1
|
Moura MR, Ceron K, Guedes JJM, Chen-Zhao R, Sica YV, Hart J, Dorman W, Portmann JM, González-del-Pliego P, Ranipeta A, Catenazzi A, Werneck FP, Toledo LF, Upham NS, Tonini JFR, Colston TJ, Guralnick R, Bowie RCK, Pyron RA, Jetz W. A phylogeny-informed characterisation of global tetrapod traits addresses data gaps and biases. PLoS Biol 2024; 22:e3002658. [PMID: 38991106 PMCID: PMC11239118 DOI: 10.1371/journal.pbio.3002658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 05/03/2024] [Indexed: 07/13/2024] Open
Abstract
Tetrapods (amphibians, reptiles, birds, and mammals) are model systems for global biodiversity science, but continuing data gaps, limited data standardisation, and ongoing flux in taxonomic nomenclature constrain integrative research on this group and potentially cause biased inference. We combined and harmonised taxonomic, spatial, phylogenetic, and attribute data with phylogeny-based multiple imputation to provide a comprehensive data resource (TetrapodTraits 1.0.0) that includes values, predictions, and sources for body size, activity time, micro- and macrohabitat, ecosystem, threat status, biogeography, insularity, environmental preferences, and human influence, for all 33,281 tetrapod species covered in recent fully sampled phylogenies. We assess gaps and biases across taxa and space, finding that shared data missing in attribute values increased with taxon-level completeness and richness across clades. Prediction of missing attribute values using multiple imputation revealed substantial changes in estimated macroecological patterns. These results highlight biases incurred by nonrandom missingness and strategies to best address them. While there is an obvious need for further data collection and updates, our phylogeny-informed database of tetrapod traits can support a more comprehensive representation of tetrapod species and their attributes in ecology, evolution, and conservation research.
Collapse
Affiliation(s)
- Mario R. Moura
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
- Departamento de Biociências, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Karoline Ceron
- Departamento de Biologia, Universidade Federal do Ceará, Fortaleza, Ceará, Brazil
| | - Jhonny J. M. Guedes
- Programa de Pós-Graduação em Ecologia e Evolução, Departamento de Ecologia, Universidade Federal de Goiás, Goiânia, Goiás, Brazil
| | - Rosana Chen-Zhao
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Yanina V. Sica
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Julie Hart
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
- New York Natural Heritage Program, State University of New York College of Environmental Science and Forestry, Albany, New York, United States of America
| | - Wendy Dorman
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
- Department of Natural Resources and Environmental Sciences (NRES), University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America
| | - Julia M. Portmann
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Pamela González-del-Pliego
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
- Rui Nabeiro Biodiversity Chair, MED Institute, Universidade de Évora, Évora, Portugal
| | - Ajay Ranipeta
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
| | - Alessandro Catenazzi
- Department of Biological Sciences, Florida International University, Miami, Florida, United States of America
| | - Fernanda P. Werneck
- Programa de Coleções Científicas Biológicas, Coordenação de Biodiversidade, Instituto Nacional de Pesquisas da Amazônia, Manaus Amazonas, Brazil
| | - Luís Felipe Toledo
- Departamento de Biologia Animal, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Nathan S. Upham
- School of Life Sciences, Arizona State University, Tempe, Arizona, United States of America
| | - João F. R. Tonini
- Department of Biology, University of Richmond, Richmond, Virginia, United States of America
| | - Timothy J. Colston
- Biology Department, University of Puerto Rico at Mayagüez, Mayagüez, Puerto Rico
| | - Robert Guralnick
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, United States of America
| | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, Berkeley, California, United States of America
| | - R. Alexander Pyron
- Department of Biological Sciences, The George Washington University, Washington DC, United States of America
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, United States of America
| |
Collapse
|
2
|
Farrell MJ, Le Guillarme N, Brierley L, Hunter B, Scheepens D, Willoughby A, Yates A, Mideo N. The changing landscape of text mining: a review of approaches for ecology and evolution. Proc Biol Sci 2024; 291:20240423. [PMID: 39082244 PMCID: PMC11289731 DOI: 10.1098/rspb.2024.0423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 06/20/2024] [Accepted: 06/20/2024] [Indexed: 08/02/2024] Open
Abstract
In ecology and evolutionary biology, the synthesis and modelling of data from published literature are commonly used to generate insights and test theories across systems. However, the tasks of searching, screening, and extracting data from literature are often arduous. Researchers may manually process hundreds to thousands of articles for systematic reviews, meta-analyses, and compiling synthetic datasets. As relevant articles expand to tens or hundreds of thousands, computer-based approaches can increase the efficiency, transparency and reproducibility of literature-based research. Methods available for text mining are rapidly changing owing to developments in machine learning-based language models. We review the growing landscape of approaches, mapping them onto three broad paradigms (frequency-based approaches, traditional Natural Language Processing and deep learning-based language models). This serves as an entry point to learn foundational and cutting-edge concepts, vocabularies, and methods to foster integration of these tools into ecological and evolutionary research. We cover approaches for modelling ecological texts, generating training data, developing custom models and interacting with large language models and discuss challenges and possible solutions to implementing these methods in ecology and evolution.
Collapse
Affiliation(s)
- Maxwell J. Farrell
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- School of Biodiversity, One Health & Veterinary Medicine, University of Glasgow, Glasgow, UK
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Nicolas Le Guillarme
- Université Grenoble Alpes, CNRS, LECA, Laboratoire d'Ecologie Alpine, Grenoble, France
| | - Liam Brierley
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Bronwen Hunter
- School of Life Sciences, University of Sussex, Brighton, UK
| | - Daan Scheepens
- Division of Biosciences, University College London, London, UK
| | | | - Andrew Yates
- Informatics Institute, University of Amsterdam, Amsterdam, The Netherlands
| | - Nicole Mideo
- Department of Ecology & Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| |
Collapse
|
3
|
Wenk EH, Sauquet H, Gallagher RV, Brownlee R, Boettiger C, Coleman D, Yang S, Auld T, Barrett R, Brodribb T, Choat B, Dun L, Ellsworth D, Gosper C, Guja L, Jordan GJ, Le Breton T, Leigh A, Lu-Irving P, Medlyn B, Nolan R, Ooi M, Sommerville KD, Vesk P, White M, Wright IJ, Falster DS. The AusTraits plant dictionary. Sci Data 2024; 11:537. [PMID: 38796535 PMCID: PMC11127939 DOI: 10.1038/s41597-024-03368-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 05/10/2024] [Indexed: 05/28/2024] Open
Abstract
Traits with intuitive names, a clear scope and explicit description are essential for all trait databases. The lack of unified, comprehensive, and machine-readable plant trait definitions limits the utility of trait databases, including reanalysis of data from a single database, or analyses that integrate data across multiple databases. Both can only occur if researchers are confident the trait concepts are consistent within and across sources. Here we describe the AusTraits Plant Dictionary (APD), a new data source of terms that extends the trait definitions included in a recent trait database, AusTraits. The development process of the APD included three steps: review and formalisation of the scope of each trait and the accompanying trait description; addition of trait metadata; and publication in both human and machine-readable forms. Trait definitions include keywords, references, and links to related trait concepts in other databases, enabling integration of AusTraits with other sources. The APD will both improve the usability of AusTraits and foster the integration of trait data across global and regional plant trait databases.
Collapse
Affiliation(s)
- Elizabeth H Wenk
- Evolution & Ecology Research Centre, University of New South Wales, Sydney, Australia.
| | - Hervé Sauquet
- Evolution & Ecology Research Centre, University of New South Wales, Sydney, Australia
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, NSW, Australia
| | - Rachael V Gallagher
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Rowan Brownlee
- Australian Research Data Commons, Caulfield East, Australia
| | - Carl Boettiger
- Department of Environmental Science, Policy, & Management, University of California, Berkeley, USA
| | - David Coleman
- Evolution & Ecology Research Centre, University of New South Wales, Sydney, Australia
- School of Natural Sciences, Macquarie University, Macquarie Park, Australia
| | - Sophie Yang
- Evolution & Ecology Research Centre, University of New South Wales, Sydney, Australia
| | - Tony Auld
- NSW Department of Planning and Environment, Parramatta, Australia
- University of Wollongong, Wollongong, Australia
- Centre for Ecosystem Science, University of New South Wales, Syndey, Australia
| | - Russell Barrett
- Evolution & Ecology Research Centre, University of New South Wales, Sydney, Australia
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, NSW, Australia
| | - Timothy Brodribb
- School of Biological Sciences, University of Tasmania, Hobart, Australia
| | - Brendan Choat
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Lily Dun
- Evolution & Ecology Research Centre, University of New South Wales, Sydney, Australia
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, NSW, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - David Ellsworth
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Carl Gosper
- Biodiversity and Conservation Science, Department of Biodiversity, Conservation and Attractions, Kensington, WA, Australia
| | - Lydia Guja
- Centre for Australian National Biodiversity Research, Canberra, Australia
- National Seed Bank, Australian National Botanic Gardens, Department of Climate Change, Energy, the Environment and Water, Canberra, Australia
| | - Gregory J Jordan
- School of Biological Sciences, University of Tasmania, Hobart, Australia
| | - Tom Le Breton
- Centre for Ecosystem Science, University of New South Wales, Syndey, Australia
| | - Andrea Leigh
- School of Life Sciences, University of Technology Sydney, Broadway, Australia
| | - Patricia Lu-Irving
- National Herbarium of NSW, Botanic Gardens of Sydney, Mount Annan, NSW, Australia
| | - Belinda Medlyn
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Rachael Nolan
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
| | - Mark Ooi
- Centre for Ecosystem Science, University of New South Wales, Syndey, Australia
| | | | - Peter Vesk
- School of Agriculture, Food and Ecosystem Sciences, University of Melbourne, Parkville, Australia
| | - Matthew White
- Arthur Rylah Institute for Environmental Research, Victorian Department of Energy, Environment and Climate Action, East Melbourne, Australia
| | - Ian J Wright
- Hawkesbury Institute for the Environment, Western Sydney University, Sydney, Australia
- School of Natural Sciences, Macquarie University, Macquarie Park, Australia
| | - Daniel S Falster
- Evolution & Ecology Research Centre, University of New South Wales, Sydney, Australia
| |
Collapse
|
4
|
Isokpehi RD, Kim Y, Krejci SE, Trivedi VD. Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential. Microorganisms 2024; 12:791. [PMID: 38674735 PMCID: PMC11052009 DOI: 10.3390/microorganisms12040791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.
Collapse
Affiliation(s)
| | - Yungkul Kim
- Oyster Microbiome Project, College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (S.E.K.); (V.D.T.)
| | | | | |
Collapse
|
5
|
Arslan D, Akdağ B, Yaşar Ç, Olivier A, Benedetti Y, Morelli F, Çiçek K. An extensive database on the traits and occurrences of amphibian species in Turkey. Sci Data 2024; 11:292. [PMID: 38486028 PMCID: PMC10940290 DOI: 10.1038/s41597-024-03101-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 02/28/2024] [Indexed: 03/18/2024] Open
Abstract
Amphibians are the most endangered taxa among vertebrates, and they face many threats during their complex life cycles. The species' life history traits and occurrence database help understand species responses against ecological factors. Consequently, the species-level-trait database has gained more prominence in recent years as a useful tool for understanding the dimensions of communities, assembly processes of communities, and conserving biodiversity at the ecosystem level against environmental changes. However, in Turkey, there are deficiencies in the knowledge of the ecological traits of amphibians compared to other vertebrate taxa, as most studies have focused on their distribution or taxonomic status. Consequently, there is a need to create such a database for future research on all known extant amphibians in Turkey. We compiled a species-level data set of species traits and occurrences for all amphibians in Turkey using 436 literature sources. We completed 36 trait categories with 5611 occurrence data for 37 amphibian species in Turkey. This study provides an open, useful, and comprehensive database for macroecological and conservation studies on amphibians in Turkey.
Collapse
Affiliation(s)
- Dilara Arslan
- Czech University of Life Sciences Prague, Faculty of Environmental Sciences, Kamýcká 129, CZ-165 00, Prague, 6, Czech Republic.
| | - Burak Akdağ
- Section of Zoology, Department of Biology, Faculty of Science, Ege University, Izmir, Turkey
| | - Çağdaş Yaşar
- Section of Zoology, Department of Biology, Faculty of Science, Ege University, Izmir, Turkey
| | - Anthony Olivier
- Tour du Valat, Institut de Recherche pour la Conservation des Zones Humides Méditerranéennes, Le Sambuc, 13200, Arles, France
| | - Yanina Benedetti
- Czech University of Life Sciences Prague, Faculty of Environmental Sciences, Kamýcká 129, CZ-165 00, Prague, 6, Czech Republic
| | - Federico Morelli
- Czech University of Life Sciences Prague, Faculty of Environmental Sciences, Kamýcká 129, CZ-165 00, Prague, 6, Czech Republic
| | - Kerim Çiçek
- Section of Zoology, Department of Biology, Faculty of Science, Ege University, Izmir, Turkey
- Natural History Application and Research Centre, Ege University, Izmir, Turkey
| |
Collapse
|
6
|
Bach A, Raub F, Höfer H, Ottermanns R, Roß-Nickoll M. ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data. Database (Oxford) 2024; 2024:baae004. [PMID: 38306294 PMCID: PMC10836506 DOI: 10.1093/database/baae004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 02/04/2024]
Abstract
The ARAMOB data repository compiles meticulously curated spider community datasets from systematical collections, ensuring a high standard of data quality. These datasets are enriched with crucial methodological data that enable the datasets to be aligned in time and space, facilitating data synthesis across studies, respectively, collections. To streamline the analysis of these datasets in a species-specific context, a suite of tailored ecological analysis tools named ARAapp has been developed. By harnessing the capabilities of ARAapp, users can systematically evaluate the spider species data housed within the ARAMOB repository, elucidating intricate relationships with a range of parameters such as vertical stratification, habitat occurrence, ecological niche parameters (moisture and shading) and phenological patterns. Database URL: ARAapp is available at www.aramob.de/en.
