1
|
Wu NC, Alton L, Bovo RP, Carey N, Currie SE, Lighton JRB, McKechnie AE, Pottier P, Rossi G, White CR, Levesque DL. Reporting guidelines for terrestrial respirometry: Building openness, transparency of metabolic rate and evaporative water loss data. Comp Biochem Physiol A Mol Integr Physiol 2024; 296:111688. [PMID: 38944270 DOI: 10.1016/j.cbpa.2024.111688] [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: 02/19/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/01/2024]
Abstract
Respirometry is an important tool for understanding whole-animal energy and water balance in relation to the environment. Consequently, the growing number of studies using respirometry over the last decade warrants reliable reporting and data sharing for effective dissemination and research synthesis. We provide a checklist guideline on five key sections to facilitate the transparency, reproducibility, and replicability of respirometry studies: 1) materials, set up, plumbing, 2) subject conditions/maintenance, 3) measurement conditions, 4) data processing, and 5) data reporting and statistics, each with explanations and example studies. Transparency in reporting and data availability has benefits on multiple fronts. Authors can use this checklist to design and report on their study, and reviewers and editors can use the checklist to assess the reporting quality of the manuscripts they review. Improved standards for reporting will enhance the value of primary studies and will greatly facilitate the ability to carry out higher quality research syntheses to address ecological and evolutionary theories.
Collapse
Affiliation(s)
- Nicholas C Wu
- Hawkesbury Institute for the Environment, Western Sydney University, New South Wales 2753, Australia.
| | - Lesley Alton
- Centre for Geometric Biology, School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia. https://twitter.com/lesley_alton
| | - Rafael P Bovo
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, United States. https://twitter.com/bovo_rp
| | - Nicholas Carey
- Marine Directorate for the Scottish Government, Aberdeen, United Kingdom
| | - Shannon E Currie
- Institute for Cell and Systems Biology, University of Hamburg, Martin-Luther-King Plz 3, 20146 Hamburg, Germany; School of Biosciences, University of Melbourne, Victoria, Australia. https://twitter.com/batsinthbelfry
| | - John R B Lighton
- Sable Systems International, North Las Vegas, NV, United States. https://twitter.com/SableSys
| | - Andrew E McKechnie
- South African Research Chair in Conservation Physiology, South African National Biodiversity Institute, South Africa; DSI-NRF Centre of Excellence at the FitzPatrick Institute, Department of Zoology and Entomology, University of Pretoria, South Africa
| | - Patrice Pottier
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, New South Wales, Australia; Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia. https://twitter.com/PatriceEcoEvo
| | - Giulia Rossi
- Department of Biology, McMaster University, Hamilton, Ontario, Canada. https://twitter.com/giuliasrossi
| | - Craig R White
- Centre for Geometric Biology, School of Biological Sciences, Monash University, Melbourne, VIC 3800, Australia
| | - Danielle L Levesque
- School of Biology and Ecology, University of Maine, Orono, ME, United States. https://twitter.com/dl_levesque
| |
Collapse
|
2
|
Pottier P, Noble DWA, Seebacher F, Wu NC, Burke S, Lagisz M, Schwanz LE, Drobniak SM, Nakagawa S. New horizons for comparative studies and meta-analyses. Trends Ecol Evol 2024; 39:435-445. [PMID: 38216408 DOI: 10.1016/j.tree.2023.12.004] [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: 09/25/2023] [Revised: 11/29/2023] [Accepted: 12/08/2023] [Indexed: 01/14/2024]
Abstract
Comparative analyses and meta-analyses are key tools to elucidate broad biological principles, yet the two approaches often appear different in purpose. We propose an integrated approach that can generate deeper insights into ecoevolutionary processes. Marrying comparative and meta-analytic approaches will allow for (i) a more accurate investigation of drivers of biological variation, (ii) a greater ability to account for sources of non-independence in experimental data, (iii) more effective control of publication bias, and (iv) improved transparency and reproducibility. Stronger integration of meta-analytic and comparative studies can also broaden the scope from species-centric investigations to community-level responses and function-valued traits (e.g., reaction norms). We illuminate commonalities, differences, and the transformative potential of combining these methodologies for advancing ecology and evolutionary biology.
Collapse
Affiliation(s)
- Patrice Pottier
- Evolution and Ecology Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia.
