Latest Articles

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  Section: Archaeology ; Topics: Archaeology, Genetics/genomics

  Evaluating commercial DNA extraction kits for bacterial community profiling in waterlogged archaeological wood

  Høier Eriksen, Anne Marie;   Müller, Oliver;   Helgå Landing, Helen; Gregory, David  

  10.24072/pcjournal.766 - Peer Community Journal, Volume 6 (2026), article no. e76

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  Understanding bacterial communities responsible for the slow biodeterioration of waterlogged archaeological wood is critical for reconstructing decay processes, predicting preservation trajectories, and informing conservation strategies. The extraction of sufficient and amplifiable bacterial DNA from waterlogged archaeological wood is essential for robust sequencing and accurate bacterial community profiling. However, DNA yield and inferred community composition can vary depending on the extraction protocol used. In this study, we evaluated the performance of three commercially available DNA extraction kits - Bead-Beat Micro AX Gravity, DNeasy PowerSoil Pro and MagAttract PowerSoil Pro DNA – on samples from a single waterlogged Neolithic wooden pole recovered from a submerged archaeological site in Denmark and preserved under anoxic conditions. Quantitative analysis showed that the Bead-beat Micro AX Gravity kit yielded the highest DNA concentrations by Qubit fluorometry and lowest PCR cycle number in quantitative PCR. Elevated DNA signals were observed in some extraction blanks during Qubit quantification; however, these blanks did not produce sequencing reads, indicating that the signal likely represented non-amplifiable material. Comparative analysis of bacterial community composition, based on 16S rRNA gene amplicon sequencing (V4 region, primers 515F/806R), revealed minimal variation between extraction methods, but distinct taxonomic profiles were observed across different sampling areas within a single archaeological wooden pole. These results indicate that while extraction protocol has limited influence on bacterial community composition in this context, spatial heterogeneity within samples can affect results. Protocols yielding higher DNA concentrations may therefore be advantageous when working with degraded archaeological materials or DNA-intensive downstream applications. However, extraction methods optimized for the recovery of highly fragmented DNA may offer additional advantages for ancient heavily degraded substrates.

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  Section: Plants ; Topics: Agricultural sciences

  Enhancing sugarcane yield resilience under a changing climate: adaptive irrigation and varietal strategies in Reunion Island

  Christina, Mathias;   Pilloni, Raphaël;   Mézino, Mickaël;   Loison, Romain;   Le Mézo, Lionel;   Poser, Christophe

  10.24072/pcjournal.764 - Peer Community Journal, Volume 6 (2026), article no. e75

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  Variations in rainfall patterns, whether in quantity or frequency, pose a significant challenge that sugarcane crops must adapt to in the context of climate change. This study aimed to assess the impact of future climate scenarios from 2015 to 2100 on sugarcane yield at a regional scale in Reunion Island and to identify adaptation practices to mitigate the impact of climate. Different irrigation regimes were tested to assess the impact on growth and future water requirements using the Mosicas sugarcane crop growth model at a 3 x 3 km resolution. High-resolution climate data for three IPCC future scenarios (RCP 2.5, 4.5, and 8.5) were obtained from the BRIO project, conducted by Météo France, the French national weather service. Results showed that, despite a favorable increase in temperature, changes in precipitation patterns resulted in minimal yield change at the island scale compared to the current period. However, the impact of climate change varied significantly across different climatic areas on the island. On the south-west coast, yields decreased significantly (by -8% and -4% on average in 2060 and 2090, respectively), while on the east and north-east coasts at high altitudes, yields increased (by +9% and +17% in 2060 and 2090). Overall, water irrigation demand increased by 15 and 24% in 2060 and 2090, respectively, on average across scenarios. It was found that irrigating non-irrigated areas reduced the negative impact of climate change, particularly in high altitudes in the south and north-east. Additionally, the simulation of more drought-resistant varieties was able to limit the negative impact of climate change in areas facing increasing water deficits without changing the irrigation regime. Finally, this study illustrated how areas currently less suitable for sugarcane production, such as high-altitude areas, will become more favorable due to climate change. Adaptation methods, such as changes in irrigation management or the adoption of more drought-tolerant varieties, were identified as effective strategies to cope with climate change and maximize the sugarcane’s potential in a more favorable temperature environment.