Collapse
Affiliation(s)
- Alexander Bach
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, Aachen 52074, Germany
| | - Florian Raub
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstr. 13, Karlsruhe 76133, Germany
| | - Hubert Höfer
- Staatliches Museum für Naturkunde Karlsruhe, Erbprinzenstr. 13, Karlsruhe 76133, Germany
| | - Richard Ottermanns
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, Aachen 52074, Germany
| | - Martina Roß-Nickoll
- Institute for Environmental Research, RWTH Aachen University, Worringerweg 1, Aachen 52074, Germany
| |
Collapse
|
7
|
Augustine SP, Bailey-Marren I, Charton KT, Kiel NG, Peyton MS. Improper data practices erode the quality of global ecological databases and impede the progress of ecological research. GLOBAL CHANGE BIOLOGY 2024; 30:e17116. [PMID: 38273575 DOI: 10.1111/gcb.17116] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 01/27/2024]
Abstract
The scientific community has entered an era of big data. However, with big data comes big responsibilities, and best practices for how data are contributed to databases have not kept pace with the collection, aggregation, and analysis of big data. Here, we rigorously assess the quantity of data for specific leaf area (SLA) available within the largest and most frequently used global plant trait database, the TRY Plant Trait Database, exploring how much of the data were applicable (i.e., original, representative, logical, and comparable) and traceable (i.e., published, cited, and consistent). Over three-quarters of the SLA data in TRY either lacked applicability or traceability, leaving only 22.9% of the original data usable compared with the 64.9% typically deemed usable by standard data cleaning protocols. The remaining usable data differed markedly from the original for many species, which led to altered interpretation of ecological analyses. Though the data we consider here make up only 4.5% of SLA data within TRY, similar issues of applicability and traceability likely apply to SLA data for other species as well as other commonly measured, uploaded, and downloaded plant traits. We end with suggested steps forward for global ecological databases, including suggestions for both uploaders to and curators of databases with the hope that, through addressing the issues raised here, we can increase data quality and integrity within the ecological community.
Collapse
Affiliation(s)
- Steven P Augustine
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul, Minnesota, USA
| | - Isaac Bailey-Marren
- Nelson Institute for Environmental Studies, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Katherine T Charton
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nathan G Kiel
- Department of Integrative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Michael S Peyton
- Department of Botany, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
8
|
Jeliazkov A, Chase JM. When Do Traits Tell More Than Species about a Metacommunity? A Synthesis across Ecosystems and Scales. Am Nat 2024; 203:E1-E18. [PMID: 38207141 DOI: 10.1086/727471] [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] [Indexed: 01/13/2024]
Abstract
AbstractLinking species traits with the variation in species assemblages across habitats has often proved useful for developing a more mechanistic understanding of species distributions in metacommunities. However, summarizing the rich tapestry of a species in all of its nuance with a few key ecological traits can also lead to an abstraction that provides less predictability than when using taxonomy alone. As a further complication, taxonomic and functional diversities can be inequitably compared, either by integrating taxonomic-level information into the calculation of how functional aspects of communities vary or by detecting spurious trait-environment relationships. To remedy this, we here synthesize analyses of 80 datasets on different taxa, ecosystems, and spatial scales that include information on abundance or presence/absence of species across sites with variable environmental conditions and the species' traits. By developing analyses that treat functional and taxonomic diversity equitably, we ask when functional diversity helps to explain metacommunity structure. We found that patterns of functional diversity explained metacommunity structure and response to environmental variation in only 25% of the datasets using a multitrait approach but up to 59% using a single-trait approach. Nevertheless, an average of only 19% (interquartile range = 0%-29%) of the traits showed a significant signal across environmental gradients. Species-level traits, as typically collected and analyzed through functional diversity patterns, often do not bring predictive advantages over what the taxonomic information already holds. While our assessment of a limited advantage of using traits to explain variation in species assemblages was largely true across ecosystems, traits played a more useful role in explaining variation when many traits were used and when trait constructs were more related to species' status, life history, and mobility. We propose future research directions to make trait-based approaches and data more helpful for inference in metacommunity ecology.
Collapse
|
9
|
Morim T, Henriques S, Vasconcelos R, Dolbeth M. A roadmap to define and select aquatic biological traits at different scales of analysis. Sci Rep 2023; 13:22947. [PMID: 38135700 PMCID: PMC10746726 DOI: 10.1038/s41598-023-50146-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Trait-based approaches are a powerful tool, as they not only improve understanding of ecological complexity and functioning but also allow comparison across different ecosystems and biogeographical regions. They may be used to unveil ecosystem processes and assess community structures, but their great potential becomes limited when dealing with scattered trait data and historically unstandardised trait nomenclature. The lack of standardisation allows authors to use the terminology of their preference, which inevitably leads to ambiguous misunderstandings and limits comparison between different studies. There have been some attempts to organise the trait vocabulary, but even these are mostly created from the perspective of a single ecosystem, which limits their applicability. In this work, we conducted a systematic literature review that identified and compiled 1127 traits across 37 datasets of fishes, invertebrates and zooplankton from freshwater, marine and transitional ecosystems. This dataset was then used to build on the Marine Species Traits Wiki and to propose a new, unified approach to a trait vocabulary based directly on readily available trait data. We propose a single standardised designation for all the different traits identified and provide a list of all the different synonyms commonly used for these traits. A roadmap to help the trait selection process is also provided, offering a guide through four main steps and important questions for choosing an adequate set of traits at the beginning of any study, which constitutes one of the main challenges in functional ecology research. Overall, this proposal will provide a solid baseline for tackling gaps in trait nomenclature and ensuring a clearer future for functional ecology studies.
Collapse
Affiliation(s)
- Teófilo Morim
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal
| | - Sofia Henriques
- IPMA - Instituto Português do Mar e da Atmosfera, Av. Dr. Alfredo Magalhães Ramalho 6, 1495-165, Algés, Portugal
- MARE - Marine and Environmental Sciences Centre & ARNET - Aquatic Research Infrastructure Network Associated Laboratory, Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisbon, Portugal
| | - Rita Vasconcelos
- IPMA - Instituto Português do Mar e da Atmosfera, Av. Dr. Alfredo Magalhães Ramalho 6, 1495-165, Algés, Portugal
| | - Marina Dolbeth
- CIIMAR - Interdisciplinary Centre of Marine and Environmental Research, Novo Edifício do Terminal de Cruzeiros do Porto de Leixões, Avenida General Norton de Matos s/n, 4450-208, Matosinhos, Portugal.
| |
Collapse
|
10
|
Deng CH, Naithani S, Kumari S, Cobo-Simón I, Quezada-Rodríguez EH, Skrabisova M, Gladman N, Correll MJ, Sikiru AB, Afuwape OO, Marrano A, Rebollo I, Zhang W, Jung S. Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. Database (Oxford) 2023; 2023:baad088. [PMID: 38079567 PMCID: PMC10712715 DOI: 10.1093/database/baad088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 10/17/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023]
Abstract
Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.
Collapse
Affiliation(s)
- Cecilia H Deng
- Molecular and Digital Breeding, New Cultivar Innovation, The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland 1025, New Zealand
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
| | - Irene Cobo-Simón
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
- Institute of Forest Science (ICIFOR-INIA, CSIC), Madrid, Spain
| | - Elsa H Quezada-Rodríguez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana-Xochimilco, Ciudad de México, México
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Maria Skrabisova
- Department of Biochemistry, Faculty of Science, Palacky University, Olomouc, Czech Republic
| | - Nick Gladman
- Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, New York, NY 11724, USA
- U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA
| | - Melanie J Correll
- Agricultural and Biological Engineering Department, University of Florida, 1741 Museum Rd, Gainesville, FL 32611, USA
| | | | | | - Annarita Marrano
- Phoenix Bioinformatics, 39899 Balentine Drive, Suite 200, Newark, CA 94560, USA
| | | | - Wentao Zhang
- National Research Council Canada, 110 Gymnasium Pl, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Sook Jung
- Department of Horticulture, Washington State University, 303c Plant Sciences Building, Pullman, WA 99164-6414, USA
| |
Collapse
|
11
|
Huang ZYX, Halliday FW, Becker DJ. Host functional traits as the nexus for multilevel infection patterns. Trends Ecol Evol 2023; 38:1125-1128. [PMID: 37684132 DOI: 10.1016/j.tree.2023.08.011] [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: 06/01/2023] [Revised: 07/27/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023]
Abstract
Understanding pathogen transmission and infection patterns at multiple biological scales is a central issue in disease ecology and evolution. Here, we suggest that functional traits of host species readily affect infection patterns of species, communities, and landscapes, and thus serve as a linkage for multilevel studies of infectious disease.
Collapse
Affiliation(s)
- Zheng Y X Huang
- School of Life Sciences, Nanjing Normal University, 210023 Nanjing, Jiangsu, China.
| | - Fletcher W Halliday
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, 8057 Zurich, Switzerland; Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, USA
| | - Daniel J Becker
- Department of Biology, University of Oklahoma, Norman, OK 73019, USA.
| |
Collapse
|
12
|
Meijer KJ, Gusmao JB, Bruil L, Franken O, Grimm IA, van der Heide T, Hijner N, Holthuijsen SJ, Hübner L, Thieltges DW, Olff H, Eriksson BK, Govers LL. The seafloor from a trait perspective. A comprehensive life history dataset of soft sediment macrozoobenthos. Sci Data 2023; 10:808. [PMID: 37978182 PMCID: PMC10656422 DOI: 10.1038/s41597-023-02728-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
Biological trait analysis (BTA) is a valuable tool for evaluating changes in community diversity and its link to ecosystem processes as well as environmental and anthropogenic perturbations. Trait-based analytical techniques like BTA rely on standardised datasets of species traits. However, there are currently only a limited number of datasets available for marine macrobenthos that contain trait data across multiple taxonomic groups. Here, we present an open-access dataset of 16 traits for 235 macrozoobenthic species recorded throughout multiple sampling campaigns of the Dutch Wadden Sea; a dynamic soft bottom system where humans have long played a substantial role in shaping the coastal environment. The trait categories included in this dataset cover a variety of life history strategies that are tightly linked to ecosystem functioning and the resilience of communities to (anthropogenic) perturbations and can advance our understanding of environmental changes and human impacts on the functioning of soft bottom systems.
Collapse
Affiliation(s)
- Kasper J Meijer
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands.
| | - Joao Bosco Gusmao
- Programa de Pós-Graduação em Geoquímica: Petróleo e Meio Ambiente (POSPETRO) Institute of Geosciences, Federal University of Bahia (IGEO, UFBA), Salvador, Bahia, Brazil
- Environmental and Marine Biology, Åbo Akademi University, 20500, Turku, Finland
| | - Lisa Bruil
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Oscar Franken
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
- NIOZ Royal Netherlands Institute for Sea Research, Department of Coastal Systems, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Ise A Grimm
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Tjisse van der Heide
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
- NIOZ Royal Netherlands Institute for Sea Research, Department of Coastal Systems, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Nadia Hijner
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Sander J Holthuijsen
- NIOZ Royal Netherlands Institute for Sea Research, Department of Coastal Systems, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
- Rijkswaterstaat Noord Nederland, P.O. Box 2232, 3500 GE, Utrecht, the Netherlands
| | - Lisa Hübner
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - David W Thieltges
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
- NIOZ Royal Netherlands Institute for Sea Research, Department of Coastal Systems, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands
| | - Han Olff
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands
| | - Britas Klemens Eriksson
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands.
| | - Laura L Govers
- Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, P.O. Box 11103, 9700 CC, Groningen, The Netherlands.
- NIOZ Royal Netherlands Institute for Sea Research, Department of Coastal Systems, P.O. Box 59, 1790 AB, Den Burg, Texel, The Netherlands.
| |
Collapse
|
13
|
Maitner B, Gallagher R, Svenning JC, Tietje M, Wenk EH, Eiserhardt WL. A global assessment of the Raunkiaeran shortfall in plants: geographic biases in our knowledge of plant traits. THE NEW PHYTOLOGIST 2023; 240:1345-1354. [PMID: 37369249 DOI: 10.1111/nph.18999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 05/03/2023] [Indexed: 06/29/2023]
Abstract
This article is part of the Special Collection ‘Global plant diversity and distribution’. See https://www.newphytologist.org/global-plant-diversity for more details.
Collapse
Affiliation(s)
- Brian Maitner
- Department of Geography, University at Buffalo, 125a Wilkeson Quadrangle, Buffalo, NY, 14261, USA
| | - Rachael Gallagher
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW, 2751, Australia
| | - Jens-Christian Svenning
- Department of Biology, Center for Ecological Dynamics in a Novel Biosphere (ECONOVO) & Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | - Melanie Tietje
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
| | - Elizabeth H Wenk
- Evolution & Ecology Research Centre, School of Biological, Earth, and Environmental Sciences, UNSW Sydney, Sydney, NSW, 2033, Australia
| | - Wolf L Eiserhardt
- Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark
- Royal Botanic Gardens, Kew, Richmond, TW9 3AE, Surrey, UK
| |
Collapse
|
14
|
Cosentino F, Castiello G, Maiorano L. A dataset on African bats' functional traits. Sci Data 2023; 10:623. [PMID: 37709808 PMCID: PMC10502069 DOI: 10.1038/s41597-023-02472-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Trait-based approaches are becoming extremely common in ecological modeling and the availability of traits databases is increasing. However, data availability is often biased towards particular regions and taxa, with many taxa (e.g., bats) often under-represented. Here, we present the AfroBaT dataset, a compilation of trait data on 320 African bat species containing 76,914 values for 86 traits focusing on morphology, reproduction, life-history, trophic ecology, and species distributions. All data were gathered from published literature following the ecological trait-data standard procedure. Missing data for both numerical and categorical traits were imputed with a machine learning approach including species phylogeny. Trophic ecology traits showed the highest coverage in the literature (72% of the species averaged over all traits), while reproductive traits the lowest. Our data imputation improved the coverage of AfroBaT especially for reproductive traits, going from 27% to 58% of the species covered. AfroBaT has a range of potential applications in macroecology and community ecology, and the availability of open-access data on African bats will enable collaboration and data-sharing among researchers.
Collapse
Affiliation(s)
- Francesca Cosentino
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy.
| | - Giorgia Castiello
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
- CREA Research Centre for Forestry and Wood, v.le Santa Margherita 80, 52100, Arezzo, Italy
| | - Luigi Maiorano
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| |
Collapse
|
15
|
Bernard C, Santos GS, Deere JA, Rodriguez-Caro R, Capdevila P, Kusch E, Gascoigne SJL, Jackson J, Salguero-Gómez R. MOSAIC - A Unified Trait Database to Complement Structured Population Models. Sci Data 2023; 10:335. [PMID: 37264011 PMCID: PMC10235418 DOI: 10.1038/s41597-023-02070-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 03/14/2023] [Indexed: 06/03/2023] Open
Abstract
Despite exponential growth in ecological data availability, broader interoperability amongst datasets is needed to unlock the potential of open access. Our understanding of the interface of demography and functional traits is well-positioned to benefit from such interoperability. Here, we introduce MOSAIC, an open-access trait database that unlocks the demographic potential stored in the COMADRE, COMPADRE, and PADRINO open-access databases. MOSAIC data were digitised and curated through a combination of existing datasets and new trait records sourced from primary literature. In its first release, MOSAIC (v. 1.0.0) includes 14 trait fields for 300 animal and plant species: biomass, height, growth determination, regeneration, sexual dimorphism, mating system, hermaphrodism, sequential hermaphrodism, dispersal capacity, type of dispersal, mode of dispersal, dispersal classes, volancy, and aquatic habitat dependency. MOSAIC includes species-level phylogenies for 1,359 species and population-specific climate data. We identify how database integration can improve our understanding of traits well-quantified in existing repositories and those that are poorly quantified (e.g., growth determination, modularity). MOSAIC highlights emerging challenges associated with standardising databases and demographic measures.
