Latest Articles

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  Section: Ecology ; Topics: Ecology, Evolution

  The biogeography of evolutionary radiations on oceanic archipelagos

  Brée, Baptiste; Matthews, Thomas J.;   Fernández-Palacios, José María;   Paroissin, Christian; Triantis, Kostas A.;   Whittaker, Robert J.;   Rigal, François  

  10.24072/pcjournal.688 - Peer Community Journal, Volume 6 (2026), article no. e21

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  Evolutionary radiations on oceanic archipelagos (ROAs) have long served as models for understanding evolutionary and ecological processes underlying species diversification. Yet, diversity patterns emerging from ROAs have received relatively little attention from biogeographers, even though characterizing the effect of key geo-environmental factors on island clade species could be important for unraveling diversification dynamics. In this study, we conducted a comparative analysis using island-specific species richness values for approximately one hundred ROAs across major oceanic archipelagos (mostly Hawaii, Canary Islands, Galápagos and Fiji) and taxa (vascular plants, invertebrates and vertebrates). Our aim was to determine whether (1) ROA species richness patterns scale as a function of key geo-environmental factors including island area, geological age, environmental heterogeneity (elevation and topographic complexity) and inter-island isolation, and (2) whether the magnitude of the effects of these factors varies across archipelagos and taxa. Our results identified elevation as a key driver of ROA species richness patterns on islands, supporting existing theoretical and empirical work that highlighted the central role of environmental heterogeneity in driving diversification on oceanic islands. As importantly, we found that the influence of geo-environmental factors varies across archipelagos and taxa, suggesting that unique archipelagic dynamics and biological traits together shape diversification differently. Our findings emphasize the value of applying biogeographical modeling at the resolution of individual radiations to improve our understanding of evolutionary processes on oceanic archipelagos.

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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.