1
|
Ricolfi L, Taylor MD, Yang Y, Lagisz M, Nakagawa S. Maternal transfer of per- and polyfluoroalkyl substances (PFAS) in wild birds: A systematic review and meta-analysis. CHEMOSPHERE 2024; 361:142346. [PMID: 38759804 DOI: 10.1016/j.chemosphere.2024.142346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Per- and polyfluoroalkyl substances (PFAS) are synthetic chemicals widely used in consumer products. PFAS can accumulate in animal tissues, resulting in biomagnification and adverse effects on wildlife, such as reproductive impairment. In bird species, PFAS are transferred from mothers to eggs along with essential nutrients and may affect embryo development. However, the extent of maternal PFAS transfer across different species and compounds remains poorly understood. Here, we conducted a systematic review and meta-analysis to quantify maternal PFAS transfer in wild birds and investigate potential sources of variation. We tested the moderating effects of compounds' physicochemical properties and biological traits of studied birds. The dataset included 505 measurements of PFAS concentration and 371 effect sizes derived from 13 studies on 16 bird species and 25 compounds. Overall, across all studies and species, we found a 41% higher concentration of PFAS in offspring than in mothers. Specifically, contaminants were concentrated in the yolk, longer and heavier compounds showed preferential transfer, larger clutch size was associated with decreased PFAS transfer and a higher transfer rate was shown in species with piscivorous and opportunistic/diverse diets. A validation assessment showed good robustness of the overall meta-analytic result. Given the crucial role of birds in maintaining ecological balance, this research article has relevant implications for modelling the impacts of PFAS on wildlife, ecosystems, and human health.
Collapse
Affiliation(s)
- Lorenzo Ricolfi
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, NSW, 2052, Australia.
| | - Matthew D Taylor
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, NSW, 2052, Australia; Port Stephens Fisheries Institute, New South Wales Department of Primary Industries, Nelson Bay, Australia; Queensland Alliance for Environmental Health Sciences, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, Australia.
| | - Yefeng Yang
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, NSW, 2052, Australia.
| | - Malgorzata Lagisz
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, NSW, 2052, Australia.
| | - Shinichi Nakagawa
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales Sydney, Sydney, NSW, 2052, Australia.
| |
Collapse
|
2
|
Morrison K, Yang Y, Santana M, Lagisz M, Nakagawa S. A systematic evidence map and bibliometric analysis of the behavioural impacts of pesticide exposure on zebrafish. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 347:123630. [PMID: 38423273 DOI: 10.1016/j.envpol.2024.123630] [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: 10/26/2023] [Revised: 01/22/2024] [Accepted: 02/20/2024] [Indexed: 03/02/2024]
Abstract
Pesticides are indispensable in agriculture and have become ubiquitous in aquatic environments. Pesticides in natural environments can cause many negative impacts on aquatic species, ranging from mortality to sub-lethal physiological and behavioural changes. The complex sub-lethal impacts of pesticides are routinely tested on model species, with zebrafish (Danio rerio) being regularly used as a behavioural model. Although behavioural ecotoxicology research using zebrafish is increasing rapidly, we lack quantitative evidence to support which pesticides have been tested and how study designs are carried out. This shortcoming not only limits the deliberate planning for future primary studies to fill the knowledge gaps but also hinders evidence synthesis. To provide quantitative evidence of what pesticides are currently studied and what study designs are used, we combined a systematic evidence map approach and bibliometric analysis. This novel method has been coined research weaving and allows us to elicit gaps and clusters in our evidence base, whilst showing connections between authors and institutions. The methodology can be summarised in five primary steps: literature searching, screening, extraction, data analysis and bibliometric analysis. We identified four areas where research on the sub-lethal effects of pesticide exposure on zebrafish is lacking. First, some widely used pesticides, such as neonicotinoids, are understudied. Second, most studies do not report important elements of the study design, namely the sex and the life-stage of the zebrafish. Third, some behaviours, such as impacts of pesticide exposure on zebrafish cognition, are underexplored. And last, we revealed through the bibliometric analysis that most of the research is conducted in developed countries and there is limited cross country co-authorships. Upon identifying these gaps, we offer solutions for each limitation, emphasizing the importance of diverse global research output and cross-country co-authorships. Our systematic evidence map and bibliometric analysis provide valuable insights for helping to guide future research, which can be used to help support evidence-based policy decisions.