Collapse
Affiliation(s)
- Connor Bernard
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom.
| | - Gabriel Silva Santos
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
- Department of Ecology, Rio de Janeiro State University, 20550-900, Rio de Janeiro, Brazil
- National Institute of the Atlantic Forest (INMA), 29650-000, Santa Teresa, Espírito Santo, Brazil
| | - Jacques A Deere
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
- Department of Evolutionary and Population Biology, Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, 1012 WX, Amsterdam, Netherlands
| | - Roberto Rodriguez-Caro
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
- Departamento de Biología Aplicada, Universidad Miguel Hernández. Av. Universidad, s/n, 03202, Elche (Alicante), Spain
| | - Pol Capdevila
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
- School of Biological Sciences, University of Bristol, 24 Tyndall Ave, Bristol, BS8 1TQ, United Kingdom
| | - Erik Kusch
- Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Arhus University, Aarhus, Denmark
- Section for Ecoinformatics & Biodiversity, Department of Biology, Arhus University, Aarhus, Denmark
| | - Samuel J L Gascoigne
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
| | - John Jackson
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
| | - Roberto Salguero-Gómez
- Department of Biology, University of Oxford, 11a Mansfield Rd, OX13SZ, Oxford, United Kingdom
- Centre for Biodiversity and Conservation Science, University of Queensland, St. Lucia, QLD, Australia
- Evolutionary Demography Laboratory, Max Plank Institute for Demographic Research, Rostock, Germany
| |
Collapse
|
16
|
Przybylska MS, Violle C, Vile D, Scheepens JF, Lacombe B, Le Roux X, Perrier L, Sales-Mabily L, Laumond M, Vinyeta M, Moulin P, Beurier G, Rouan L, Cornet D, Vasseur F. AraDiv: a dataset of functional traits and leaf hyperspectral reflectance of Arabidopsis thaliana. Sci Data 2023; 10:314. [PMID: 37225767 DOI: 10.1038/s41597-023-02189-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 04/27/2023] [Indexed: 05/26/2023] Open
Abstract
Data from functional trait databases have been increasingly used to address questions related to plant diversity and trait-environment relationships. However, such databases provide intraspecific data that combine individual records obtained from distinct populations at different sites and, hence, environmental conditions. This prevents distinguishing sources of variation (e.g., genetic-based variation vs. phenotypic plasticity), a necessary condition to test for adaptive processes and other determinants of plant phenotypic diversity. Consequently, individual traits measured under common growing conditions and encompassing within-species variation across the occupied geographic range have the potential to leverage trait databases with valuable data for functional and evolutionary ecology. Here, we recorded 16 functional traits and leaf hyperspectral reflectance (NIRS) data for 721 widely distributed Arabidopsis thaliana natural accessions grown in a common garden experiment. These data records, together with meteorological variables obtained during the experiment, were assembled to create the AraDiv dataset. AraDiv is a comprehensive dataset of A. thaliana's intraspecific variability that can be explored to address questions at the interface of genetics and ecology.
Collapse
Affiliation(s)
- Maria Stefania Przybylska
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France.
| | - Cyrille Violle
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Denis Vile
- LEPSE, Univ Montpellier, INRAE, Institut Agro Montpellier, Montpellier, France
| | - J F Scheepens
- Plant Evolutionary Ecology, Institute of Ecology, Evolution and Diversity, Faculty of Biological Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 13, 60438, Frankfurt am Main, Germany
| | - Benoit Lacombe
- IPSIM, Univ Montpellier, CNRS, INRAE, Institut Agro Montpellier, Montpellier, France
| | - Xavier Le Roux
- Microbial Ecology Centre, UMR 1418 INRAE, UMR 5557 CNRS, INRAE, CNRS, University Lyon 1, University of Lyon, VetAgroSup, Villeurbanne, France
| | - Lisa Perrier
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | | | | - Mariona Vinyeta
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Pierre Moulin
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Gregory Beurier
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Lauriane Rouan
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | - Denis Cornet
- CIRAD, UMR AGAP Institut, F-34398, Montpellier, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, F-34398, Montpellier, France
| | | |
Collapse
|
17
|
Froidevaux JSP, Toshkova N, Barbaro L, Benítez-López A, Kerbiriou C, Le Viol I, Pacifici M, Santini L, Stawski C, Russo D, Dekker J, Alberdi A, Amorim F, Ancillotto L, Barré K, Bas Y, Cantú-Salazar L, Dechmann DKN, Devaux T, Eldegard K, Fereidouni S, Furmankiewicz J, Hamidovic D, Hill DL, Ibáñez C, Julien JF, Juste J, Kaňuch P, Korine C, Laforge A, Legras G, Leroux C, Lesiński G, Mariton L, Marmet J, Mata VA, Mifsud CM, Nistreanu V, Novella-Fernandez R, Rebelo H, Roche N, Roemer C, Ruczyński I, Sørås R, Uhrin M, Vella A, Voigt CC, Razgour O. A species-level trait dataset of bats in Europe and beyond. Sci Data 2023; 10:253. [PMID: 37137926 PMCID: PMC10156679 DOI: 10.1038/s41597-023-02157-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 04/17/2023] [Indexed: 05/05/2023] Open
Abstract
Knowledge of species' functional traits is essential for understanding biodiversity patterns, predicting the impacts of global environmental changes, and assessing the efficiency of conservation measures. Bats are major components of mammalian diversity and occupy a variety of ecological niches and geographic distributions. However, an extensive compilation of their functional traits and ecological attributes is still missing. Here we present EuroBaTrait 1.0, the most comprehensive and up-to-date trait dataset covering 47 European bat species. The dataset includes data on 118 traits including genetic composition, physiology, morphology, acoustic signature, climatic associations, foraging habitat, roost type, diet, spatial behaviour, life history, pathogens, phenology, and distribution. We compiled the bat trait data obtained from three main sources: (i) a systematic literature and dataset search, (ii) unpublished data from European bat experts, and (iii) observations from large-scale monitoring programs. EuroBaTrait is designed to provide an important data source for comparative and trait-based analyses at the species or community level. The dataset also exposes knowledge gaps in species, geographic and trait coverage, highlighting priorities for future data collection.
Collapse
Affiliation(s)
- Jérémy S P Froidevaux
- University of Stirling, Biological and Environmental Sciences, Faculty of Natural Sciences, FK9 4LJ, Stirling, UK.
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France.
- School of Biological Sciences, University of Bristol, Life Sciences Building, BS8 1TQ, Bristol, UK.
| | - Nia Toshkova
- Institute of Biodiversity and Ecosystem Research, Bulgarian Academy of Sciences, 1 Tsar Osvoboditel Blvd., 1000, Sofia, Bulgaria
- National Museum of Natural History at the Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Luc Barbaro
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- DYNAFOR, INRAE-INPT, University of Toulouse, Castanet-Tolosan, France
| | - Ana Benítez-López
- Integrative Ecology Group, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
- Department of Zoology, University of Granada, Granada, Spain
| | - Christian Kerbiriou
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Isabelle Le Viol
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Michela Pacifici
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Luca Santini
- Department of Biology and Biotechnologies "Charles Darwin", Sapienza University of Rome, Rome, Italy
| | - Clare Stawski
- Department of Biology, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
- School of Science, Technology and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - Danilo Russo
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Università degli Studi di Napoli Federico II, via Università, 100, 80055, Portici (Napoli), Italy.
| | - Jasja Dekker
- Jasja Dekker Dierecologie BV, Arnhem, the Netherlands
| | - Antton Alberdi
- Center for Evolutionary Hologenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Francisco Amorim
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Leonardo Ancillotto
- Laboratory of Animal Ecology and Evolution (AnEcoEvo), Dipartimento di Agraria, Università degli Studi di Napoli Federico II, via Università, 100, 80055, Portici (Napoli), Italy
| | - Kévin Barré
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Yves Bas
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- CEFE, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Lisette Cantú-Salazar
- Luxembourg Institute of Science and Technology, Environmental Research and Innovation, 41 rue du Brill, L-4422, Belvaux, Luxemburg
| | - Dina K N Dechmann
- Max Planck Institute of Animal Behavior, Department of Migration, Am Obstberg 1, 78315, Radolfzell, Germany
- University of Konstanz, Department of Biology, Universitätsstr. 10, 78464, Konstanz, Germany
| | - Tiphaine Devaux
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Katrine Eldegard
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432, Ås, Norway
| | - Sasan Fereidouni
- Research Institute of Wildlife Ecology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Joanna Furmankiewicz
- Department of Behavioural Ecology, Faculty of Biological Sciences, University of Wroclaw, Sienkiewicza 21, 50-335, Wroclaw, Poland
| | - Daniela Hamidovic
- Ministry of Economy and Sustainable Development, Institute for Environment and Nature, Radnička cesta 80, HR-10000, Zagreb, Croatia
- Croatian Biospeleological Society, Rooseveltov trg 6, HR-10000, Zagreb, Croatia
| | - Davina L Hill
- School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Carlos Ibáñez
- Department Evolutionary Ecology, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
| | - Jean-François Julien
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Javier Juste
- Department Evolutionary Ecology, Estación Biológica de Doñana (EBD-CSIC), Sevilla, Spain
- CIBER de Epidemiología y Salud Pública, CIBERESP, 28220, Madrid, Spain
| | - Peter Kaňuch
- Institute of Forest Ecology, Slovak Academy of Sciences, Zvolen, Slovakia
| | - Carmi Korine
- Mitrani Department of Desert Ecology, Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, 8499000, Midreshet Ben-Gurion, Israel
| | - Alexis Laforge
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Gaëlle Legras
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Camille Leroux
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- Auddicé Biodiversité- ZAC du Chevalement, 5 rue des Molettes, 59286, Roost-Warendin, France
| | - Grzegorz Lesiński
- Institute of Animal Science, Warsaw University of Life Sciences (SGGW), Ciszewskiego 8, 02-787, Warsaw, Poland
| | - Léa Mariton
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie (IMPMC), Sorbonne Université, CNRS, MNHN, IRD, 61 Rue Buffon, 75005, Paris, France
| | - Julie Marmet
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
| | - Vanessa A Mata
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
| | - Clare M Mifsud
- Conservation Biology Research Group, Biology Department, University of Malta, MSD2080, Msida, Malta
| | | | - Roberto Novella-Fernandez
- Technical University of Munich, Terrestrial Ecology Research Group, Department for Life Science Systems, School of Life Sciences, Freising, Germany
| | - Hugo Rebelo
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, 4485-661, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661, Vairão, Portugal
- ESS, Polytechnic Institute of Setúbal, Campus do IPS - Estefanilha, 2910-761, Setúbal, Portugal
| | - Niamh Roche
- Bat Conservation Ireland, Carmichael House, 4-7, North Brunswick Street, Dublin, D07 RHA8, Ireland
| | - Charlotte Roemer
- Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), CNRS, MNHN, Sorbonne-Université, 29900 Concarneau, 75005, Paris, France
- CEFE, Univ. Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Ireneusz Ruczyński
- Mammal Research Institute Polish Academy of Sciences, Stoczek 1, 17-230, Białowieża, Poland
| | - Rune Sørås
- Department of Biology, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Marcel Uhrin
- Institute of Biology and Ecology, Faculty of Science, P. J, Šafárik University in Košice, Košice, Slovakia
| | - Adriana Vella
- Conservation Biology Research Group, Biology Department, University of Malta, MSD2080, Msida, Malta
| | - Christian C Voigt
- Department Evolutionary Ecology, Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, 10315, Berlin, Germany
| | - Orly Razgour
- Biosciences, University of Exeter, Streatham Campus, Hatherly Laboratories, Prince of Wales Road, Exeter, EX4 4PS, UK.
| |
Collapse
|
18
|
Staton T, Girling RD, Redak RA, Smith SM, Allison JD. Can morphological traits explain species-specific differences in meta-analyses? A case study of forest beetles. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023:e2838. [PMID: 36911981 DOI: 10.1002/eap.2838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 02/08/2023] [Accepted: 02/15/2023] [Indexed: 05/17/2023]
Abstract
Meta-analyses have become a valuable tool with which to synthesize effects across studies, but in ecology and evolution, they are often characterized by high heterogeneity, where effect sizes vary between studies. Much of this heterogeneity can be attributed to species-specific differences in responses to predictor variables. Here, we aimed to incorporate a novel trait-based approach to explain species-specific differences in a meta-analysis by testing the ability of morphological traits to explain why the effectiveness of flight-intercept trap design varies according to beetle species, a critical issue in forest pest management. An existing morphological trait database for forest beetles was supplemented, providing trait data for 97 species, while data from a previous meta-analysis on capture rates of bark or woodboring beetles according to different trap designs were updated. We combined these sources by including nine morphological traits as moderators in meta-analysis models, for five different components of trap design. Traits were selected based on theoretical hypotheses relating to beetle movement, maneuverability, and sensory perception. We compared the performance of morphological traits as moderators versus guild, taxonomic family, and null meta-analysis models. Morphological traits for the effect of trap type (panel vs. multiple-funnel) on beetle capture rates improved model fit (AICc ), reduced within-study variance (σ2 ), and explained more variation (McFadden's pseudo-R2 ) compared with null, guild, and taxonomic family models. For example, morphological trait models explained 10% more of the variance (pseudo-R2 ) when compared with a null model. However, using traits was less informative to explain how detailed elements of trap design such as surface treatment and color influence capture rates. The reduction of within-study variance when accounting for morphological traits demonstrates their potential value for explaining species-specific differences. Morphological traits associated with flight efficiency, maneuverability, and eye size were particularly informative for explaining the effectiveness of trap type. This could lead to improved predictability of optimal trap design according to species. Therefore, morphological traits could be a valuable tool for understanding species-specific differences in community ecology, but other causes of heterogeneity across studies, such as forest type and structure, require further investigation.