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  Section: Archaeology ; Topics: Archaeology

  palimpsestR: An R Package for the Identification and Probabilistic Decomposition of Archaeological Palimpsests

  Cocca, Enzo;   Montagnetti, Roberto;   Cattani, Maurizio  

  10.24072/pcjournal.762 - Peer Community Journal, Volume 6 (2026), article no. e74

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  This paper presents palimpsestr, an R package and Shiny application dedicated to the identification and probabilistic decomposition of archaeological palimpsests — deposits in which material from multiple occupation phases is superimposed and partially intermixed. Such deposits represent one of the most persistent analytical challenges in field archaeology, and existing tools (Harris Matrix recording systems, k-means spatial clustering, GIS overlays) typically address only one evidence domain at a time. palimpsestr implements the Stratigraphic Entanglement Field (SEF) framework, which integrates four evidence domains — horizontal coordinates, vertical elevation, chronological range, and cultural class — into a single diagonal-covariance Gaussian mixture model fitted by Expectation-Maximisation. The model is augmented with optional taphonomic weighting and stratigraphic entanglement penalties derived from the Harris Matrix. Three interpretable diagnostics — the Stratigraphic Entanglement Index (SEI), Excavation Stratigraphic Energy (ESE), and Palimpsest Dissolution Index (PDI) — allow practitioners to assess deposit coherence, detect potentially redeposited finds, and evaluate the reliability of chronological attribution at the find, unit, and phase levels. The framework supports archaeologists in three principal interpretive tasks: assessing the reliability and coherence of stratigraphic units (distinguishing genuine palimpsests from recording errors); identifying intrusive finds with respect to both their typology and their stratigraphic position; and providing the basis for future statistical estimation of type longevity (the duration of use of pottery and material categories). The package supports CSV/TSV/Excel/SQLite/PostgreSQL data import, GIS export to GeoPackage via the sf package, publication-quality plots via ggplot2 and interactive plots via plotly, and includes a built-in Shiny dashboard for non-programmatic use. Since the original release the statistical core has been substantially refined: the cultural class is now modelled as a per-phase categorical distribution (a Gaussian-times-multinomial mixed-type mixture) rather than as one-hot Gaussian columns, so that stratigraphic units are no longer split across phases by typology; the spatial and vertical similarity kernels are bounded and scale-invariant; the domain weights enter the likelihood and can be cross-validated; a uniform noise component yields a genuine posterior probability of intrusion and shields phase estimates from outliers; and optional treatments propagate per-find dating uncertainty and apply the stratigraphic constraint as a dynamically updated Neighborhood-EM field. The intrusion diagnostic also distinguishes the direction of the chronological mismatch (residual vs. latent-feature), and a companion helper (recommend_setup()) inspects a dataset and reports when its recording resolution limits the achievable inference. We present an overview of the application's functions and demonstrate its use through a case study at the multi-period Roman villa of Poggio Gramignano (Lugnano in Teverina, Italy). We also discuss the methodological assumptions of the SEF framework — in particular the implicit assumption of horizontal stratigraphy and the dependence of phase resolution on the spatial and chronological recording resolution of the data — and outline planned developments.

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  Section: Archaeology ; Topics: Archaeology

  Detecting Temporal Relations in Archaeology: Model and Algorithms

  Levy, Eythan  

  10.24072/pcjournal.761 - Peer Community Journal, Volume 6 (2026), article no. e73

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   This paper addresses the question of finding the optimal temporal relation between two time-periods, in the presence of uncertainties regarding their boundaries (i.e. unknown or bounded start/end). It proposes a fast algorithmic solution, implementated in the Python language, and an archaeological case study related to the Early Bronze Age in the Levant. Open-source Python implementations of our data model and algorithms can be downloaded on the author’s GitHub repository. Our solution is also implemented in the latest version (v. 3) of the ChronoLog modelling tool (https://chrono.ulb.be/).