Collapse
Affiliation(s)
- Kyle Morrison
- Ecology & Evolution Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia.
| | - Yefeng Yang
- Ecology & Evolution Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Manuela Santana
- Marine Ecology Laboratory, Centre for Marine Studies, Federal University of Paraná, Paraná, Brazil
| | - Malgorzata Lagisz
- Ecology & Evolution Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia; Theoretical Sciences Visiting Program, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Shinichi Nakagawa
- Ecology & Evolution Research Centre, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia; Theoretical Sciences Visiting Program, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| |
Collapse
|
3
|
Macartney EL, Morrison K, Snook RR, Lagisz M, Nakagawa S. Intra-specific correlations between ejaculate traits and competitive fertilization success: a meta-analysis across species and fertilization modes. Evolution 2024; 78:497-510. [PMID: 38146674 DOI: 10.1093/evolut/qpad229] [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: 08/21/2023] [Revised: 12/04/2023] [Accepted: 12/21/2023] [Indexed: 12/27/2023]
Abstract
Understanding of how selection can act on traits that improve competitiveness and subsequent paternity has advanced, including the idea that internal and external fertilization presents different environments that may select differentially on ejaculate traits. However, no studies have quantitatively synthesized the intra-specific relationships between these traits and paternity. Therefore, we conducted a meta-analysis across 52 papers to determine which ejaculate traits positively correlate with paternity share and how these correlations vary with fertilization mode. Overall, most ejaculate traits were positively associated with paternity, with the notable exception of sperm length. Sub-analyses on sperm number, sperm length, and sperm velocity revealed no statistical differences between fertilization modes in the relationship between traits and paternity when all effect sizes across species were combined. However, in a sub-analysis on fish species only, we found evidence that sperm velocity may be more important in external fertilizers. We also observed differences in the importance of phylogenetic relatedness and some species-specific differences. Our results suggest that while most ejaculate traits should be under positive directional selection in both internal and external fertilizers, sperm length may be subject to more nuanced selection pressures. Overall, we highlight important patterns of intra-specific relationships between ejaculate traits and competitive fertilization success.
Collapse
Affiliation(s)
- Erin L Macartney
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Kyle Morrison
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Rhonda R Snook
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Malgorzata Lagisz
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
- Theoretical Sciences Visiting Program, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Shinichi Nakagawa
- Evolution and Ecology Research Centre, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
- Theoretical Sciences Visiting Program, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| |
Collapse
|
4
|
Fredston AL, Lowndes JSS. Welcoming More Participation in Open Data Science for the Oceans. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:537-549. [PMID: 37418835 DOI: 10.1146/annurev-marine-041723-094741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2023]
Abstract
Open science is a global movement happening across all research fields. Enabled by technology and the open web, it builds on years of efforts by individuals, grassroots organizations, institutions, and agencies. The goal is to share knowledge and broaden participation in science, from early ideation to making research outputs openly accessible to all (open access). With an emphasis on transparency and collaboration, the open science movement dovetails with efforts to increase diversity, equity, inclusion, and belonging in science and society. The US Biden-Harris Administration and many other US government agencies have declared 2023 the Year of Open Science, providing a great opportunity to boost participation in open science for the oceans. For researchers day-to-day, open science is a critical piece of modern analytical workflows with increasing amounts of data. Therefore, we focus this article on open data science-the tooling and people enabling reproducible, transparent, inclusive practices for data-intensive research-and its intersection with the marine sciences. We discuss the state of various dimensions of open science and argue that technical advancements have outpaced our field's culture change to incorporate them. Increasing inclusivity and technical skill building are interlinked and must be prioritized within the marine science community to find collaborative solutions for responding to climate change and other threats to marine biodiversity and society.
Collapse
Affiliation(s)
- Alexa L Fredston
- Department of Ocean Sciences, University of California, Santa Cruz, California, USA;
| | - Julia S Stewart Lowndes
- National Center for Ecological Analysis and Synthesis, University of California, Santa Barbara, California, USA
| |
Collapse
|
5
|
Nakagawa S, Lagisz M, Yang Y, Drobniak SM. Finding the right power balance: Better study design and collaboration can reduce dependence on statistical power. PLoS Biol 2024; 22:e3002423. [PMID: 38190355 PMCID: PMC10773938 DOI: 10.1371/journal.pbio.3002423] [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] [Indexed: 01/10/2024] Open
Abstract
Power analysis currently dominates sample size determination for experiments, particularly in grant and ethics applications. Yet, this focus could paradoxically result in suboptimal study design because publication biases towards studies with the largest effects can lead to the overestimation of effect sizes. In this Essay, we propose a paradigm shift towards better study designs that focus less on statistical power. We also advocate for (pre)registration and obligatory reporting of all results (regardless of statistical significance), better facilitation of team science and multi-institutional collaboration that incorporates heterogenization, and the use of prospective and living meta-analyses to generate generalizable results. Such changes could make science more effective and, potentially, more equitable, helping to cultivate better collaborations.