Collapse
Affiliation(s)
- Tom Staton
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
- Institute of Forestry & Conservation, University of Toronto, Toronto, Ontario, Canada
- Natural Resources Canada, Canadian Forest Service, Great Lakes Forestry Centre, Sault Ste Marie, Ontario, Canada
| | - Robbie D Girling
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Richard A Redak
- Department of Entomology, University of California Riverside, Riverside, California, USA
| | - Sandy M Smith
- Institute of Forestry & Conservation, University of Toronto, Toronto, Ontario, Canada
| | - Jeremy D Allison
- Institute of Forestry & Conservation, University of Toronto, Toronto, Ontario, Canada
- Natural Resources Canada, Canadian Forest Service, Great Lakes Forestry Centre, Sault Ste Marie, Ontario, Canada
| |
Collapse
|
19
|
Recknagel F. Cyberinfrastructure for sourcing and processing ecological data. ECOL INFORM 2023. [DOI: 10.1016/j.ecoinf.2023.102039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
|
20
|
deCastro-Arrazola I, Andrew NR, Berg MP, Curtsdotter A, Lumaret JP, Menéndez R, Moretti M, Nervo B, Nichols ES, Sánchez-Piñero F, Santos AMC, Sheldon KS, Slade EM, Hortal J. A trait-based framework for dung beetle functional ecology. J Anim Ecol 2023; 92:44-65. [PMID: 36443916 PMCID: PMC10099951 DOI: 10.1111/1365-2656.13829] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 09/27/2022] [Indexed: 11/30/2022]
Abstract
Traits are key for understanding the environmental responses and ecological roles of organisms. Trait approaches to functional ecology are well established for plants, whereas consistent frameworks for animal groups are less developed. Here we suggest a framework for the study of the functional ecology of animals from a trait-based response-effect approach, using dung beetles as model system. Dung beetles are a key group of decomposers that are important for many ecosystem processes. The lack of a trait-based framework tailored to this group has limited the use of traits in dung beetle functional ecology. We review which dung beetle traits respond to the environment and affect ecosystem processes, covering the wide range of spatial, temporal and biological scales at which they are involved. Dung beetles show trait-based responses to variation in temperature, water, soil properties, trophic resources, light, vegetation structure, competition, predation and parasitism. Dung beetles' influence on ecosystem processes includes trait-mediated effects on nutrient cycling, bioturbation, plant growth, seed dispersal, other dung-based organisms and parasite transmission, as well as some cases of pollination and predation. We identify 66 dung beetle traits that are either response or effect traits, or both, pertaining to six main categories: morphology, feeding, reproduction, physiology, activity and movement. Several traits pertain to more than one category, in particular dung relocation behaviour during nesting or feeding. We also identify 136 trait-response and 77 trait-effect relationships in dung beetles. No response to environmental stressors nor effect over ecological processes were related with traits of a single category. This highlights the interrelationship between the traits shaping body-plans, the multi-functionality of traits, and their role linking responses to the environment and effects on the ecosystem. Despite current developments in dung beetle functional ecology, many knowledge gaps remain, and there are biases towards certain traits, functions, taxonomic groups and regions. Our framework provides the foundations for the thorough development of trait-based dung beetle ecology. It also serves as an example framework for other taxa.
Collapse
Affiliation(s)
- Indradatta deCastro-Arrazola
- Germans Cabot Franciscans 48, Bunyola, Spain.,Departamento de Zoología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Nigel R Andrew
- Insect Ecology Lab, Natural History Museum, University of New England, Armidale, New South Wales, Australia
| | - Matty P Berg
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
| | - Alva Curtsdotter
- Insect Ecology Lab, Natural History Museum, University of New England, Armidale, New South Wales, Australia
| | | | - Rosa Menéndez
- Lancaster Environment Centre, Lancaster University, Lancaster, UK
| | - Marco Moretti
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Beatrice Nervo
- Department of Life Sciences and Systems Biology, University of Torino, Torino, Italy
| | | | | | - Ana M C Santos
- Terrestrial Ecology Group (TEG-UAM), Departamento de Ecología, Universidad Autónoma de Madrid, Madrid, Spain.,Centro de Investigación en Biodiversidad y Cambio Global (CIBC-UAM), Universidad Autónoma de Madrid, Madrid, Spain
| | - Kimberly S Sheldon
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, United States
| | - Eleanor M Slade
- Asian School of the Environment, Nanyang Technological University, Singapore, Singapore
| | - Joaquín Hortal
- Department of Biogeography and Global Change, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain.,Departamento de Ecologia, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Brazil.,cE3c - Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, Lisbon, Portugal
| |
Collapse
|
21
|
Agosti D, Benichou L, Addink W, Arvanitidis C, Catapano T, Cochrane G, Dillen M, Döring M, Georgiev T, Gérard I, Groom Q, Kishor P, Kroh A, Kvaček J, Mergen P, Mietchen D, Pauperio J, Sautter G, Penev L. Recommendations for use of annotations and persistent identifiers in taxonomy and biodiversity publishing. RESEARCH IDEAS AND OUTCOMES 2022. [DOI: 10.3897/rio.8.e97374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The paper summarises many years of discussions and experience of biodiversity publishers, organisations, research projects and individual researchers, and proposes recommendations for implementation of persistent identifiers for article metadata, structural elements (sections, subsections, figures, tables, references, supplementary materials and others) and data specific to biodiversity (taxonomic treatments, treatment citations, taxon names, material citations, gene sequences, specimens, scientific collections) in taxonomy and biodiversity publishing. The paper proposes best practices on how identifiers should be used in the different cases and on how they can be minted, cited, and expressed in the backend article XML to facilitate conversion to and further re-use of the article content as FAIR data. The paper also discusses several specific routes for post-publication re-use of semantically enhanced content through large biodiversity data aggregators such as the Global Biodiversity Information Facility (GBIF), the International Nucleotide Sequence Database Collaboration (INSDC) and others, and proposes specifications of both identifiers and XML tags to be used for that purpose. A summary table provides an account and overview of the recommendations. The guidelines are supported with examples from the existing publishing practices.
Collapse
|
22
|
Lintulaakso K, Tatti N, Žliobaitė I. Quantifying mammalian diets. Mamm Biol 2022. [DOI: 10.1007/s42991-022-00323-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
AbstractWe propose a quantitative approach for categorising mammalian diets based on the taxonomy of food items and parts consumed (the form of food). Our analysis covers 82% of the mammalian species alive today. The diet information comes from different data sources—textbooks, datasets and peer-reviewed literature and includes a transformation of narrative quantitative data into qualitative data. We link a database on nutrient composition of diet items of the quantitative diet data and analyse the distribution of macronutrients of diets across taxonomic groups and map them to the dental morphology of the eaters. The results show associations between dental complexity and the concentrations of some nutrients. Our analysis highlights omnivory as a multi-faceted concept—there are many kinds of omnivores within the dietary space we report. The developed dataset and the proposed approach relating the chemical composition of diets offers a basis for future comparative studies of living and fossil mammals. With this study, we make the accompanying large-scale dietary data publicly available online (https://www.mammalbase.net).
Collapse
|
23
|
Mora-Cross M, Morales-Carmiol A, Chen-Huang T, Barquero-Pérez M. Essential Biodiversity Variables: extracting plant phenological data from specimen labels using machine learning. RESEARCH IDEAS AND OUTCOMES 2022. [DOI: 10.3897/rio.8.e86012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Essential Biodiversity Variables (EBVs) make it possible to evaluate and monitor the state of biodiversity over time at different spatial scales. Its development is led by the Group on Earth Observations Biodiversity Observation Network (GEO BON) to harmonize, consolidate and standardize biodiversity data from varied biodiversity sources. This document presents a mechanism to obtain baseline data to feed the Species Traits Variable Phenology or other biodiversity indicators by extracting species characters and structure names from morphological descriptions of specimens and classifying such descriptions using machine learning (ML).
A workflow that performs Named Entity Recognition (NER) and Classification of morphological descriptions using ML algorithms was evaluated with excellent results. It was implemented using Python, Pytorch, Scikit-Learn, Pomegranate, Python-crfsuite, and other libraries applied to 106,804 herbarium records from the National Biodiversity Institute of Costa Rica (INBio). The text classification results were almost excellent (F1 score between 96% and 99%) using three traditional ML methods: Multinomial Naive Bayes (NB), Linear Support Vector Classification (SVC), and Logistic Regression (LR). Furthermore, results extracting names of species morphological structures (e.g., leaves, trichomes, flowers, petals, sepals) and character names (e.g., length, width, pigmentation patterns, and smell) using NER algorithms were competitive (F1 score between 95% and 98%) using Hidden Markov Models (HMM), Conditional Random Fields (CRFs), and Bidirectional Long Short Term Memory Networks with CRF (BI-LSTM-CRF).
Collapse
|
24
|
Chaudhary VB, Holland EP, Charman-Anderson S, Guzman A, Bell-Dereske L, Cheeke TE, Corrales A, Duchicela J, Egan C, Gupta MM, Hannula SE, Hestrin R, Hoosein S, Kumar A, Mhretu G, Neuenkamp L, Soti P, Xie Y, Helgason T. What are mycorrhizal traits? Trends Ecol Evol 2022; 37:573-581. [PMID: 35504748 DOI: 10.1016/j.tree.2022.04.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/02/2022] [Accepted: 04/06/2022] [Indexed: 12/29/2022]
Abstract
Traits are inherent properties of organisms, but how are they defined for organismal networks such as mycorrhizal symbioses? Mycorrhizal symbioses are complex and diverse belowground symbioses between plants and fungi that have proved challenging to fit into a unified and coherent trait framework. We propose an inclusive mycorrhizal trait framework that classifies traits as morphological, physiological, and phenological features that have functional implications for the symbiosis. We further classify mycorrhizal traits by location - plant, fungus, or the symbiosis - which highlights new questions in trait-based mycorrhizal ecology designed to charge and challenge the scientific community. This new framework is an opportunity for researchers to interrogate their data to identify novel insights and gaps in our understanding of mycorrhizal symbioses.
Collapse
Affiliation(s)
- V Bala Chaudhary
- Department of Environmental Studies, Dartmouth College, Hanover, NH 03755, USA.
| | | | | | - Aidee Guzman
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Lukas Bell-Dereske
- Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague, Czech Republic
| | - Tanya E Cheeke
- School of Biological Sciences, Washington State University, Richland, WA 99354, USA
| | - Adriana Corrales
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá 110151, Colombia
| | - Jessica Duchicela
- Departamento de Ciencias de la Vida, Universidad de las Fuerzas Armadas ESPE, Sangolquí 171103, Ecuador
| | - Cameron Egan
- Department of Biology, Okanagan College, 1000 KLO Rd, Kelowna, BC, Canada V1Y 4X8
| | - Manju M Gupta
- Department of Biology, University of Delhi, Sri Aurobindo College, Delhi 110017, India
| | - S Emilia Hannula
- Institute of Environmental Sciences, Leiden University, Leiden 2333, The Netherlands
| | - Rachel Hestrin
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Shabana Hoosein
- Department of Forest and Rangeland Stewardship, Colorado State University, Fort Collins, CO 80523, USA
| | - Amit Kumar
- Institute of Ecology, Faculty of Sustainability, Leuphana University of Lüneburg, 21335 Lüneburg, Germany
| | - Genet Mhretu
- Department of Biology, Mekelle University, Mekelle 231, Ethiopia
| | - Lena Neuenkamp
- University of Bern, Institute of Plant Sciences, Berne 3013, Switzerland; Department of Ecology and Multidisciplinary Institute for Environment Studies 'Ramon Margalef', University of Alicante, Alicante 03009, Spain
| | - Pushpa Soti
- Biology Department, University of Texas Rio Grande Valley, Edinburg, TX 78539, USA
| | - Yichun Xie
- School of Life Sciences, The Chinese University of Hong Kong, Hong Kong SAR 999077
| | | |
Collapse
|
25
|
Farrell MJ, Brierley L, Willoughby A, Yates A, Mideo N. Past and future uses of text mining in ecology and evolution. Proc Biol Sci 2022; 289:20212721. [PMID: 35582795 PMCID: PMC9114983 DOI: 10.1098/rspb.2021.2721] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Ecology and evolutionary biology, like other scientific fields, are experiencing an exponential growth of academic manuscripts. As domain knowledge accumulates, scientists will need new computational approaches for identifying relevant literature to read and include in formal literature reviews and meta-analyses. Importantly, these approaches can also facilitate automated, large-scale data synthesis tasks and build structured databases from the information in the texts of primary journal articles, books, grey literature, and websites. The increasing availability of digital text, computational resources, and machine-learning based language models have led to a revolution in text analysis and natural language processing (NLP) in recent years. NLP has been widely adopted across the biomedical sciences but is rarely used in ecology and evolutionary biology. Applying computational tools from text mining and NLP will increase the efficiency of data synthesis, improve the reproducibility of literature reviews, formalize analyses of research biases and knowledge gaps, and promote data-driven discovery of patterns across ecology and evolutionary biology. Here we present recent use cases from ecology and evolution, and discuss future applications, limitations and ethical issues.
Collapse
Affiliation(s)
- Maxwell J. Farrell
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| | - Liam Brierley
- Department of Health Data Science, University of Liverpool, Liverpool, UK
| | - Anna Willoughby
- Odum School of Ecology, University of Georgia, Athens, GA, USA,Center for the Ecology of Infectious Diseases, University of Georgia, Athens, GA, USA
| | - Andrew Yates
- University of Amsterdam, Amsterdam, The Netherlands
| | - Nicole Mideo
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Canada
| |
Collapse
|
26
|
Junker RR, Albrecht J, Becker M, Keuth R, Farwig N, Schleuning M. Towards an animal economics spectrum for ecosystem research. Funct Ecol 2022. [DOI: 10.1111/1365-2435.14051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert R. Junker
- Evolutionary Ecology of Plants Department of Biology University of Marburg 35043 Marburg Germany
- Department of Environment and Biodiversity University of Salzburg 5020 Salzburg Austria
| | - Jörg Albrecht
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F) Senckenberganlage 25 60325 Frankfurt am Main Germany
| | - Marcel Becker
- Conservation Ecology Department of Biology University of Marburg 35043 Marburg Germany
| | - Raya Keuth
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F) Senckenberganlage 25 60325 Frankfurt am Main Germany
| | - Nina Farwig
- Conservation Ecology Department of Biology University of Marburg 35043 Marburg Germany
| | - Matthias Schleuning
- Senckenberg Biodiversity and Climate Research Centre (SBiK‐F) Senckenberganlage 25 60325 Frankfurt am Main Germany
| |
Collapse
|
27
|
Heger T, Zarrieß S, Algergawy A, Jeschke J, König-Ries B. INAS: Interactive Argumentation Support for the Scientific Domain of Invasion Biology. RESEARCH IDEAS AND OUTCOMES 2022. [DOI: 10.3897/rio.8.e80457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Developing a precise argument is not an easy task. In real-world argumentation scenarios, arguments presented in texts (e.g. scientific publications) often constitute the end result of a long and tedious process. A lot of work on computational argumentation has focused on analyzing and aggregating these products of argumentation processes, i.e. argumentative texts. In this project, we adopt a complementary perspective: we aim to develop an argumentation machine that supports users during the argumentation process in a scientific context, enabling them to follow ongoing argumentation in a scientific community and to develop their own arguments. To achieve this ambitious goal, we will focus on a particular phase of the scientific argumentation process, namely the initial phase of claim or hypothesis development. According to argumentation theory, the starting point of an argument is a claim, and also data that serves as a basis for the claim. In scientific argumentation, a carefully developed and thought-through hypothesis (which we see as Toulmin's "claim'' in a scientific context) is often crucial for researchers to be able to conduct a successful study and, in the end, present a new, high-quality finding or argument. Thus, an initial hypothesis needs to be specific enough that a researcher can test it based on data, but, at the same time, it should also relate to previous general claims made in the community. We investigate how argumentation machines can (i) represent concrete and more abstract knowledge on hypotheses and their underlying concepts, (ii) model the process of hypothesis refinement, including data as a basis of refinement, and (iii) interactively support a user in developing her own hypothesis based on these resources. This project will combine methods from different disciplines: natural language processing, knowledge representation and semantic web, philosophy of science and -- as an example for a scientific domain -- invasion biology. Our starting point is an existing resource in invasion biology that organizes and relates core hypotheses in the field and associates them to meta-data for more than 1000 scientific publications, which was developed over the course of several years based on manual analysis. This network, however, is currently static (i.e. needs substantial manual curation to be extended to incorporate new claims) and, moreover, is not easily accessible for users who miss specific background and domain knowledge in invasion biology. Our goal is to develop (i) a semantic model for representing knowledge on concepts and hypotheses, such that also non-expert users can use the network; (ii) a tool that automatically computes links from publication abstracts (and data) to these hypotheses; and (iii) an interactive system that supports users in refining their initial, potentially underdeveloped hypothesis.
