Latest Articles

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  Section: Ecology ; Topics: Ecology, Evolution

  The SORTEE guidelines for data and code quality control in ecology and evolutionary biology

  Pick, Joel L;   Allen, Bethany J;   Bachelot, Benedicte;   Bairos-Novak, Kevin R;   Brand, Jack A;   Class, Barbara;   Dallas, Tad;   D'Amelio, Pietro B;   Fenollosa, Erola;   Fernández-Juricic, Esteban;   Gomes, Dylan G E;   Grainger, Matthew J;   Guillemaud, Thomas;   John, Christian;   Krasnow, Ruby;   Lagisz, Malgorzata;   Lequime, Sebastian;   Maynard, Daniel S;   Nakagawa, Shinichi;   O'Dea, Rose E;   Paquet, Matthieu;   Petitjean, Quentin;   Sánchez-Tójar, Alfredo;   van Dis, Natalie E;   Wilson, Laura A B;   Ivimey-Cook, Edward R  

  10.24072/pcjournal.687 - Peer Community Journal, Volume 6 (2026), article no. e20

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  Open data and code are crucial to increasing transparency and reproducibility, and in building trust in scientific research. However, despite an increasing number of journals in ecology and evolutionary biology mandating for data and code to be archived alongside published articles, the amount and quality of archived data and code, and subsequent reproducibility of results, has remained worryingly low. As a result, a handful of journals have recruited dedicated data editors, whose role is to help authors increase the overall quality of archived data and code. There is, however, a general lack of consensus around what a data editor should check, how to do it, and to what level of detail, and the process is often vague and hidden from readers and authors alike. Here, with the input from multiple data editors across several journals in ecology and evolutionary biology, we establish and describe the first standardised guidelines for Data and Code Quality Control on behalf of the Society for Open, Reliable, and Transparent Ecology and Evolutionary Biology (SORTEE). We then introduce the SORTEE-led guidelines as a flexible six-stage framework that journals can implement incrementally and/or apply on a case-by-case basis, particularly when some checks (e.g., computational reproducibility) are not feasible (e.g., proprietary software). We conclude with practical advice for journals and authors, arguing that flexible adoption of these standardised guidelines will improve the consistency and transparency of the data editor process for readers, authors, data editors, and the wider scientific community.

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  Section: Ecotoxicology & Environmental Chemistry ; Topics: Ecology, Environmental sciences

  Exposure to a mixture of organic pollutants in a threatened freshwater turtle Emys orbicularis: effects of age, sex, and temporal variation

  Merleau, Leslie-Anne;   Lourdais, Olivier;   Olivier, Anthony;   Vittecoq, Marion;   Alliot, Fabrice;   Traore, Sira; Leray, Carole; Goutte, Aurélie  

  10.24072/pcjournal.684 - Peer Community Journal, Volume 6 (2026), article no. e19

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  Freshwater ecosystems constitute major sinks for organic contaminants, increasing anthropogenic pressures and threatening the unique biodiversity they harbour. In addition to persistent legacy compounds, such as polychlorinated biphenyls (PCBs) and organochlorine pesticides (OCPs), various pollutants are less persistent but are chronically released, including polycyclic aromatic hydrocarbons (PAHs), phthalate diesters (PAEs), pyrethroid pesticides, and insect repellent. Heretofore, these pollutants have received insufficient attention in freshwater reptiles, considering their potential to trigger detrimental effects on organisms. During two years (2019 and 2020), we quantified plasma levels of 46 compounds from 7 chemical families in two monitored populations of the protected European pond turtle (Emys orbicularis) in the Camargue wetland, France. PAHs and PAEs were found predominantly and concomitantly, with similar occurrences and levels in the two populations. We observed similar inter-annual variations in PAHs and PAEs with differences between males and females, highlighting the need for a better assessment of the role of sex in the exposure pathway and the toxicokinetics of contaminants, especially in turtles. The negative relationship between PAH levels and age, as well as the high intra-individual variation in levels of both contaminant families, provides further evidence of limited bioaccumulation of these pollutants in the blood of E. orbicularis. This could be explained by the metabolic biotransformation of parent compounds, highlighting the need to quantify the levels of PAH metabolites and phthalate monoesters. Finally, our work underscores the importance of long-term monitoring to better determine the vulnerability of turtle populations already exposed to a wide range of contaminants.

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  Section: Genomics ; Topics: Genetics/genomics

  Genome of Trichoderma gamsii strain T035, a promising beneficial fungus in agriculture

  Colou, Justine;   Brémand, Etienne;   Robin, Alwena;   Bastide, Franck;   Guillemette, Thomas  

  10.24072/pcjournal.686 - Peer Community Journal, Volume 6 (2026), article no. e18

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  Trichoderma gamsii is a filamentous fungus widely recognized for its beneficial roles in agriculture, particularly for its ability to suppress plant pathogens and enhance crop health. However, genomic resources for this species remain scarce, limiting functional and applied studies. Here, we report the high-quality genome of T. gamsii strain T035, a promising biocontrol strain with significant antagonistic activity against several pathogens in vitro. The assembly consisted of 16 sequences, including near 7 chromosome-scale sequences, with an N50 value of 7.2 Mbp and a total assembly length of 38.8 Mbp. This genome represents the most complete T. gamsii assembly to date and will provide a valuable resource to facilitate the exploration of molecular mechanisms underlying biocontrol and support the development of sustainable plant protection strategies.

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  Section: Archaeology ; Topics: Archaeology, Computer sciences

  The impact of normal mapping on the appearance of geometrically simplified archaeological 3D models

  Costopoulos, Stefanos; Papaioannou, Georgios  

  10.24072/pcjournal.683 - Peer Community Journal, Volume 6 (2026), article no. e17

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  A great challenge in 3D digitization and modelling lies in striking a balance between surface detail and model size, while accommodating the geometric information representation requirements of diverse archaeological practices. 3D meshes that contain a high polygon count severely impact storage requirements, data transmission, and 3D rendering. It is therefore typical for high-resolution digitized objects and modelled assets alike to be sub-sampled and simplified into levels of detail (LODs) to match the requirements of the intended applications. By doing so, however, geometric detail is lost, negatively affecting the model’s visual fidelity during 3D visualization. Normal mapping offers a reliable and practical solution to this challenge by transferring surface orientation data from the original, detailed models into simplified versions. This approach preserves the key visual characteristics present on the surface of a high-detail model, without reintroducing geometric complexity into the simplified structure. In archaeological contexts, where both accuracy and accessibility are important, normal mapping enables lightweight models to maintain the perceptual qualities of high-resolution originals, while supporting diverse visualization applications, from analytical inspection to public dissemination. In this paper, our proposed methodology explores the robustness of detail transfer through normal mapping on simplified archaeological models, highlighting its effectiveness as a tool for efficient cultural heritage visualization and immersive applications. The study claims that normal-mapped models can effectively stand in for the original high-detail scans in a variety of scenarios, thus offering a viable and efficient alternative to the demanding storage and transmission of high-fidelity 3D models.