Collapse
Affiliation(s)
- Shinichi Nakagawa
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
- Theoretical Sciences Visiting Program, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Malgorzata Lagisz
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
- Theoretical Sciences Visiting Program, Okinawa Institute of Science and Technology Graduate University, Onna, Japan
| | - Yefeng Yang
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Szymon M. Drobniak
- Evolution & Ecology Research Centre and School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
- Institute of Environmental Sciences, Jagiellonian University, Kraków, Poland
| |
Collapse
|
6
|
Stransky N, Ganser K, Quintanilla-Martinez L, Gonzalez-Menendez I, Naumann U, Eckert F, Koch P, Huber SM, Ruth P. Efficacy of combined tumor irradiation and K Ca3.1-targeting with TRAM-34 in a syngeneic glioma mouse model. Sci Rep 2023; 13:20604. [PMID: 37996600 PMCID: PMC10667541 DOI: 10.1038/s41598-023-47552-4] [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: 05/24/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023] Open
Abstract
The intermediate-conductance calcium-activated potassium channel KCa3.1 has been proposed to be a new potential target for glioblastoma treatment. This study analyzed the effect of combined irradiation and KCa3.1-targeting with TRAM-34 in the syngeneic, immune-competent orthotopic SMA-560/VM/Dk glioma mouse model. Whereas neither irradiation nor TRAM-34 treatment alone meaningfully prolonged the survival of the animals, the combination significantly prolonged the survival of the mice. We found an irradiation-induced hyperinvasion of glioma cells into the brain, which was inhibited by concomitant TRAM-34 treatment. Interestingly, TRAM-34 did neither radiosensitize nor impair SMA-560's intrinsic migratory capacities in vitro. Exploratory findings hint at increased TGF-β1 signaling after irradiation. On top, we found a marginal upregulation of MMP9 mRNA, which was inhibited by TRAM-34. Last, infiltration of CD3+, CD8+ or FoxP3+ T cells was not impacted by either irradiation or KCa3.1 targeting and we found no evidence of adverse events of the combined treatment. We conclude that concomitant irradiation and TRAM-34 treatment is efficacious in this preclinical glioma model.
Collapse
Affiliation(s)
- Nicolai Stransky
- Department of Radiation Oncology, University of Tübingen, Hoppe-Seyler-Str. 3, 72076, Tübingen, Germany
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, 72076, Tübingen, Germany
| | - Katrin Ganser
- Department of Radiation Oncology, University of Tübingen, Hoppe-Seyler-Str. 3, 72076, Tübingen, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Neuropathology, Comprehensive Cancer Center, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany
| | - Irene Gonzalez-Menendez
- Institute of Pathology and Neuropathology, Comprehensive Cancer Center, Eberhard Karls University of Tübingen, 72076, Tübingen, Germany
- Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", Eberhard Karls University, Tübingen, Germany
| | - Ulrike Naumann
- Molecular Neurooncology, Hertie Institute for Clinical Brain Research and Center Neurology, University of Tübingen, 72076, Tübingen, Germany
- Faculty of Medicine University, Gene and RNA Therapy Center (GRTC), Tübingen, Germany
| | - Franziska Eckert
- Department of Radiation Oncology, University of Tübingen, Hoppe-Seyler-Str. 3, 72076, Tübingen, Germany
- Department of Radiation Oncology, Comprehensive Cancer Center, Medical University Vienna, AKH, Wien, Austria
| | - Pierre Koch
- Department of Pharmaceutical/Medicinal Chemistry II, Institute of Pharmacy, University of Regensburg, 93040, Regensburg, Germany
| | - Stephan M Huber
- Department of Radiation Oncology, University of Tübingen, Hoppe-Seyler-Str. 3, 72076, Tübingen, Germany.
