Latest Articles

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  Section: Genomics ; Topics: Genetics/genomics, Evolution

  Comparing DNA extraction methods for successful PacBio HiFi sequencing: a case study of the freshwater mussel Anodonta anatina (Bivalvia: Unionidae)

  Giulio, Marco R.;   Lergster, Urs; Feulner, Philine G. D.;   Weber, Alexandra A.-T.  

  10.24072/pcjournal.733 - Peer Community Journal, Volume 6 (2026), article no. e57

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  High-quality reference genomes are increasingly recognized as essential resources in biodiversity genomics and conservation. However, successful DNA extraction and long-read sequencing remain highly organism-dependent. Molluscs, a diverse phylum of invertebrates, pose particular challenges due to the presence of inhibitory compounds and the difficulty of obtaining high-molecular-weight DNA, often necessitating careful optimization of extraction protocols. Here, we present a case study on the freshwater mussel Anodonta anatina (Bivalvia: Unionidae), evaluating two preservation methods, six DNA extraction protocols, and two post-extraction clean-up steps for their effects on DNA quality and PacBio HiFi sequencing yield from foot tissue of a single individual. The PacBio Nanobind and CTAB protocols produced high-quality DNA from fresh tissue but performed poorly on flash-frozen tissue. Post-extraction clean-up generally degraded DNA and did not improve sequencing yield. Unexpectedly, the column-based Omega Mollusc Kit, although not designed for high-molecular-weight DNA, performed better than the PacBio-recommended Nanobind kit and the manual CTAB method on flash-frozen tissue. It generated high DNA quantity and purity, sufficient integrity for HiFi sequencing, and appeared to remove contaminants effectively. While the resulting DNA may be too fragmented for ultra-long read sequencing, the Omega Mollusc Kit offers a practical, cost-effective first approach for testing DNA extraction and PacBio sequencing in flash-frozen A. anatina foot tissue. When fresh tissue is available, Nanobind or CTAB were the best-performing options in our comparison. Overall, our results provide a practical starting point for protocol selection, while acknowledging that validation across other mollusc species, tissue types, and preservation methods remains important. This strategy could reduce the need for extensive protocol optimization and facilitate future mollusc genomics efforts.

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  Section: Archaeology ; Topics: Archaeology, Anthropology, Computer sciences ; Conference: CAA2025

  Experimental interpretation of ancient games through playtesting

  Tsilogiannis, Angelos; Konstantakis, Markos;   Vosinakis, Spyros  

  10.24072/pcjournal.738 - Peer Community Journal, Volume 6 (2026), article no. e56

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  Reconstructing the rules of ancient games remains one of archaeology’s most intricate interpretive challenges. While surviving boards and pieces provide tangible evidence, the logic of play, rules, roles, and goals have largely vanished. Traditional reconstructions rely on text and comparisons to better known games, yet these methods seldom capture the experiential and social dimensions of ancient gameplay. This paper presents an experimental framework designed to explore how such systems might emerge through play itself. Using Ludus Latrunculorum (“The Game of Little Soldiers”) as a case study, participants engaged in iterative, co-creative sessions where they invented, refined, and transmitted rules across successive lineages of play. The resulting games revealed recurring mechanics that closely parallel known reconstructions of Ludus Latrunculorum. While the outcomes do not claim historical accuracy, they demonstrate how collective experimentation can illuminate the cognitive and social processes underlying the development of structured games in antiquity. The study thus proposes experimental play as a complementary archaeological tool for examining how rulesets evolve, stabilize, and reflect the societies that produce them.

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  Section: Mathematical & Computational Biology ; Topics: Biophysics and computational biology, Computer sciences

  Accelerating k-mer-based sequence filtering

  Martayan, Igor;   Vandamme, Léa;   Constantinides, Bede;   Cazaux, Bastien;   Paperman, Charles;   Limasset, Antoine  

  10.24072/pcjournal.735 - Peer Community Journal, Volume 6 (2026), article no. e55

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  Motivation. The exponential growth of global sequencing data repositories presents both analytical challenges and opportunities. While k-mer-based indexing has improved scalability over traditional alignment for identifying relevant documents, pinpointing the exact sequences matching numerous queries remains a hurdle. In particular, searching for numerous k-mers with a single large query or multiple distinct queries strains existing exact matching tools, whose performance scales poorly with an increasing number of patterns. At the same time, indexing entire vast datasets for infrequent or ad-hoc searches is often resource-prohibitive. Designing fast methods for matching a large number of k-mers without exhaustive pre-indexing is therefore critical.  Contributions. We propose an efficient solution to the problem of k-mer-based sequence filtering: given a set of k-mers of interests and a threshold, quickly evaluate whether an arbitrary sequence has a number of k-mer matches above or below the threshold. Our approach demonstrates how minimizer-based based sketching, alongside SIMD acceleration, can enhance the performance of streaming searches, and is implemented as a Rust tool named K2Rmini. On a consumer laptop, K2Rmini is able to filter long reads at 2 Gbp/s.  Availability. https://github.com/Malfoy/K2Rmini.

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  Section: Ecology ; Topics: Ecology, Statistics

  Uncovering the relative movements of ecological trajectories

  Djeghri, Nicolas;   Gauthier, Olivier; Sturbois, Anthony;   Meiners, Scott J.;   Allen, Robert B.;   De Cáceres, Miquel  

  10.24072/pcjournal.736 - Peer Community Journal, Volume 6 (2026), article no. e54

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  Movement analogies are often employed by ecologists to describe how ecological dynamics relate to one another. For instance, two communities whose similarity increases in time may be said to converge. Here we argue that the movement analogies used by ecologists to compare ecological dynamics could be enriched with other notions such as “pursuit” or “parallel” movements, if accompanied by appropriate statistical testing. By building on the framework of Ecological Trajectory Analysis, we present here Relative Trajectory Movement Assessment (RTMA), a framework to detect and qualify relative movements in ecological dynamics defined as trajectories in multivariate space. Using synthetic trajectory data, we illustrate how RTMA can reveal a diverse range of relative movements beyond the convergence and divergence patterns already recognized in ecology. We exemplify the use of RTMA on real ecological datasets describing 1) old field successional dynamics in eastern North America and 2) temporal patterns in tree size structure of a New Zealand forest. RTMA provides ecologists with a new way of describing and comparing ecological dynamics that could be widely applied, from plot-scale dynamics to the effects of global change.