| | - Daniel W A Noble
- Division of Ecology and Evolution, Research School of Biology, College of Science, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Frank Seebacher
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
| | - Nicholas C Wu
- Hawkesbury Institute for the Environment, Western Sydney University, New South Wales, Australia
| | - Samantha Burke
- Evolution and Ecology Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Malgorzata Lagisz
- Evolution and Ecology Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia; Theoretical Sciences Visiting Program, Okinawa Institute of Science and Technology Graduate University, Onna 904-0495, Japan
| | - Lisa E Schwanz
- Evolution and Ecology Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Szymon M Drobniak
- Evolution and Ecology Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia; Institute of Environmental Sciences, Jagiellonian University, Krakow, Poland
| | - Shinichi Nakagawa
- Evolution and Ecology Centre, School of Biological, Earth, and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia; Theoretical Sciences Visiting Program, Okinawa Institute of Science and Technology Graduate University, Onna 904-0495, Japan
| |
Collapse
|
3
|
Downie AT, Wu NC, Cramp RL, Franklin CE. Sublethal consequences of ultraviolet radiation exposure on vertebrates: Synthesis through meta-analysis. GLOBAL CHANGE BIOLOGY 2023; 29:6620-6634. [PMID: 37366045 DOI: 10.1111/gcb.16848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/26/2023] [Indexed: 06/28/2023]
Abstract
Ultraviolet radiation (UVR) from the sun is a natural daytime stressor for vertebrates in both terrestrial and aquatic ecosystems. UVR effects on the physiology of vertebrates manifest at the cellular level, but have bottom-up effects at the tissue level and on whole-animal performance and behaviours. Climate change and habitat loss (i.e. loss of shelter from UVR) could interact with and exacerbate the genotoxic and cytotoxic impacts of UVR on vertebrates. Therefore, it is important to understand the range and magnitude of effects that UVR can have on a diversity of physiological metrics, and how these may be shaped by taxa, life stage or geographical range in the major vertebrate groups. Using a meta-analytical approach, we used 895 observations from 47 different vertebrate species (fish, amphibian, reptile and bird), and 51 physiological metrics (i.e. cellular, tissue and whole-animal metrics), across 73 independent studies, to elucidate the general patterns of UVR effects on vertebrate physiology. We found that while UVR's impacts on vertebrates are generally negative, fish and amphibians were the most susceptible taxa, adult and larvae were the most susceptible life stages, and animals inhabiting temperate and tropical latitudes were the most susceptible to UVR stress. This information is critical to further our understanding of the adaptive capacity of vulnerable taxon to UVR stress, and the wide-spread sublethal physiological effects of UVR on vertebrates, such as DNA damage and cellular stress, which may translate up to impaired growth and locomotor performance. These impairments to individual fitness highlighted by our study may potentially cause disruptions at the ecosystem scale, especially if the effects of this pervasive diurnal stressor are exacerbated by climate change and reduced refuge due to habitat loss and degradation. Therefore, conservation of habitats that provide refuge to UVR stress will be critical to mitigate stress from this pervasive daytime stressor.
Collapse
Affiliation(s)
- Adam T Downie
- School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Nicholas C Wu
- Hawkesbury Institute for the Environment, Western Sydney University, Richmond, New South Wales, Australia
| | - Rebecca L Cramp
- School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| | - Craig E Franklin
- School of Biological Sciences, The University of Queensland, St. Lucia, Queensland, Australia
| |
Collapse
|
4
|
Wu NC. Pathogen load predicts host functional disruption: A meta‐analysis of an amphibian fungal panzootic. Funct Ecol 2023. [DOI: 10.1111/1365-2435.14245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Nicholas C. Wu
- Hawkesbury Institute for the Environment Western Sydney University Richmond New South Wales Australia
| |
Collapse
|
5
|
Gavgani HN, Grotewold E, Gray J. Methodology for Constructing a Knowledgebase for Plant Gene Regulation Information. Methods Mol Biol 2023; 2698:277-300. [PMID: 37682481 DOI: 10.1007/978-1-0716-3354-0_17] [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: 09/09/2023]
Abstract
The amount of biological data is growing at a rapid pace as many high-throughput omics technologies and data pipelines are developed. This is resulting in the growth of databases for DNA and protein sequences, gene expression, protein accumulation, structural, and localization information. The diversity and multi-omics nature of such bioinformatic data requires well-designed databases for flexible organization and presentation. Besides general-purpose online bioinformatic databases, users need narrowly focused online databases to quickly access a meaningful collection of related data for their research. Here, we describe the methodology used to implement a plant gene regulatory knowledgebase, with data, query, and tool features, as well as the ability to expand to accommodate future datasets. We exemplify this methodology for the GRASSIUS knowledgebase, but it is applicable to developing and updating similar plant gene regulatory knowledgebases. GRASSIUS organizes and presents gene regulatory data from grass species with a central focus on maize (Zea mays). The main class of data presented include not only the families of transcription factors (TFs) and co-regulators (CRs) but also protein-DNA interaction data, where available.
Collapse
Affiliation(s)
- Hadi Nayebi Gavgani
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
- Dandelions Therapeutics Inc., San Francisco, CA, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA
| | - John Gray
- Department of Biological Sciences, University of Toledo, Toledo, OH, USA.
| |
Collapse
|
6
|
Abstract
Rising temperatures represent a significant threat to the survival of ectothermic animals. As such, upper thermal limits represent an important trait to assess the vulnerability of ectotherms to changing temperatures. For instance, one may use upper thermal limits to estimate current and future thermal safety margins (i.e., the proximity of upper thermal limits to experienced temperatures), use this trait together with other physiological traits in species distribution models, or investigate the plasticity and evolvability of these limits for buffering the impacts of changing temperatures. While datasets on thermal tolerance limits have been previously compiled, they sometimes report single estimates for a given species, do not present measures of data dispersion, and are biased towards certain parts of the globe. To overcome these limitations, we systematically searched the literature in seven languages to produce the most comprehensive dataset to date on amphibian upper thermal limits, spanning 3,095 estimates across 616 species. This resource will represent a useful tool to evaluate the vulnerability of amphibians, and ectotherms more generally, to changing temperatures.
Collapse
|
7
|
Franklin CE, Patek SN, Wright PA. Looking to the future: Building New Paradigms in Comparative Physiology and Biomechanics. J Exp Biol 2022; 225:274422. [PMID: 35258620 DOI: 10.1242/jeb.244096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|