| | - Peter Ruth
- Department of Pharmacology, Toxicology and Clinical Pharmacy, Institute of Pharmacy, University of Tübingen, 72076, Tübingen, Germany
| |
Collapse
|
7
|
Kohrs FE, Auer S, Bannach-Brown A, Fiedler S, Haven TL, Heise V, Holman C, Azevedo F, Bernard R, Bleier A, Bössel N, Cahill BP, Castro LJ, Ehrenhofer A, Eichel K, Frank M, Frick C, Friese M, Gärtner A, Gierend K, Grüning DJ, Hahn L, Hülsemann M, Ihle M, Illius S, König L, König M, Kulke L, Kutlin A, Lammers F, Mehler DMA, Miehl C, Müller-Alcazar A, Neuendorf C, Niemeyer H, Pargent F, Peikert A, Pfeuffer CU, Reinecke R, Röer JP, Rohmann JL, Sánchez-Tójar A, Scherbaum S, Sixtus E, Spitzer L, Straßburger VM, Weber M, Whitmire CJ, Zerna J, Zorbek D, Zumstein P, Weissgerber TL. Eleven strategies for making reproducible research and open science training the norm at research institutions. eLife 2023; 12:e89736. [PMID: 37994903 PMCID: PMC10666927 DOI: 10.7554/elife.89736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/07/2023] [Indexed: 11/24/2023] Open
Abstract
Reproducible research and open science practices have the potential to accelerate scientific progress by allowing others to reuse research outputs, and by promoting rigorous research that is more likely to yield trustworthy results. However, these practices are uncommon in many fields, so there is a clear need for training that helps and encourages researchers to integrate reproducible research and open science practices into their daily work. Here, we outline eleven strategies for making training in these practices the norm at research institutions. The strategies, which emerged from a virtual brainstorming event organized in collaboration with the German Reproducibility Network, are concentrated in three areas: (i) adapting research assessment criteria and program requirements; (ii) training; (iii) building communities. We provide a brief overview of each strategy, offer tips for implementation, and provide links to resources. We also highlight the importance of allocating resources and monitoring impact. Our goal is to encourage researchers - in their roles as scientists, supervisors, mentors, instructors, and members of curriculum, hiring or evaluation committees - to think creatively about the many ways they can promote reproducible research and open science practices in their institutions.
Collapse
Affiliation(s)
- Friederike E Kohrs
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité - Universitätsmedizin BerlinBerlinGermany
| | - Susann Auer
- Department of Plant Physiology, Faculty of Biology, Technische Universität DresdenDresdenGermany
| | - Alexandra Bannach-Brown
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité - Universitätsmedizin BerlinBerlinGermany
| | - Susann Fiedler
- Department Strategy & Innovation, Vienna University of Economics and BusinessViennaAustria
| | - Tamarinde Laura Haven
- Danish Centre for Studies in Research & Research Policy, Department of Political Science, Aarhus UniversityAarhusDenmark
| | | | - Constance Holman
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité - Universitätsmedizin BerlinBerlinGermany
| | - Flavio Azevedo
- Saxony Center for Criminological ResearchChemnitzGermany
- University of CambridgeCambridgeUnited Kingdom
| | - René Bernard
- NeuroCure Cluster of Excellence, Charité - Universitätsmedizin BerlinBerlinGermany
| | - Arnim Bleier
- Department for Computational Social Sciences, GESIS - Leibniz Institute for the Social SciencesCologneGermany
| | - Nicole Bössel
- Department of Psychiatry and Psychotherapy, University Medicine GreifswaldGreifswaldGermany
| | | | | | - Adrian Ehrenhofer
- Institute of Solid Mechanics & Dresden Center for Intelligent Materials, Technische Universität DresdenDresdenGermany
| | - Kristina Eichel
- Department of Education and Psychology, Freie Universität BerlinBerlinGermany
| | | | - Claudia Frick
- Institute of Information Science, Technische Hochschule KölnKölnGermany
| | - Malte Friese
- Department of Psychology, Saarland UniversitySaarbrückenGermany
| | - Anne Gärtner
- Department of Psychology, Technische Universität DresdenDresdenGermany
| | - Kerstin Gierend
- Department of Biomedical Informatics at the Center for Preventive Medicine and Digital Health, Medical Faculty Mannheim, Heidelberg UniversityHeidelbergGermany
| | - David Joachim Grüning
- Department of Psychology, Heidelberg UniversityHeidelbergGermany
- Department of Survey Development and Methodology, GESIS – Leibniz Institute for the Social SciencesMannheimGermany
| | - Lena Hahn
- Department of Social Psychology, Universität TrierTrierGermany
| | - Maren Hülsemann
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité - Universitätsmedizin BerlinBerlinGermany