Collapse
|
28
|
Potapov AM, Beaulieu F, Birkhofer K, Bluhm SL, Degtyarev MI, Devetter M, Goncharov AA, Gongalsky KB, Klarner B, Korobushkin DI, Liebke DF, Maraun M, Mc Donnell RJ, Pollierer MM, Schaefer I, Shrubovych J, Semenyuk II, Sendra A, Tuma J, Tůmová M, Vassilieva AB, Chen T, Geisen S, Schmidt O, Tiunov AV, Scheu S. Feeding habits and multifunctional classification of soil‐associated consumers from protists to vertebrates. Biol Rev Camb Philos Soc 2022; 97:1057-1117. [DOI: 10.1111/brv.12832] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/31/2021] [Accepted: 01/05/2022] [Indexed: 12/17/2022]
Affiliation(s)
- Anton M. Potapov
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Frédéric Beaulieu
- Canadian National Collection of Insects, Arachnids and Nematodes, Agriculture and Agri‐Food Canada Ottawa ON K1A 0C6 Canada
| | - Klaus Birkhofer
- Department of Ecology Brandenburg University of Technology Karl‐Wachsmann‐Allee 6 03046 Cottbus Germany
| | - Sarah L. Bluhm
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Maxim I. Degtyarev
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Miloslav Devetter
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Anton A. Goncharov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Konstantin B. Gongalsky
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Bernhard Klarner
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Daniil I. Korobushkin
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Dana F. Liebke
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Mark Maraun
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Rory J. Mc Donnell
- Department of Crop and Soil Science Oregon State University Corvallis OR 97331 U.S.A
| | - Melanie M. Pollierer
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Ina Schaefer
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
| | - Julia Shrubovych
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
- Institute of Systematics and Evolution of Animals PAS Slawkowska 17 Pl 31‐016 Krakow Poland
- State Museum Natural History of NAS of Ukraine Teatralna 18 79008 Lviv Ukraine
| | - Irina I. Semenyuk
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
- Joint Russian‐Vietnamese Tropical Center №3 Street 3 Thang 2, Q10 Ho Chi Minh City Vietnam
| | - Alberto Sendra
- Colecciones Entomológicas Torres‐Sala, Servei de Patrimoni Històric, Ajuntament de València València Spain
- Departament de Didàctica de les Cièncias Experimentals i Socials, Facultat de Magisteri Universitat de València València Spain
| | - Jiri Tuma
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
- Biology Centre CAS, Institute of Entomology Branisovska 1160/31 370 05 Ceske Budejovice Czech Republic
| | - Michala Tůmová
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Anna B. Vassilieva
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Ting‐Wen Chen
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology Na Sádkách 702/7 37005 České Budějovice Czech Republic
| | - Stefan Geisen
- Department of Nematology Wageningen University & Research 6700ES Wageningen The Netherlands
| | - Olaf Schmidt
- UCD School of Agriculture and Food Science University College Dublin Belfield Dublin 4 Ireland
| | - Alexei V. Tiunov
- A.N. Severtsov Institute of Ecology and Evolution, Russian Academy of Sciences Leninsky Prospect 33 119071 Moscow Russia
| | - Stefan Scheu
- J.F. Blumenbach Institute of Zoology and Anthropology University of Göttingen Untere Karspüle 2 37073 Göttingen Germany
- Centre of Biodiversity and Sustainable Land Use Büsgenweg 1 37077 Göttingen Germany
| |
Collapse
|
29
|
Pekár S, Wolff JO, Černecká Ľ, Birkhofer K, Mammola S, Lowe EC, Fukushima CS, Herberstein ME, Kučera A, Buzatto BA, Djoudi EA, Domenech M, Enciso AV, Piñanez Espejo YMG, Febles S, García LF, Gonçalves-Souza T, Isaia M, Lafage D, Líznarová E, Macías-Hernández N, Magalhães I, Malumbres-Olarte J, Michálek O, Michalik P, Michalko R, Milano F, Munévar A, Nentwig W, Nicolosi G, Painting CJ, Pétillon J, Piano E, Privet K, Ramírez MJ, Ramos C, Řezáč M, Ridel A, Růžička V, Santos I, Sentenská L, Walker L, Wierucka K, Zurita GA, Cardoso P. The World Spider Trait database: a centralized global open repository for curated data on spider traits. Database (Oxford) 2021; 2021:baab064. [PMID: 34651181 PMCID: PMC8517500 DOI: 10.1093/database/baab064] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/13/2021] [Accepted: 09/23/2021] [Indexed: 11/12/2022]
Abstract
Spiders are a highly diversified group of arthropods and play an important role in terrestrial ecosystems as ubiquitous predators, which makes them a suitable group to test a variety of eco-evolutionary hypotheses. For this purpose, knowledge of a diverse range of species traits is required. Until now, data on spider traits have been scattered across thousands of publications produced for over two centuries and written in diverse languages. To facilitate access to such data, we developed an online database for archiving and accessing spider traits at a global scale. The database has been designed to accommodate a great variety of traits (e.g. ecological, behavioural and morphological) measured at individual, species or higher taxonomic levels. Records are accompanied by extensive metadata (e.g. location and method). The database is curated by an expert team, regularly updated and open to any user. A future goal of the growing database is to include all published and unpublished data on spider traits provided by experts worldwide and to facilitate broad cross-taxon assays in functional ecology and comparative biology. Database URL:https://spidertraits.sci.muni.cz/.
Collapse
Affiliation(s)
- Stano Pekár
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czechia
| | - Jonas O Wolff
- Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, Greifswald 17489, Germany
- Department of Biological Sciences, Macquarie University, 6 Wally’s Walk, Sydney, NSW 2109, Australia
| | - Ľudmila Černecká
- Slovak Academy of Sciences, Institute of Forest Ecology, Ľ. Štúra 2, Zvolen 960 01, Slovak Republic
| | - Klaus Birkhofer
- Department of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Konrad-Wachsmann-Allee 6, Cottbus 03046, Germany
| | - Stefano Mammola
- Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History LUOMUS, University of Helsinki, Pohjoinen Rautatiekatu 13, Helsinki 00014, Finland
- Molecular Ecology Group (MEG), Water Research Institute (IRSA), National Research Council (CNR), Corso Tonolli, 50, Pallanza 28922, Italy
| | - Elizabeth C Lowe
- Department of Biological Sciences, Macquarie University, 6 Wally’s Walk, Sydney, NSW 2109, Australia
| | - Caroline S Fukushima
- Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History LUOMUS, University of Helsinki, Pohjoinen Rautatiekatu 13, Helsinki 00014, Finland
| | - Marie E Herberstein
- Department of Biological Sciences, Macquarie University, 6 Wally’s Walk, Sydney, NSW 2109, Australia
| | - Adam Kučera
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czechia
| | - Bruno A Buzatto
- Department of Biological Sciences, Macquarie University, 6 Wally’s Walk, Sydney, NSW 2109, Australia
- School of Biological Sciences, University of Western Australia, 35 Stirling highway, Crawley, WA 6009, Australia
| | - El Aziz Djoudi
- Department of Ecology, Brandenburg University of Technology Cottbus-Senftenberg, Konrad-Wachsmann-Allee 6, Cottbus 03046, Germany
| | - Marc Domenech
- Department of Evolutionary Biology, Ecology and Environmental Sciences & Biodiversity Research Institute (IRBio), Universitat de Barcelona, Av. Diagonal 643, Barcelona 08028, Spain
| | | | | | - Sara Febles
- Grupo de Investigaciones Entomológicas de Tenerife (GIET), C/ San Eulogio 15, 1º, La Laguna, Canary Islands 38108, Spain
| | - Luis F García
- Centro Universitario Regional del Este, Universidad de la República, Ruta 8 Km 282, Treinta y Tres, Uruguay
| | - Thiago Gonçalves-Souza
- Department of Biology, Ecological Synthesis and Biodiversity Conservation Lab, Federal Rural University of Pernambuco, Dom Manuel de Medeiros, s/n, Dois Irmãos—CEP, Recife, PE 50710-270, Brazil
| | - Marco Isaia
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina, 13, Turin 10123, Italy
| | - Denis Lafage
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du General Leclerc, Rennes 35042, France
| | - Eva Líznarová
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czechia
| | - Nuria Macías-Hernández
- Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History LUOMUS, University of Helsinki, Pohjoinen Rautatiekatu 13, Helsinki 00014, Finland
- Departamento de Biología Animal, Edafología y Geología, Universidad de La Laguna, La Laguna, Tenerife 38206, Spain
| | - Ivan Magalhães
- Division of Arachnology, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’—CONICET, Av. Ángel Gallardo 470, Buenos Aires C1405DJR, Argentina
| | - Jagoba Malumbres-Olarte
- Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History LUOMUS, University of Helsinki, Pohjoinen Rautatiekatu 13, Helsinki 00014, Finland
- CE3C—Centre for Ecology, Evolution and Environmental Changes, Azorean Biodiversity Group and Universidade dos Açores, Angra do Heroísmo, Azores, Portugal
| | - Ondřej Michálek
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czechia
| | - Peter Michalik
- Zoological Institute and Museum, University of Greifswald, Loitzer Str. 26, Greifswald 17489, Germany
| | - Radek Michalko
- Department of Forest Ecology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemědělská 3, Brno 613 00, Czech Republic
| | - Filippo Milano
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina, 13, Turin 10123, Italy
| | - Ana Munévar
- Instituto de Biología Subtropical (UNAM-CONICET), Puerto Iguazú, Argentina
| | - Wolfgang Nentwig
- Institute of Ecology and Evolution, University of Bern, Baltzerstrasse 6, Bern 3012, Switzerland
| | - Giuseppe Nicolosi
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina, 13, Turin 10123, Italy
| | - Christina J Painting
- Te Aka Mātuatua School of Science, University of Waikato, Private Bag 3105, Hamilton 3240, New Zealand
| | - Julien Pétillon
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du General Leclerc, Rennes 35042, France
| | - Elena Piano
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina, 13, Turin 10123, Italy
| | - Kaïna Privet
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du General Leclerc, Rennes 35042, France
| | - Martín J Ramírez
- Division of Arachnology, Museo Argentino de Ciencias Naturales ‘Bernardino Rivadavia’—CONICET, Av. Ángel Gallardo 470, Buenos Aires C1405DJR, Argentina
| | - Cândida Ramos
- Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History LUOMUS, University of Helsinki, Pohjoinen Rautatiekatu 13, Helsinki 00014, Finland
| | - Milan Řezáč
- Crop Research Institute, Drnovská 507, Prague 6 CZ-16106, Czechia
| | - Aurélien Ridel
- UMR CNRS 6553 ECOBIO, Université de Rennes 1, 263 Avenue du General Leclerc, Rennes 35042, France
| | - Vlastimil Růžička
- Biology Centre, Czech Academy of Sciences, Institute of Entomology, Branišovská 31, České Budějovice 370 05, Czechia
| | - Irene Santos
- Grupo de Investigaciones Entomológicas de Tenerife (GIET), C/ San Eulogio 15, 1º, La Laguna, Canary Islands 38108, Spain
- Island Ecology and Evolution Research Group, Instituto de Productos Naturales y Agrobiología (IPNA-CSIC), La Laguna, Tenerife, Canary Islands 38206, Spain
| | - Lenka Sentenská
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Kotlářská 2, Brno 611 37, Czechia
| | - Leilani Walker
- Natural Sciences, Auckland War Memorial Museum, Parnell, Auckland 1010, New Zealand
| | - Kaja Wierucka
- Department of Biological Sciences, Macquarie University, 6 Wally’s Walk, Sydney, NSW 2109, Australia
- Department of Anthropology, University of Zürich, Winterthurerstrasse 190, Zürich 8057, Switzerland
| | | | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research, Finnish Museum of Natural History LUOMUS, University of Helsinki, Pohjoinen Rautatiekatu 13, Helsinki 00014, Finland
| |
Collapse
|
30
|
Doherty JF, Chai X, Cope LE, de Angeli Dutra D, Milotic M, Ni S, Park E, Filion A. The rise of big data in disease ecology. Trends Parasitol 2021; 37:1034-1037. [PMID: 34602364 DOI: 10.1016/j.pt.2021.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/03/2021] [Accepted: 09/08/2021] [Indexed: 10/20/2022]
Abstract
Big data have become readily available to explore patterns in large-scale disease ecology. However, the rate at which these public databases are exploited remains unknown. We highlight trends in big data usage in disease ecology during the past decade and encourage researchers to integrate big data into their study framework.
