Latest Articles

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  Section: Ecology ; Topics: Ecology

  Urbanisation and habitat loss favour thermophilic and monogynous ant species

  Finand, Basile;   Monnin, Thibaud;   Bocquet, Céline; Bultelle, Angélique; Fédérici, Pierre;   Darmedru, Léa; Gouffault, Solène; Ledamoisel, Joséphine; Loeuille, Nicolas  

  10.24072/pcjournal.775 - Peer Community Journal, Volume 6 (2026), article no. e83

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  Environmental changes such as urbanisation and related habitat loss and fragmentation profoundly impact ecological communities by altering habitats, resources, and microclimates. Yet, the impacts of the resulting environmental conditions on metacommunity dynamics, ranging from species sorting to mass effects, remain a subject of debate. Ants, with diverse life histories and strong ecological effects, are ideal model species to study these pressures. We investigated the response of ant communities, including taxonomic and functional diversity, to urbanisation and habitat fragmentation in the Paris region, comparing wooded areas in 25 urban parks vs. 24 rural forests outside the city. We found a clear difference in species composition between urban and rural environments, with a higher prevalence of thermophilic species and a tendency for monogyny in the city. Forest communities were homogeneous across the size levels we studied, while park communities differed noticeably depending on park size, with larger parks harbouring more species. Our findings suggest that urbanisation selects specific ant traits and favours more thermophilic species, thereby increasing the mean thermal preference of urban communities. These selective effects influence which species can colonise and survive in different patches, shaping metacommunity structure and potentially affecting the resilience of ant communities under climate change.

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  Section: Genomics ; Topics: Genetics/genomics, Microbiology, Computer sciences

  ViroSeek: a viral detection pipeline for second-generation sequencing

  Berger, Audric;   Lefebvre, Margaux J.M.;   Dainat, Jacques;   Jiolle, Davy;   Moltini-Conclois, Isabelle;   Talignani, Loic;   Mastriani, Emilio;   Cornelie, Sylvie;   Berthet, Nicolas;   Paupy, Christophe  

  10.24072/pcjournal.767 - Peer Community Journal, Volume 6 (2026), article no. e82

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  Arbovirus emergences represent a rising public health issue and are exacerbated by climate change and globalization. Virome analysis has become a key approach for monitoring and managing infectious diseases, yet existing tools often remain technically complex and inaccessible to non-specialists. In this context, we present ViroSeek, a reproducible and accessible bioinformatics pipeline specifically designed for the taxonomic analysis of second-generation sequencing data from target-enriched libraries. ViroSeek performs a series of automated steps: quality control, trimming, host and bacterial sequence removal, assembly, taxonomic assignment, read remapping for quantification, and PCR duplicate removal. The whole process is designed to produce a clear, usable viral taxonomy table that is suitable for diversity studies. ViroSeek was empirically validated on enriched control samples containing a known panel of viruses. All the expected viruses were correctly detected. Bacterial and host contaminant sequences were effectively removed. The pipeline is freely available and fully documented, supporting its adoption and adaptation by the research community.

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  Section: Archaeology ; Topics: Archaeology, Paleontology, Computer sciences

  Computational simulations of potential Pachycrocuta bite damage based on a ~1.2 Ma ravaged hippopotamus femur from Fuente Nueva 3 (Orce, Granada, Spain)

  Courtenay, Lloyd A.;   Serrano-Ramos, Alexia;   Saarinen, Juha;   Viranta, Suvi;   Barsky, Deborah;   Jiménez-Arenas, Juan-Manuel;   Yravedra, José  

  10.24072/pcjournal.771 - Peer Community Journal, Volume 6 (2026), article no. e81

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  Understanding the behaviour and interactions of extinct carnivoran species present a significant challenge in archaeological and palaeontological research, often limited by numerous constraints in the fossil record. Here we analyse a hippopotamus femur that presents extensive damage by carnivorans, recovered from the open-air site Fuente Nueva 3 ($\sim$1.2 Ma, Orce, Granada, Spain). Given the extent of furrowing, the potential agents known in the palaeolandscape, and a number of additional theoretical features, we believe this bone to have been consumed by an extinct species of giant hyena; Pachycrocuta brevirostris. Leveraging the use of advanced microscopic techniques to digitise the tooth marks observed on this specimen in three dimensions, the present study utilises artificially intelligent algorithms to then simulate the possible morphological variability of this carnivoran. This allows us to propose a characterisation of Pachycrocuta brevirostris tooth pit morphology, so as to construct a proposal for a diagnostic reference sample of this species. If our findings are correct, they underscore the importance tooth mark size has on identifying the activity of Pachycrocuta, revealing the giant hyena to have produced remarkably large, deep, and circular tooth pits on dense cortical bone.

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  Section: Plants ; Topics: Agricultural sciences, Biophysics and computational biology, Plant biology

  A multi-scale dataset combining 3D plant architecture, leaf gas exchange, and whole-plant fluxes in young oil palm under controlled climate scenarios

  Perez, Raphael P. A.;   Torrelli, Valentin; Roques, Sandrine;   Devidal, Sébastien; Piel, Clément;   Landais, Damien; Ramel, Merlin; Arsouze, Thomas;   Lamour, Julien;   Caliman, Jean-Pierre; Vezy, Rémi  

  10.24072/pcjournal.773 - Peer Community Journal, Volume 6 (2026), article no. e80

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  Functional-structural plant models simulate plant responses to environmental conditions, but their development and evaluation are often limited by the lack of datasets combining detailed architectural and physiological measurements. Here, we present a comprehensive dataset acquired from four oil palm plants (Elaeis guinnensis) grown under controlled and contrasting climate scenarios. The dataset includes (i) three-dimensional reconstructions of plant architecture derived from terrestrial lidar point clouds, (ii) leaf-level gas exchange measurements used to parameterize photosynthesis and stomatal conductance models, and (iii) continuous plant-scale measurements of CO₂ and H₂O fluxes obtained in a microcosm under precisely monitored and manipulated environmental conditions (light, temperature, humidity, and CO₂ concentration) across height climate scenarios. By combining detailed structural data with physiological measurements at both leaf and whole-plant scales, this database has been designed to build and evaluate digital twins (or shadows) of plants functioning under controlled conditions. It provides a valuable resource for calibrating biophysical models (light interception and photosynthesis), benchmarking model predictions across scales, and investigating the consistency between leaf-level parameterization and plant-level fluxes. All data and processing workflows are openly available, facilitating reuse for model development, evaluation, and intercomparison in plant and crop modelling communities.