| | - Malika Ihle
- LMU Open Science Center, Department of Psychology, LMU MunichMunichGermany
| | - Sabrina Illius
- ICAN Institute for Cognitive and Affective Neuroscience, Department of Psychology, Faculty of Human Sciences, Medical School HamburgHamburgGermany
| | - Laura König
- Faculty of Life Sciences: Food, Nutrition and Health, University of BayreuthBayreuthGermany
| | - Matthias König
- Institute for Biology, Institute for Theoretical Biology, Humboldt-University BerlinBerlinGermany
| | - Louisa Kulke
- Developmental Psychology with Educational Psychology, University of BremenBremenGermany
| | - Anton Kutlin
- Max Planck Institute for the Physics of Complex SystemsDresdenGermany
| | - Fritjof Lammers
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ)HeidelbergGermany
| | - David MA Mehler
- Department of Psychiatry, Psychotherapy and Psychosomatics, Medical School, RWTH Aachen UniversityAachenGermany
| | - Christoph Miehl
- Computation in Neural Circuits, Max Planck Institute for Brain ResearchFrankfurtGermany
| | - Anett Müller-Alcazar
- ICAN Institute for Cognitive and Affective Neuroscience, Department of Psychology, Faculty of Human Sciences, Medical School HamburgHamburgGermany
| | - Claudia Neuendorf
- Hector-Institute for Education Sciences and Psychology, Eberhard Karls, University of TübingenTübingenGermany
| | - Helen Niemeyer
- Department of Education and Psychology, Freie Universität BerlinBerlinGermany
| | | | - Aaron Peikert
- Center for Lifespan Psychology, Max Planck Institute for Human DevelopmentBerlinGermany
| | - Christina U Pfeuffer
- Department of Psychology, Catholic University of Eichstätt-IngolstadtEichstättGermany
| | - Robert Reinecke
- Institute of Geography, Johannes Gutenberg-University MainzMainzGermany
| | - Jan Philipp Röer
- Department of Psychology and Psychotherapy, Witten/Herdecke UniversityWittenGermany
| | - Jessica L Rohmann
- Scientific Directorate, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC)BerlinGermany
| | | | - Stefan Scherbaum
- Department of Psychology, Technische Universität DresdenDresdenGermany
| | - Elena Sixtus
- Empirical Childhood Research, University of PotsdamPotsdamGermany
| | | | - Vera Maren Straßburger
- Department of Psychology, Medical School HamburgHamburgGermany
- Charité - Universitätsmedizin Berlin, Gender in Medicine (GiM)BerlinGermany
| | - Marcel Weber
- Department of Psychology, Saarland UniversitySaarbrückenGermany
| | - Clarissa J Whitmire
- Max Delbrück Center for Molecular Medicine in the Helmholtz AssociationBerlinGermany
- Neuroscience Research Center, Charité-Universitätsmedizin BerlinBerlinGermany
| | - Josephine Zerna
- Department of Psychology, Technische Universität DresdenDresdenGermany
| | - Dilara Zorbek
- International Graduate Program Medical Neurosciences, Charité – Universitätsmedizin BerlinBerlinGermany
| | | | - Tracey L Weissgerber
- QUEST Center for Responsible Research, Berlin Institute of Health at Charité - Universitätsmedizin BerlinBerlinGermany
| |
Collapse
|
8
|
Geis L, d’Errico F, Jordan FM, Brenet M, Queffelec A. Multiproxy analysis of Upper Palaeolithic lustrous gravels supports their anthropogenic use. PLoS One 2023; 18:e0291552. [PMID: 37910580 PMCID: PMC10619837 DOI: 10.1371/journal.pone.0291552] [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: 11/22/2022] [Accepted: 09/01/2023] [Indexed: 11/03/2023] Open
Abstract
Upper Palaeolithic sites in southwestern France attributed to the Upper Gravettian and the Solutrean yielded sub spherical gravels with a highly shiny appearance that have intrigued researchers since the 1930s. In this work, we analyze specimens from five sites, including the recently excavated Solutrean site of Landry, to establish whether their presence in archaeological layers and peculiar aspect are due to natural processes or human agency. We study the spatial distribution of gravels at Landry and submit archaeological gravels from the five sites, natural formations, Landry sediment sieving, and polishing experiments with a rotary tumbling machine to morphometric, colorimetric, microscopic, and textural analyses. Our results indicate the lustrous gravels found at the five sites result from deliberate selection and suggest their shiny appearance is the consequence of human agency, possibly resulting from prolonged contact with a soft material such as animal skin. Ethnographic accounts indicate that these gravels may have been used for magico-religious ritual purposes (charms, sorcery, divination etc.), in games, as elements of musical instruments, and as items serving other social and personal purposes. We argue that these objects reflect a cultural innovation emerged during the Gravettian and continued into the Solutrean.