Collapse
Affiliation(s)
| | - Xuhong Chai
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Laurie E Cope
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | | | - Marin Milotic
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Steven Ni
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Eunji Park
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Antoine Filion
- Department of Zoology, University of Otago, Dunedin, New Zealand.
| |
Collapse
|
31
|
Jochum M, Barnes AD, Brose U, Gauzens B, Sünnemann M, Amyntas A, Eisenhauer N. For flux's sake: General considerations for energy-flux calculations in ecological communities. Ecol Evol 2021; 11:12948-12969. [PMID: 34646445 PMCID: PMC8495806 DOI: 10.1002/ece3.8060] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 07/26/2021] [Accepted: 07/30/2021] [Indexed: 11/18/2022] Open
Abstract
Global change alters ecological communities with consequences for ecosystem processes. Such processes and functions are a central aspect of ecological research and vital to understanding and mitigating the consequences of global change, but also those of other drivers of change in organism communities. In this context, the concept of energy flux through trophic networks integrates food-web theory and biodiversity-ecosystem functioning theory and connects biodiversity to multitrophic ecosystem functioning. As such, the energy-flux approach is a strikingly effective tool to answer central questions in ecology and global-change research. This might seem straight forward, given that the theoretical background and software to efficiently calculate energy flux are readily available. However, the implementation of such calculations is not always straight forward, especially for those who are new to the topic and not familiar with concepts central to this line of research, such as food-web theory or metabolic theory. To facilitate wider use of energy flux in ecological research, we thus provide a guide to adopting energy-flux calculations for people new to the method, struggling with its implementation, or simply looking for background reading, important resources, and standard solutions to the problems everyone faces when starting to quantify energy fluxes for their community data. First, we introduce energy flux and its use in community and ecosystem ecology. Then, we provide a comprehensive explanation of the single steps towards calculating energy flux for community data. Finally, we discuss remaining challenges and exciting research frontiers for future energy-flux research.
Collapse
Affiliation(s)
- Malte Jochum
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiologyLeipzig UniversityLeipzigGermany
| | | | - Ulrich Brose
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiodiversityUniversity of JenaJenaGermany
| | - Benoit Gauzens
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiodiversityUniversity of JenaJenaGermany
| | - Marie Sünnemann
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiologyLeipzig UniversityLeipzigGermany
| | - Angelos Amyntas
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiodiversityUniversity of JenaJenaGermany
| | - Nico Eisenhauer
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
- Institute of BiologyLeipzig UniversityLeipzigGermany
| |
Collapse
|
32
|
Crane M, Silva I, Grainger MJ, Gale GA. Limitations and gaps in global bat wing morphology trait data. Mamm Rev 2021. [DOI: 10.1111/mam.12270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matt Crane
- Conservation Ecology Program King Mongkut’s University of Technology Thonburi 49 Thakham, Bangkhuntien Bangkok10150Thailand
| | - Inês Silva
- Center for Advanced Systems Understanding (CASUS) Am Untermarkt 20 Görlitz02826Germany
- Helmholtz‐Zentrum Dresden‐Rossendorf (HZDR) Bautzner Landstraße 400 Dresden01328Germany
| | - Matthew J. Grainger
- Norwegian Institute for Nature Research Postbox 5685 Torgarden Trondheim7485Norway
| | - George A. Gale
- Conservation Ecology Program King Mongkut’s University of Technology Thonburi 49 Thakham, Bangkhuntien Bangkok10150Thailand
| |
Collapse
|
33
|
Wood ZT, Wiegardt AK, Barton KL, Clark JD, Homola JJ, Olsen BJ, King BL, Kovach AI, Kinnison MT. Meta-analysis: Congruence of genomic and phenotypic differentiation across diverse natural study systems. Evol Appl 2021; 14:2189-2205. [PMID: 34603492 PMCID: PMC8477602 DOI: 10.1111/eva.13264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 06/02/2021] [Accepted: 06/06/2021] [Indexed: 01/17/2023] Open
Abstract
Linking genotype to phenotype is a primary goal for understanding the genomic underpinnings of evolution. However, little work has explored whether patterns of linked genomic and phenotypic differentiation are congruent across natural study systems and traits. Here, we investigate such patterns with a meta-analysis of studies examining population-level differentiation at subsets of loci and traits putatively responding to divergent selection. We show that across the 31 studies (88 natural population-level comparisons) we examined, there was a moderate (R 2 = 0.39) relationship between genomic differentiation (F ST ) and phenotypic differentiation (P ST ) for loci and traits putatively under selection. This quantitative relationship between P ST and F ST for loci under selection in diverse taxa provides broad context and cross-system predictions for genomic and phenotypic adaptation by natural selection in natural populations. This context may eventually allow for more precise ideas of what constitutes "strong" differentiation, predictions about the effect size of loci, comparisons of taxa evolving in nonparallel ways, and more. On the other hand, links between P ST and F ST within studies were very weak, suggesting that much work remains in linking genomic differentiation to phenotypic differentiation at specific phenotypes. We suggest that linking genotypes to specific phenotypes can be improved by correlating genomic and phenotypic differentiation across a spectrum of diverging populations within a taxon and including wide coverage of both genomes and phenomes.
Collapse
Affiliation(s)
- Zachary T. Wood
- School of Biology and EcologyUniversity of MaineOronoMEUSA
- Maine Center for Genetics in the EnvironmentOronoMEUSA
| | - Andrew K. Wiegardt
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Kayla L. Barton
- Department of Molecular & Biomedical SciencesUniversity of MaineOronoMEUSA
| | - Jonathan D. Clark
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Jared J. Homola
- Department of Fisheries and WildlifeMichigan State UniversityEast LansingMIUSA
| | - Brian J. Olsen
- Maine Center for Genetics in the EnvironmentOronoMEUSA
- Department of Wildlife, Fisheries, and Conservation BiologyUniversity of MaineOronoMEUSA
| | - Benjamin L. King
- Department of Molecular & Biomedical SciencesUniversity of MaineOronoMEUSA
| | - Adrienne I. Kovach
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNHUSA
| | - Michael T. Kinnison
- School of Biology and EcologyUniversity of MaineOronoMEUSA
- Maine Center for Genetics in the EnvironmentOronoMEUSA
| |
Collapse
|
34
|
Vanderbilt K, Gries C. Integrating long-tail data: How far are we? ECOL INFORM 2021. [DOI: 10.1016/j.ecoinf.2021.101372] [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]
|
35
|
Culina A, Adriaensen F, Bailey LD, Burgess MD, Charmantier A, Cole EF, Eeva T, Matthysen E, Nater CR, Sheldon BC, Sæther B, Vriend SJG, Zajkova Z, Adamík P, Aplin LM, Angulo E, Artemyev A, Barba E, Barišić S, Belda E, Bilgin CC, Bleu J, Both C, Bouwhuis S, Branston CJ, Broggi J, Burke T, Bushuev A, Camacho C, Campobello D, Canal D, Cantarero A, Caro SP, Cauchoix M, Chaine A, Cichoń M, Ćiković D, Cusimano CA, Deimel C, Dhondt AA, Dingemanse NJ, Doligez B, Dominoni DM, Doutrelant C, Drobniak SM, Dubiec A, Eens M, Einar Erikstad K, Espín S, Farine DR, Figuerola J, Kavak Gülbeyaz P, Grégoire A, Hartley IR, Hau M, Hegyi G, Hille S, Hinde CA, Holtmann B, Ilyina T, Isaksson C, Iserbyt A, Ivankina E, Kania W, Kempenaers B, Kerimov A, Komdeur J, Korsten P, Král M, Krist M, Lambrechts M, Lara CE, Leivits A, Liker A, Lodjak J, Mägi M, Mainwaring MC, Mänd R, Massa B, Massemin S, Martínez‐Padilla J, Mazgajski TD, Mennerat A, Moreno J, Mouchet A, Nakagawa S, Nilsson J, Nilsson JF, Cláudia Norte A, van Oers K, Orell M, Potti J, Quinn JL, Réale D, Kristin Reiertsen T, Rosivall B, Russell AF, Rytkönen S, Sánchez‐Virosta P, Santos ESA, Schroeder J, Senar JC, Seress G, Slagsvold T, Szulkin M, Teplitsky C, Tilgar V, Tolstoguzov A, Török J, Valcu M, Vatka E, Verhulst S, Watson H, Yuta T, Zamora‐Marín JM, Visser ME. Connecting the data landscape of long-term ecological studies: The SPI-Birds data hub. J Anim Ecol 2021; 90:2147-2160. [PMID: 33205462 PMCID: PMC8518542 DOI: 10.1111/1365-2656.13388] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/01/2020] [Indexed: 01/20/2023]
Abstract
The integration and synthesis of the data in different areas of science is drastically slowed and hindered by a lack of standards and networking programmes. Long-term studies of individually marked animals are not an exception. These studies are especially important as instrumental for understanding evolutionary and ecological processes in the wild. Furthermore, their number and global distribution provides a unique opportunity to assess the generality of patterns and to address broad-scale global issues (e.g. climate change). To solve data integration issues and enable a new scale of ecological and evolutionary research based on long-term studies of birds, we have created the SPI-Birds Network and Database (www.spibirds.org)-a large-scale initiative that connects data from, and researchers working on, studies of wild populations of individually recognizable (usually ringed) birds. Within year and a half since the establishment, SPI-Birds has recruited over 120 members, and currently hosts data on almost 1.5 million individual birds collected in 80 populations over 2,000 cumulative years, and counting. SPI-Birds acts as a data hub and a catalogue of studied populations. It prevents data loss, secures easy data finding, use and integration and thus facilitates collaboration and synthesis. We provide community-derived data and meta-data standards and improve data integrity guided by the principles of Findable, Accessible, Interoperable and Reusable (FAIR), and aligned with the existing metadata languages (e.g. ecological meta-data language). The encouraging community involvement stems from SPI-Bird's decentralized approach: research groups retain full control over data use and their way of data management, while SPI-Birds creates tailored pipelines to convert each unique data format into a standard format. We outline the lessons learned, so that other communities (e.g. those working on other taxa) can adapt our successful model. Creating community-specific hubs (such as ours, COMADRE for animal demography, etc.) will aid much-needed large-scale ecological data integration.
Collapse
|
36
|
Moretti M, Fontana S, Carscadden KA, MacIvor JS. Reproductive trait differences drive offspring production in urban cavity-nesting bees and wasps. Ecol Evol 2021; 11:9932-9948. [PMID: 34367550 PMCID: PMC8328425 DOI: 10.1002/ece3.7537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/11/2021] [Accepted: 03/16/2021] [Indexed: 11/24/2022] Open
Abstract
The contrasting and idiosyncratic changes in biodiversity that have been documented across urbanization gradients call for a more mechanistic understanding of urban community assembly. The reproductive success of organisms in cities should underpin their population persistence and the maintenance of biodiversity in urban landscapes. We propose that exploring individual-level reproductive traits and environmental drivers of reproductive success could provide the necessary links between environmental conditions, offspring production, and biodiversity in urban areas. For 3 years, we studied cavity-nesting solitary bees and wasps in four urban green space types across Toronto, Canada. We measured three reproductive traits of each nest: the total number of brood cells, the proportion of parasite-free cells, and the proportion of non-emerged brood cells that were parasite-free. We determined (a) how reproductive traits, trait diversity and offspring production respond to multiple environmental variables and (b) how well reproductive trait variation explains the offspring production of single nests, by reflecting the different ways organisms navigate trade-offs between gathering of resources and exposure to parasites. Our results showed that environmental variables were poor predictors of mean reproductive trait values, trait diversity, and offspring production. However, offspring production was highly positively correlated with reproductive trait evenness and negatively correlated with trait richness and divergence. This suggests that a narrow range of reproductive traits are optimal for reproduction, and the even distribution of individual reproductive traits across those optimal phenotypes is consistent with the idea that selection could favor diverse reproductive strategies to reduce competition. This study is novel in its exploration of individual-level reproductive traits and its consideration of multiple axes of urbanization. Reproductive trait variation did not follow previously reported biodiversity-urbanization patterns; the insensitivity to urbanization gradients raise questions about the role of the spatial mosaic of habitats in cities and the disconnections between different metrics of biodiversity.
Collapse
Affiliation(s)
- Marco Moretti
- Biodiversity and Conservation BiologySwiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Simone Fontana
- Biodiversity and Conservation BiologySwiss Federal Research Institute WSLBirmensdorfSwitzerland
- Nature Conservation and Landscape EcologyUniversity of FreiburgFreiburgGermany
| | - Kelly A. Carscadden
- Department of Ecology and Evolutionary BiologyUniversity of ColoradoBoulderCOUSA
| | - J. Scott MacIvor
- Department of Biological SciencesUniversity of Toronto ScarboroughTorontoONCanada
| |
Collapse
|
37
|
Crane M, Silva I, Marshall BM, Strine CT. Lots of movement, little progress: a review of reptile home range literature. PeerJ 2021; 9:e11742. [PMID: 34322323 PMCID: PMC8300531 DOI: 10.7717/peerj.11742] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/17/2021] [Indexed: 11/20/2022] Open
Abstract
Reptiles are the most species-rich terrestrial vertebrate group with a broad diversity of life history traits. Biotelemetry is an essential methodology for studying reptiles as it compensates for several limitations when studying their natural history. We evaluated trends in terrestrial reptile spatial ecology studies focusing upon quantifying home ranges for the past twenty years. We assessed 290 English-language reptile home range studies published from 2000-2019 via a structured literature review investigating publications' study location, taxonomic group, methodology, reporting, and analytical techniques. Substantial biases remain in both location and taxonomic groups in the literature, with nearly half of all studies (45%) originating from the USA. Snakes were most often studied, and crocodiles were least often studied, while testudines tended to have the greatest within study sample sizes. More than half of all studies lacked critical methodological details, limiting the number of studies for inclusion in future meta-analyses (55% of studies lacked information on individual tracking durations, and 51% lacked sufficient information on the number of times researchers recorded positions). Studies continue to rely on outdated methods to quantify space-use (including Minimum Convex Polygons and Kernel Density Estimators), often failing to report subtleties regarding decisions that have substantial impact on home range area estimates. Moving forward researchers can select a suite of appropriate analytical techniques tailored to their research question (dynamic Brownian Bridge Movement Models for within sample interpolation, and autocorrelated Kernel Density Estimators for beyond sample extrapolation). Only 1.4% of all evaluated studies linked to available and usable telemetry data, further hindering scientific consensus. We ultimately implore herpetologists to adopt transparent reporting practices and make liberal use of open data platforms to maximize progress in the field of reptile spatial ecology.
