are identified to species (88%), and collectively Tallo includes data for 5163 species distributed across 1453 genera and 187 plant families. The database is publicly archived under a CC-BY 4.0 licence and can be access from: https://doi.org/10.5281/zenodo.6637599. To demonstrate its value, here we present three case studies that highlight how the Tallo database can be used to address a range of theoretical and applied questions in ecology-from testing the predictions of metabolic scaling theory, to exploring the limits of tree allometric plasticity along environmental gradients and modelling global variation in maximum attainable tree height. In doing so, we provide a key resource for field ecologists, remote sensing researchers and the modelling community working together to better understand the role that trees play in regulating the terrestrial carbon cycle.

Published
2022

8. Trait ecology of startup plants

Author

Julian Schrader, Daniel Falster, and Mark Westoby

Subjects
Plant Leaves, Ecology, Physiology, Seedlings, Plant Science, Plants
Abstract

Startup plants include seedlings and basal and epicormic resprouts. It has long been held that startups have different strategies from adult plants, but theory for what trait differences to expect is limited and not yet quantitatively tested. Three applicable concepts are analogous to human startup firms, R-shift, and trait-growth theory. All three suggest startups should be built with lower construction costs than established plants. This appears to be almost always true in terms of leaf mass per area (LMA), though many comparisons are complicated by the startups growing in lower light. Trait-growth theory predicts LMA should increase progressively with height or total leaf area, driven by higher conductive-pathway costs associated with each unit leaf area, and by greater reward from slowing leaf turnover. Basal resprouts often have somewhat higher LMA than seedlings, but possibly this is simply because they are larger. A number of eminently testable questions are identified. Prospects are good for a theoretically cogent and field-tested body of knowledge about plant startups.

Published
2022

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