Collapse
Affiliation(s)
- Lila Geis
- CNRS, UMR5199, Pacea, Université de Bordeaux, Pessac, France
| | - Francesco d’Errico
- CNRS, UMR5199, Pacea, Université de Bordeaux, Pessac, France
- Centre for Early Sapiens Behaviour (SapienCE), Department of Archaeology, History, Cultural Studies and Religion, University of Bergen, Bergen, Norway
| | - Fiona M. Jordan
- Department of Anthropology and Archaeology, University of Bristol, Bristol, England
| | - Michel Brenet
- CNRS, UMR5199, Pacea, Université de Bordeaux, Pessac, France
- Inrap Nouvelle-Aquitaine Outre-mer, Pôle mixte de Recherches Archéologiques, Campagne, France
| | - Alain Queffelec
- CNRS, UMR5199, Pacea, Université de Bordeaux, Pessac, France
| |
Collapse
|
9
|
Ivimey-Cook ER, Pick JL, Bairos-Novak KR, Culina A, Gould E, Grainger M, Marshall BM, Moreau D, Paquet M, Royauté R, Sánchez-Tójar A, Silva I, Windecker SM. Implementing code review in the scientific workflow: Insights from ecology and evolutionary biology. J Evol Biol 2023; 36:1347-1356. [PMID: 37812156 DOI: 10.1111/jeb.14230] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/08/2023] [Accepted: 09/12/2023] [Indexed: 10/10/2023]
Abstract
Code review increases reliability and improves reproducibility of research. As such, code review is an inevitable step in software development and is common in fields such as computer science. However, despite its importance, code review is noticeably lacking in ecology and evolutionary biology. This is problematic as it facilitates the propagation of coding errors and a reduction in reproducibility and reliability of published results. To address this, we provide a detailed commentary on how to effectively review code, how to set up your project to enable this form of review and detail its possible implementation at several stages throughout the research process. This guide serves as a primer for code review, and adoption of the principles and advice here will go a long way in promoting more open, reliable, and transparent ecology and evolutionary biology.
Collapse
Affiliation(s)
- Edward R Ivimey-Cook
- School of Biodiversity, One Health and Veterinary Medicine, University of Glasgow, Glasgow, UK
| | - Joel L Pick
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Kevin R Bairos-Novak
- Australian Research Council Centre of Excellence for Coral Reef Studies & College of Science and Engineering, James Cook University, Townsville, Queensland, Australia
| | - Antica Culina
- Rudjer Boskovic Institute, Zagreb, Croatia
- Netherlands Institute of Ecology, NIOO-KNAW, Wageningen, the Netherlands
| | - Elliot Gould
- School of Ecosystem and Forest Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | | | - Benjamin M Marshall
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, UK
| | - David Moreau
- School of Psychology, Centre for Brain Research, University of Auckland, Auckland, New Zealand
| | - Matthieu Paquet
- Institute of Mathematics of Bordeaux, University of Bordeaux, CNRS, Bordeaux INP, Talence, France
| | - Raphaël Royauté
- Université ParisSaclay, INRAE, AgroParisTech, UMR EcoSys, Palaiseau, France
| | | | - Inês Silva
- Center for Advanced Systems Understanding (CASUS), Helmholtz-Zentrum Dresden-Rossendorf e.V. (HZDR), Görlitz, Germany
| | - Saras M Windecker
- School of Ecosystem and Forest Sciences, University of Melbourne, Melbourne, Victoria, Australia
| |
Collapse
|
10
|
Kiermer V. Authorship practices must evolve to support collaboration and open science. PLoS Biol 2023; 21:e3002364. [PMID: 37831717 PMCID: PMC10599500 DOI: 10.1371/journal.pbio.3002364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/25/2023] [Indexed: 10/15/2023] Open
Abstract
Journal authorship practices have not sufficiently evolved to reflect the way research is now done. Improvements to support teams, collaboration, and open science are urgently needed.
Collapse
Affiliation(s)
- Veronique Kiermer
- Public Library of Science, San Francisco, California, United States of America
| |
Collapse
|