Collapse
Affiliation(s)
- Matthew Crane
- Conservation Ecology Program, King Mongkut’s Institute of Technology Thonburi, Bangkok, Bangkhuntien / Bangkok, Thailand
| | - Inês Silva
- (CASUS), Center for Advanced Systems Understanding, Görlitz, Germany
- (HZDR), Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - Benjamin M. Marshall
- School of Biology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| | - Colin T. Strine
- School of Biology, Suranaree University of Technology, Nakhon Ratchasima, Thailand
| |
Collapse
|
38
|
Krug RM, Petchey OL. Metadata Made Easy: Develop and Use Domain-Specific Metadata Schemes by following the dmdScheme approach. Ecol Evol 2021; 11:9174-9181. [PMID: 34306613 PMCID: PMC8293710 DOI: 10.1002/ece3.7764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/22/2021] [Accepted: 05/14/2021] [Indexed: 11/24/2022] Open
Abstract
Metadata plays an essential role in the long-term preservation, reuse, and interoperability of data. Nevertheless, creating useful metadata can be sufficiently difficult and weakly enough incentivized that many datasets may be accompanied by little or no metadata. One key challenge is, therefore, how to make metadata creation easier and more valuable. We present a solution that involves creating domain-specific metadata schemes that are as complex as necessary and as simple as possible. These goals are achieved by co-development between a metadata expert and the researchers (i.e., the data creators). The final product is a bespoke metadata scheme into which researchers can enter information (and validate it) via the simplest of interfaces: a web browser application and a spreadsheet.We provide the R package dmdScheme (dmdScheme: An R package for working with domain specific MetaData schemes (Version v0.9.22), 2019) for creating a template domain-specific scheme. We describe how to create a domain-specific scheme from this template, including the iterative co-development process, and the simple methods for using the scheme, and simple methods for quality assessment, improvement, and validation.The process of developing a metadata scheme following the outlined approach was successful, resulting in a metadata scheme which is used for the data generated in our research group. The validation quickly identifies forgotten metadata, as well as inconsistent metadata, therefore improving the quality of the metadata. Multiple output formats are available, including XML.Making the provision of metadata easier while also ensuring high quality must be a priority for data curation initiatives. We show how both objectives are achieved by close collaboration between metadata experts and researchers to create domain-specific schemes. A near-future priority is to provide methods to interface domain-specific schemes with general metadata schemes, such as the Ecological Metadata Language, to increase interoperability.
Collapse
Affiliation(s)
- Rainer M. Krug
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichZurichSwitzerland
| | - Owen L. Petchey
- Department of Evolutionary Biology and Environmental StudiesUniversity of ZürichZurichSwitzerland
| |
Collapse
|
39
|
Hagge J, Müller J, Birkemoe T, Buse J, Christensen RHB, Gossner MM, Gruppe A, Heibl C, Jarzabek-Müller A, Seibold S, Siitonen J, Soutinho JG, Sverdrup-Thygeson A, Thorn S, Drag L. What does a threatened saproxylic beetle look like? Modelling extinction risk using a new morphological trait database. J Anim Ecol 2021; 90:1934-1947. [PMID: 33942309 DOI: 10.1111/1365-2656.13512] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 04/22/2021] [Indexed: 11/30/2022]
Abstract
The extinction of species is a non-random process, and understanding why some species are more likely to go extinct than others is critical for conservation efforts. Functional trait-based approaches offer a promising tool to achieve this goal. In forests, deadwood-dependent (saproxylic) beetles comprise a major part of threatened species, but analyses of their extinction risk have been hindered by the availability of suitable morphological traits. To better understand the mechanisms underlying extinction in insects, we investigated the relationships between morphological features and the extinction risk of saproxylic beetles. Specifically, we hypothesised that species darker in colour, with a larger and rounder body, a lower mobility, lower sensory perception and more robust mandibles are at higher risk. We first developed a protocol for morphological trait measurements and present a database of 37 traits for 1,157 European saproxylic beetle species. Based on 13 selected, independent traits characterising aspects of colour, body shape, locomotion, sensory perception and foraging, we used a proportional-odds multiple linear mixed-effects model to model the German Red List categories of 744 species as an ordinal index of extinction risk. Six out of 13 traits correlated significantly with extinction risk. Larger species as well as species with a broad and round body had a higher extinction risk than small, slim and flattened species. Species with short wings had a higher extinction risk than those with long wings. On the contrary, extinction risk increased with decreasing wing load and with higher mandibular aspect ratio (shorter and more robust mandibles). Our study provides new insights into how morphological traits, beyond the widely used body size, determine the extinction risk of saproxylic beetles. Moreover, our approach shows that the morphological characteristics of beetles can be comprehensively represented by a selection of 13 traits. We recommend them as a starting point for functional analyses in the rapidly growing field of ecological and conservation studies of deadwood.
Collapse
Affiliation(s)
- Jonas Hagge
- Forest Nature Conservation, Georg-August-University Göttingen, Göttingen, Germany.,Forest Nature Conservation, Northwest German Forest Research Institute, Münden, Germany
| | - Jörg Müller
- Bavarian Forest National Park, Grafenau, Germany.,Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Rauhenebrach, Germany
| | - Tone Birkemoe
- The Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Aas, Norway
| | - Jörn Buse
- Black Forest National Park, Freudenstadt, Germany
| | | | - Martin M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.,ETH Zurich, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, Zurich, Switzerland
| | - Axel Gruppe
- Chair of Zoology, Entomology Research Group, Technical University of Munich, Freising, Germany
| | | | | | - Sebastian Seibold
- Ecosystem Dynamics and Forest Management Group, Department of Ecology and Ecosystem Management, Technical University of Munich, Freising, Germany.,Berchtesgaden National Park, Berchtesgaden, Germany
| | - Juha Siitonen
- Natural Resources Institute Finland (Luke), Helsinki, Finland
| | | | - Anne Sverdrup-Thygeson
- The Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Aas, Norway
| | - Simon Thorn
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Rauhenebrach, Germany
| | - Lukas Drag
- Field Station Fabrikschleichach, Department of Animal Ecology and Tropical Biology, Biocenter, University of Würzburg, Rauhenebrach, Germany
| |
Collapse
|
40
|
Lenters TP, Henderson A, Dracxler CM, Elias GA, Kamga SM, Couvreur TL, Kissling WD. Integration and harmonization of trait data from plant individuals across heterogeneous sources. ECOL INFORM 2021. [DOI: 10.1016/j.ecoinf.2020.101206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
41
|
|
42
|
Parravicini V, Casey JM, Schiettekatte NMD, Brandl SJ, Pozas-Schacre C, Carlot J, Edgar GJ, Graham NAJ, Harmelin-Vivien M, Kulbicki M, Strona G, Stuart-Smith RD. Delineating reef fish trophic guilds with global gut content data synthesis and phylogeny. PLoS Biol 2020; 18:e3000702. [PMID: 33370276 PMCID: PMC7793298 DOI: 10.1371/journal.pbio.3000702] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 01/08/2021] [Accepted: 12/03/2020] [Indexed: 11/19/2022] Open
Abstract
Understanding species' roles in food webs requires an accurate assessment of their trophic niche. However, it is challenging to delineate potential trophic interactions across an ecosystem, and a paucity of empirical information often leads to inconsistent definitions of trophic guilds based on expert opinion, especially when applied to hyperdiverse ecosystems. Using coral reef fishes as a model group, we show that experts disagree on the assignment of broad trophic guilds for more than 20% of species, which hampers comparability across studies. Here, we propose a quantitative, unbiased, and reproducible approach to define trophic guilds and apply recent advances in machine learning to predict probabilities of pairwise trophic interactions with high accuracy. We synthesize data from community-wide gut content analyses of tropical coral reef fishes worldwide, resulting in diet information from 13,961 individuals belonging to 615 reef fish. We then use network analysis to identify 8 trophic guilds and Bayesian phylogenetic modeling to show that trophic guilds can be predicted based on phylogeny and maximum body size. Finally, we use machine learning to test whether pairwise trophic interactions can be predicted with accuracy. Our models achieved a misclassification error of less than 5%, indicating that our approach results in a quantitative and reproducible trophic categorization scheme, as well as high-resolution probabilities of trophic interactions. By applying our framework to the most diverse vertebrate consumer group, we show that it can be applied to other organismal groups to advance reproducibility in trait-based ecology. Our work thus provides a viable approach to account for the complexity of predator-prey interactions in highly diverse ecosystems.
Collapse
Affiliation(s)
- Valeriano Parravicini
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL,” Perpignan, France
| | - Jordan M. Casey
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL,” Perpignan, France
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, Texas, United States of America
| | - Nina M. D. Schiettekatte
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL,” Perpignan, France
| | - Simon J. Brandl
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL,” Perpignan, France
- Department of Marine Science, University of Texas at Austin, Marine Science Institute, Port Aransas, Texas, United States of America
- Centre for the Synthesis and Analysis of Biodiversity (CESAB), Institut Bouisson Bertrand, Montpellier, France
| | - Chloé Pozas-Schacre
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL,” Perpignan, France
| | - Jérémy Carlot
- PSL Université Paris: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan, France
- Laboratoire d’Excellence “CORAIL,” Perpignan, France
| | - Graham J. Edgar
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | | | | | - Michel Kulbicki
- UMR Entropie, LabEx Corail, IRD, Université de Perpignan, Perpignan, France
| | - Giovanni Strona
- University of Helsinki, Department of Bioscience, Helsinki, Finland
| | - Rick D. Stuart-Smith
- Centre for the Synthesis and Analysis of Biodiversity (CESAB), Institut Bouisson Bertrand, Montpellier, France
| |
Collapse
|
43
|
Callaghan CT, Poore AGB, Mesaglio T, Moles AT, Nakagawa S, Roberts C, Rowley JJL, VergÉs A, Wilshire JH, Cornwell WK. Three Frontiers for the Future of Biodiversity Research Using Citizen Science Data. Bioscience 2020. [DOI: 10.1093/biosci/biaa131] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AbstractCitizen science is fundamentally shifting the future of biodiversity research. But although citizen science observations are contributing an increasingly large proportion of biodiversity data, they only feature in a relatively small percentage of research papers on biodiversity. We provide our perspective on three frontiers of citizen science research, areas that we feel to date have had minimal scientific exploration but that we believe deserve greater attention as they present substantial opportunities for the future of biodiversity research: sampling the undersampled, capitalizing on citizen science's unique ability to sample poorly sampled taxa and regions of the world, reducing taxonomic and spatial biases in global biodiversity data sets; estimating abundance and density in space and time, develop techniques to derive taxon-specific densities from presence or absence and presence-only data; and capitalizing on secondary data collection, moving beyond data on the occurrence of single species and gain further understanding of ecological interactions among species or habitats. The contribution of citizen science to understanding the important biodiversity questions of our time should be more fully realized.
Collapse
Affiliation(s)
- Corey T Callaghan
- Centre for Ecosystem Science, School of Biological, Earth, and Environmental Sciences, University of New South Wales
- Ecology and Evolution Research Centre, School of Biological, Earth, and Environmental Sciences, also at the University of New South Wales
| | - Alistair G B Poore
- Ecology and Evolution Research Centre, School of Biological, Earth, and Environmental Sciences, also at the University of New South Wales
| | - Thomas Mesaglio
- Centre for Ecosystem Science, School of Biological, Earth, and Environmental Sciences, University of New South Wales
| | - Angela T Moles
- Ecology and Evolution Research Centre, School of Biological, Earth, and Environmental Sciences, also at the University of New South Wales
| | - Shinichi Nakagawa
- Ecology and Evolution Research Centre, School of Biological, Earth, and Environmental Sciences, also at the University of New South Wales
| | - Christopher Roberts
- Centre for Ecosystem Science, School of Biological, Earth, and Environmental Sciences, University of New South Wales
| | - Jodi J L Rowley
- Australian Museum Research Institute, part of the Australian Museum, Sydney, New South Wales, Australia
| | - Adriana VergÉs
- Ecology and Evolution Research Centre, School of Biological, Earth, and Environmental Sciences, also at the University of New South Wales
| | - John H Wilshire
- Centre for Ecosystem Science, School of Biological, Earth, and Environmental Sciences, University of New South Wales
| | - William K Cornwell
- Centre for Ecosystem Science, School of Biological, Earth, and Environmental Sciences, University of New South Wales
| |
Collapse
|
44
|
Callaghan CT, Benedetti Y, Wilshire JH, Morelli F. Avian trait specialization is negatively associated with urban tolerance. OIKOS 2020. [DOI: 10.1111/oik.07356] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Corey T. Callaghan
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences; UNSW Sydney Sydney NSW 2052 Australia
- Community Ecology & Conservation Research Group, Faculty of Environmental Sciences, Czech Univ. of Life Sciences Prague Prague Czech Republic
| | - Yanina Benedetti
- Dept of Applied Geoinformatics and Spatial Planning, Faculty of Environmental Sciences, Czech Univ. of Life Sciences Prague Prague Czech Republic
| | - John H. Wilshire
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences; UNSW Sydney Sydney NSW 2052 Australia
- Centre for Biodiversity and Global Change, Ecology and Evolutionary Biology Dept, Yale Univ. New Haven CT USA
| | - Federico Morelli
- Dept of Applied Geoinformatics and Spatial Planning, Faculty of Environmental Sciences, Czech Univ. of Life Sciences Prague Prague Czech Republic
- Faculty of Biological Sciences, Univ. of Zielona Góra Zielona Góra Poland
| |
Collapse
|
45
|
Fukushima CS, Mammola S, Cardoso P. Global wildlife trade permeates the Tree of Life. BIOLOGICAL CONSERVATION 2020; 247:108503. [PMID: 32454527 PMCID: PMC7237378 DOI: 10.1016/j.biocon.2020.108503] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 05/27/2023]
Abstract
Legal and illegal wildlife trade is a multibillion dollar industry that is driving several species toward extinction. Even though wildlife trade permeates the Tree of Life, most analyses to date focused on the trade of a small selection of charismatic vertebrate species. Given that vertebrate taxa represent only 3% of described species, this is a significant bias that prevents the development of comprehensive conservation strategies. In this short contribution, we discuss the significance of global wildlife trade considering the full diversity of organisms for which data are available in the IUCN database. We emphasize the importance of being fast and effective in filling the knowledge gaps about non-vertebrate life forms, in order to achieve an in-depth understanding of global trading patterns across the full canopy of the Tree of Life, and not just its most appealing twig.
