Latest Articles

Section: Archaeology ; Topics: Archaeology

The Application of graphic visualization filters for Historical-Archaeological Studies. A case of study: “Mesas del Esparragal”, Alcalá de Los Gazules, Cádiz (Spain)

Catalán González, Francisco Javier

10.24072/pcjournal.575 - Peer Community Journal, Volume 5 (2025), article no. e66.
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The aim of this article consists in a presentation and a comparison of filters for the detection of archaeological structures developed through open-source Geographical Information Systems tools applied to the surface of the archaeological site known as Mesas del Esparragal, located in the municipality of Alcalá de los Gazules (Cádiz, Spain). The site, identified by some researchers as Lascuta because of its relationship with the famous Lascuta Bronze, has exceptional characteristics in terms of its strategic position for controlling the territory. For this reason, the Romans at the hands of the consul Lucius Emilius Paulus, were able to establish their camp in this important place with the aim of putting down the uprising perpetuated by the city of Hasta Regia. For this purpose, the data obtained through the LiDAR sensor collected by the National Plan for Aerial Orthophotography (PNOA) will be used. These data will be classified by means of the LASTools complement and later a series of filters will be made through the Relief Visualization Toolbox (RVT) software and the SAGA software, with the purpose of comparing them and determining which filter or filters are the most appropriate when locating possible archaeological structures under the surface. The filters to be compared are: The Three-directional Hillshade, the Simple Local Relief Model (SLRM) and the Red Relief Image Map (RRIM).
Section: Genomics ; Topics: Genetics/genomics

Draft genome and transcriptomic sequence data of three invasive insect species

Lombaert, Eric; Klopp, Christophe; Blin, Aurélie; Annonay, Gwenolah; Iampietro, Carole; Lluch, Jérôme; Sallaberry, Marine; Valière, Sophie; Poloni, Riccardo; Joron, Mathieu; Deleury, Emeline

10.24072/pcjournal.568 - Peer Community Journal, Volume 5 (2025), article no. e65.
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Cydalima perspectalis (the box tree moth), Leptoglossus occidentalis (the western conifer seed bug), and Tecia solanivora (the Guatemalan tuber moth) are three economically harmful invasive insect species. This study presents their genomic and transcriptomic sequences, generated through whole-genome sequencing, RNA-seq transcriptomic data, and Hi-C sequencing. The resulting genome assemblies exhibit good quality, providing valuable insights into these species. The genome sizes are 500.4 Mb for C. perspectalis, 1.74 Gb for L. occidentalis, and 623.3 Mb for T. solanivora. These datasets are available in the NCBI Sequence Read Archive (BioProject PRJNA1140410) and serve as essential resources for population genomics studies and the development of effective pest management strategies, addressing significant gaps in the understanding of invasive insect species.
Section: Zoology ; Topics: Agricultural sciences, Ecology

Intra- and interspecific variations in flight performance of oak-associated Agrilinae (Coleoptera: Buprestidae) using computerised flight mills

Le Souchu, Elodie; Sallé, Aurélien; Bankhead-Dronnet, Stéphanie; Laparie, Mathieu; Sauvard, Daniel

10.24072/pcjournal.560 - Peer Community Journal, Volume 5 (2025), article no. e64.
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Several Agrilinae species (Coleoptera: Buprestidae) are thermophilous forest borers, and some are also major invasive pests. They are expected to be favoured by climate change and the global deterioration of forest health, and expand their range and damage. Flight behaviour and performance of these insects are poorly known despite their critical role in dispersal and their relevance to management. This study aimed to assess intra- and interspecific variability in active flight of several Agrilinae species and effects of sex and mass on this variability. We assessed the flight performance of eleven oak-associated species (nine Agrilus, one Coraebus, one Meliboeus) plus one herb-associated Agrilus. Computer-monitored flight mills were used to measure flight parameters of 250 beetles. Overall, flight capacities were rather homogeneous among species, with a dominance of poor flyers and only Coraebus undatus showed outstanding performance. Beetles generally performed several short flight bouts within one trial, and only a few individuals sustained long flight. The maximal total distance covered across multiple assays until death ranged from 170 to 16 097 m, with a median between 35 and 966 m (excluding individuals that never flew). Add to this interspecific variability, flight distances varied greatly among individuals, but were not influenced by sex. Preflight body mass had mixed effects depending on the species, presumably related to dispersal patterns. In our experimental conditions, most species had limited average dispersal capacities over multiple flight trials. Overall, long-distance dispersal and colonisation events probably depend on a small proportion of individuals which largely exceeded the median performance.
Section: Genomics ; Topics: Evolution, Genetics/genomics

Particular sequence characteristics induce bias in the detection of polymorphic transposable element insertions

Verneret, Marie; Le, Van Anthony; Faraut, Thomas; Turpin, Jocelyn; Lerat, Emmanuelle

10.24072/pcjournal.570 - Peer Community Journal, Volume 5 (2025), article no. e63.
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Transposable elements (TEs) have an important role in genome evolution but are challenging for bioinformatics detection due to their repetitive nature and ability to move and replicate within genomes. New sequencing technologies now enable the characterization of nucleotide and structural variations within species. Among them, TE polymorphism is critical to identify as it may influence species adaptation or trigger diseases. Despite the development of numerous bioinformatic programs, identifying the most effective tool is challenging due to non-overlapping results and varying efficiency across studies. Benchmarking efforts have highlighted some of the limitations of these tools, often evaluated on either real or simulated data. However, real data may be incomplete or contain unannotated TEs, while simulated data may not accurately reflect real genomes. This study introduces a simulation method generating data based on real genomes to control all genomic parameters. Evaluating several TE polymorphic detection tools using data from Drosophila melanogaster and Arabidopsis thaliana, our study investigates factors like copy size, sequence divergence, and GC content that influence detection efficiency. Our results indicate that only a few programs perform satisfactorily and that all are sensitive to TE and genomic characteristics that may differ according to the species considered. Using Bos taurus population data as a case study to identify polymorphic LTR-retrotransposon insertions, we found low-frequency insertions particularly challenging to detect due to a high number of false positives. Increased sequencing coverage improved sensitivity but reduced precision. Our work underscores the importance of selecting appropriate tools and thresholds according to the specific research questions.

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The network image was drawn by Martin Grandjean: A force-based network visualization CC BY-SA