Collapse
Affiliation(s)
- Caroline Sayuri Fukushima
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of Helsinki, Helsinki, Finland
| | - Stefano Mammola
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of Helsinki, Helsinki, Finland
- Molecular Ecology Group (MEG), IRSA-Water Research Institute, National Research Council, Verbania Pallanza, Italy
| | - Pedro Cardoso
- Laboratory for Integrative Biodiversity Research (LIBRe), Finnish Museum of Natural History (LUOMUS), University of Helsinki, Helsinki, Finland
| |
Collapse
|
46
|
Morelli F, Benedetti Y, Callaghan CT. Ecological specialization and population trends in European breeding birds. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e00996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
|
47
|
Verde Arregoitia LD, Teta P, D’Elía G. Patterns in research and data sharing for the study of form and function in caviomorph rodents. J Mammal 2020; 101:604-612. [PMID: 32454535 PMCID: PMC7236905 DOI: 10.1093/jmammal/gyaa002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/27/2019] [Indexed: 11/16/2022] Open
Abstract
The combination of morphometrics, phylogenetic comparative methods, and open data sets has renewed interest in relating morphology to adaptation and ecological opportunities. Focusing on the Caviomorpha, a well-studied mammalian group, we evaluated patterns in research and data sharing in studies relating form and function. Caviomorpha encompasses a radiation of rodents that is diverse both taxonomically and ecologically. We reviewed 41 publications investigating ecomorphology in this group. We recorded the type of data used in each study and whether these data were made available, and we re-digitized all provided data. We tracked two major lines of information: collections material examined and trait data for morphological and ecological traits. Collectively, the studies considered 63% of extant caviomorph species; all extant families and genera were represented. We found that species-level trait data rarely were provided. Specimen-level data were even less common. Morphological and ecological data were too heterogeneous and sparse to aggregate into a single data set, so we created relational tables with the data. Additionally, we concatenated all specimen lists into a single data set and standardized all relevant data for phylogenetic hypotheses and gene sequence accessions to facilitate future morphometric and phylogenetic comparative research. This work highlights the importance and ongoing use of scientific collections, and it allows for the integration of specimen information with species trait data. Recientemente ha resurgido el interés por estudiar la relación entre morfología, ecología, y adaptación. Esto se debe al desarrollo de nuevas herramientas morfométricas y filogenéticas, y al acceso a grandes bases de datos para estudios comparados. Revisamos 41 publicaciones sobre ecomorfología de roedores caviomorfos, un grupo diverso y bien estudiado, para evaluar los patrones de investigación y la transparencia para la liberación de datos. Registramos los tipos de datos que se utilizaron para cada estudio y si los datos están disponibles. Cuando estos datos se compartieron, los redigitalizamos. Nos enfocamos en los ejemplares consultados, y en datos que describen rasgos ecológicos y morfológicos para las especies estudiadas. Los estudios que revisamos abarcan el 63% de las especies de caviomorfos que actualmente existen. Encontramos que raramente fueron compartidos los datos que se tomaron para especies, y menos aún para ejemplares. Los datos morfológicos y ecológicos eran demasiado heterogéneos e exiguos para consolidar en un solo banco de datos; debido a esta circunstancia, creamos tablas relacionales con los datos. Además, enlazamos todas las listas individuales de especímenes para crear un solo banco de datos y estandarizamos todos los datos pertinentes a hipótesis filogenéticas, así como los números de acceso de secuencias genéticas, para así facilitar eventuales estudios comparados de morfometría y filogenia. Este trabajo resalta la importancia de las colecciones científicas y documenta su uso, además permitiendo la futura integración de datos derivados de ejemplares con datos sobre rasgos ecomorfológicos a nivel de especie.
Collapse
Affiliation(s)
- Luis D Verde Arregoitia
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Campus Isla Teja, Valdivia CP, Chile
| | - Pablo Teta
- División Mastozoología, Museo Argentino de Ciencias Naturales “Bernardino Rivadavia”, Ciudad Autónoma de Buenos Aires, Argentina
| | - Guillermo D’Elía
- Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Campus Isla Teja, Valdivia CP, Chile
| |
Collapse
|
48
|
Gallagher RV, Falster DS, Maitner BS, Salguero-Gómez R, Vandvik V, Pearse WD, Schneider FD, Kattge J, Poelen JH, Madin JS, Ankenbrand MJ, Penone C, Feng X, Adams VM, Alroy J, Andrew SC, Balk MA, Bland LM, Boyle BL, Bravo-Avila CH, Brennan I, Carthey AJR, Catullo R, Cavazos BR, Conde DA, Chown SL, Fadrique B, Gibb H, Halbritter AH, Hammock J, Hogan JA, Holewa H, Hope M, Iversen CM, Jochum M, Kearney M, Keller A, Mabee P, Manning P, McCormack L, Michaletz ST, Park DS, Perez TM, Pineda-Munoz S, Ray CA, Rossetto M, Sauquet H, Sparrow B, Spasojevic MJ, Telford RJ, Tobias JA, Violle C, Walls R, Weiss KCB, Westoby M, Wright IJ, Enquist BJ. Open Science principles for accelerating trait-based science across the Tree of Life. Nat Ecol Evol 2020; 4:294-303. [PMID: 32066887 DOI: 10.1038/s41559-020-1109-6] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Accepted: 01/10/2020] [Indexed: 01/22/2023]
Abstract
Synthesizing trait observations and knowledge across the Tree of Life remains a grand challenge for biodiversity science. Species traits are widely used in ecological and evolutionary science, and new data and methods have proliferated rapidly. Yet accessing and integrating disparate data sources remains a considerable challenge, slowing progress toward a global synthesis to integrate trait data across organisms. Trait science needs a vision for achieving global integration across all organisms. Here, we outline how the adoption of key Open Science principles-open data, open source and open methods-is transforming trait science, increasing transparency, democratizing access and accelerating global synthesis. To enhance widespread adoption of these principles, we introduce the Open Traits Network (OTN), a global, decentralized community welcoming all researchers and institutions pursuing the collaborative goal of standardizing and integrating trait data across organisms. We demonstrate how adherence to Open Science principles is key to the OTN community and outline five activities that can accelerate the synthesis of trait data across the Tree of Life, thereby facilitating rapid advances to address scientific inquiries and environmental issues. Lessons learned along the path to a global synthesis of trait data will provide a framework for addressing similarly complex data science and informatics challenges.
Collapse
Affiliation(s)
- Rachael V Gallagher
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia.
| | - Daniel S Falster
- Evolution and Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Brian S Maitner
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Roberto Salguero-Gómez
- Department of Zoology, Oxford University, Oxford, UK.,Centre for Biodiversity and Conservation Science, University of Queensland, Brisbane, Queensland, Australia.,Evolutionary Demography Laboratory, Max Plank Institute for Demographic Research, Rostock, Germany
| | - Vigdis Vandvik
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway
| | - William D Pearse
- Ecology Center and Department of Biology, Utah State University, Logan, UT, USA
| | | | - Jens Kattge
- Max Planck Institute for Biogeochemistry, Jena, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | | | - Joshua S Madin
- Hawai'i Institute of Marine Biology, University of Hawai'i at Manoa, Manoa, HI, USA
| | - Markus J Ankenbrand
- Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,Center for Computational and Theoretical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,Comprehensive Heart Failure Center, University Hospital Wuerzburg, Wuerzburg, Germany
| | - Caterina Penone
- Institute of Plant Sciences, University of Bern, Bern, Switzerland
| | - Xiao Feng
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Vanessa M Adams
- Discipline of Geography and Spatial Sciences, University of Tasmania, Hobart, Tasmania, Australia
| | - John Alroy
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Samuel C Andrew
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Meghan A Balk
- Bio5 Institute, University of Arizona, Tucson, AZ, USA
| | - Lucie M Bland
- School of Life and Environmental Sciences, Centre for Integrative Ecology, Deakin University, Geelong, Victoria, Australia
| | - Brad L Boyle
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Catherine H Bravo-Avila
- Department of Biology, University of Miami, Miami, FL, USA.,Fairchild Tropical Botanic Garden, Coral Gables, FL, USA
| | - Ian Brennan
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Alexandra J R Carthey
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Renee Catullo
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Brittany R Cavazos
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Dalia A Conde
- Species360 Conservation Science Alliance, Bloomington, MN, USA.,Interdisciplinary Center on Population Dynamics, University of Southern Denmark, Odense, Denmark.,Department of Biology, University of Southern Denmark, Odense, Denmark
| | - Steven L Chown
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Belen Fadrique
- Department of Biology, University of Miami, Miami, FL, USA
| | - Heloise Gibb
- Department of Ecology, Environment and Evolution and Centre for Future Landscapes, La Trobe University, Melbourne, Victoria, Australia
| | - Aud H Halbritter
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway
| | - Jennifer Hammock
- National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - J Aaron Hogan
- International Center for Tropical Botany, Department of Biological Sciences, Florida International University, Miami, FL, USA
| | - Hamish Holewa
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Michael Hope
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Canberra, Australian Capital Territory, Australia
| | - Colleen M Iversen
- Climate Change Science Institute and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Malte Jochum
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.,Institute of Plant Sciences, University of Bern, Bern, Switzerland.,Institute of Biology, Leipzig University, Leipzig, Germany
| | - Michael Kearney
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Alexander Keller
- Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,Center for Computational and Theoretical Biology, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Paula Mabee
- Department of Biology, University of South Dakota, Vermillion, SD, USA
| | - Peter Manning
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt, Germany
| | - Luke McCormack
- Center for Tree Science, The Morton Arboretum, Lisle, IL, USA
| | - Sean T Michaletz
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daniel S Park
- Department of Organismic and Evolutionary Biology and Harvard University Herbaria, Harvard University, Cambridge, MA, USA
| | - Timothy M Perez
- Department of Biology, University of Miami, Miami, FL, USA.,Fairchild Tropical Botanic Garden, Coral Gables, FL, USA
| | - Silvia Pineda-Munoz
- School of Biological Sciences and School of Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Courtenay A Ray
- School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Maurizio Rossetto
- National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia.,Queensland Alliance of Agriculture and Food Innovation, University of Queensland, Brisbane, Queensland, Australia
| | - Hervé Sauquet
- Evolution and Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.,National Herbarium of New South Wales, Royal Botanic Gardens and Domain Trust, Sydney, New South Wales, Australia.,Ecologie Systématique Evolution, Univ. Paris-Sud, CNRS, AgroParisTech, Universite Paris-Saclay, Orsay, France
| | - Benjamin Sparrow
- TERN / School of Biological Sciences, Faculty of Science, The University of Adelaide, Adelaide, South Australia, Australia
| | - Marko J Spasojevic
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
| | - Richard J Telford
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,Bjerknes Centre for Climate Research, University of Bergen, Bergen, Norway
| | - Joseph A Tobias
- Department of Life Sciences, Imperial College London, London, UK
| | - Cyrille Violle
- CEFE, CNRS, Univ Montpellier, Université Paul Valéry Montpellier, Montpellier, France
| | | | | | - Mark Westoby
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Ian J Wright
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Brian J Enquist
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Santa Fe Institute, Santa Fe, NM, USA
| |
Collapse
|
49
|
Schleuning M, Neuschulz EL, Albrecht J, Bender IMA, Bowler DE, Dehling DM, Fritz SA, Hof C, Mueller T, Nowak L, Sorensen MC, Böhning-Gaese K, Kissling WD. Trait-Based Assessments of Climate-Change Impacts on Interacting Species. Trends Ecol Evol 2020; 35:319-328. [PMID: 31987640 DOI: 10.1016/j.tree.2019.12.010] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 12/04/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022]
Abstract
Plant-animal interactions are fundamentally important in ecosystems, but have often been ignored by studies of climate-change impacts on biodiversity. Here, we present a trait-based framework for predicting the responses of interacting plants and animals to climate change. We distinguish three pathways along which climate change can impact interacting species in ecological communities: (i) spatial and temporal mismatches in the occurrence and abundance of species, (ii) the formation of novel interactions and secondary extinctions, and (iii) alterations of the dispersal ability of plants. These pathways are mediated by three kinds of functional traits: response traits, matching traits, and dispersal traits. We propose that incorporating these traits into predictive models will improve assessments of the responses of interacting species to climate change.
Collapse
Affiliation(s)
- Matthias Schleuning
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany.
| | - Eike Lena Neuschulz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Jörg Albrecht
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - Irene M A Bender
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany; Institute of Biology, Geobotany and Botanical Garden, Martin-Luther-University Halle-Wittenberg, 06108 Halle, Germany
| | - Diana E Bowler
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - D Matthias Dehling
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch 8140, New Zealand
| | - Susanne A Fritz
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Department of Biological Sciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Christian Hof
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Terrestrial Ecology Research Group, Technical University of Munich, Hans-Carl-von-Carlowitz-Platz 2, 85354 Freising, Germany
| | - Thomas Mueller
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Department of Biological Sciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Larissa Nowak
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Department of Biological Sciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Marjorie C Sorensen
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Department of Biological Sciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany; Department of Integrative Biology, University of Guelph, 50 Stone Rd. E., Guelph, ON, Canada N1G 2W1
| | - Katrin Böhning-Gaese
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany; Department of Biological Sciences, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - W Daniel Kissling
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94240, 1090, GE, Amsterdam, The Netherlands
| |
Collapse
|
50
|
Berzaghi F, Wright IJ, Kramer K, Oddou-Muratorio S, Bohn FJ, Reyer CPO, Sabaté S, Sanders TGM, Hartig F. Towards a New Generation of Trait-Flexible Vegetation Models. Trends Ecol Evol 2019; 35:191-205. [PMID: 31882280 DOI: 10.1016/j.tree.2019.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/15/2019] [Accepted: 11/25/2019] [Indexed: 12/17/2022]
Abstract
Plant trait variability, emerging from eco-evolutionary dynamics that range from alleles to macroecological scales, is one of the most elusive, but possibly most consequential, aspects of biodiversity. Plasticity, epigenetics, and genetic diversity are major determinants of how plants will respond to climate change, yet these processes are rarely represented in current vegetation models. Here, we provide an overview of the challenges associated with understanding the causes and consequences of plant trait variability, and review current developments to include plasticity and evolutionary mechanisms in vegetation models. We also present a roadmap of research priorities to develop a next generation of vegetation models with flexible traits. Including trait variability in vegetation models is necessary to better represent biosphere responses to global change.
Collapse
Affiliation(s)
- Fabio Berzaghi
- Laboratory for Sciences of Climate and Environment (LSCE) - UMR CEA/CNRS/UVSQ, Gif-sur-Yvette 91191, France; Department of Biological Sciences, Macquarie University, Sydney, NSW 2022, Australia; Dipartimento per la Innovazione nei sistemi Biologici, Agroalimentari e Forestali, University of Tuscia, Viterbo 01100, Italy.
| | - Ian J Wright
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2022, Australia
| | - Koen Kramer
- Wageningen University and Research, Droevendaalse steeg 4, 6700AA Wageningen, The Netherlands
| | | | - Friedrich J Bohn
- Karlsruhe Institute of Technology, Institute for Meteorology and Climate Research, Atmospheric Environmental Research (IMK-IFU), Kreuzeckbahnstrasse 19, Garmisch-Partenkirchen 82467, Germany; Helmholtz Centre for Environmental Research - UFZ, Permoserstraße 15, Leipzig 04318, Germany
| | - Christopher P O Reyer
- Potsdam Institute for Climate Impact Research (PIK), Member of the Leibniz Association, PO Box 60 12 03, D-14412 Potsdam, Germany
| | - Santiago Sabaté
- Department of Evolutionary Biology, Ecology, and Environmental Sciences, University of Barcelona (UB), Barcelona 08028, Spain; CREAF (Center for Ecological Research and Forestry Applications), Cerdanyola del Vallès 08193, Spain
| | - Tanja G M Sanders
- Thuenen Institut of Forest Ecosystems, Alfred-Moeller-Str. 1, Haus 41/42, 16225 Eberswalde, Germany
| | - Florian Hartig
- Theoretical Ecology, Faculty of Biology and Preclinical Medicine, University of Regensburg, Universitätsstraße 3, 93053, Regensburg, Germany
| |
Collapse
|