Latest Articles

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  Section: Evolutionary Biology ; Topics: Evolution, Ecology, Paleontology

  prepR4pcm: An R package for preparing data and trees for phylogenetic comparative methods

  Nakagawa, Shinichi;   Ortega, Santiago;   Mizuno, Ayumi;   Santos, Eduardo S. A.;   Lagisz, Malgorzata;   Jain, Bhavya;   Celeste, Jimuel Jr;   Poo Hernandez, Sergio  

  10.24072/pcjournal.809 - Peer Community Journal, Volume 6 (2026), article no. e104

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  Phylogenetic comparative methods require species names in a trait dataset to match tip labels in a phylogenetic tree. Yet this apparently simple prerequisite is often one of the most fragile steps in a comparative workflow. Names may differ because of, for example, formatting, taxonomic revisions, synonyms, or spelling errors. If these differences are resolved informally, species can be lost from analyses, and the reasons for their loss can be difficult to reconstruct. Here, we present $\texttt{prepR4pcm}$, an R package for preparing data and trees for phylogenetic comparative methods. The package reconciles species names through a staged procedure: exact matching, normalised matching, synonym lookup with local taxonomic databases, and optional fuzzy matching for likely spelling errors. Each decision is stored in a reconciliation object with the original name, matched name, match type, confidence score, and a short explanation. This object turns name matching from a hidden preprocessing step into an auditable part of the analysis. $\texttt{prepR4pcm}$ also supports the points where comparative workflows need human judgement. Users can inspect unresolved names, accept or reject suggested matches, add manual corrections, apply taxonomy crosswalks (which link names across taxonomic systems), compare reconciliation runs, and generate reports. The package then returns a matched data frame and pruned tree with the same species set, ready for phylogenetic generalised least squares, phylogenetic mixed models, phylogenetic meta-analysis, and related workflows. If users do not yet have a tree, $\texttt{prepR4pcm}$ can retrieve trees from several sources, date trees when suitable information is available, and format tree-source citations. We illustrate the workflow using bundled datasets with realistic name mismatches. $\texttt{prepR4pcm}$ is available at the CRAN (Comprehensive R Archive Network) with documentation and vignettes covering data and tree reconciliation, tree retrieval, multi-tree workflows, and phylogenetic meta-analysis.

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  Section: Health & Movement Sciences ; Topics: Neuroscience, Psychological and cognitive sciences, Physiology

  On the importance of effort perception in stroke care: From evidence to an ideal care pathway – An opinion paper

  Charonitis, Maëlle;   Collette, Fabienne;   Pageaux, Benjamin  

  10.24072/pcjournal.810 - Peer Community Journal, Volume 6 (2026), article no. e103

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  Post-stroke rehabilitation has traditionally relied on objective assessments of motor and cognitive abilities. However, one crucial factor remains largely overlooked in current practice: the perception of effort, that is, the conscious experience of task intensity and difficulty. Effort perception is strongly influenced by internal states such as fatigue and pain, two symptoms frequently reported after stroke, even in the absence of major neurological deficits. While these symptoms are often treated separately, they converge into a shared experience: that of heightened perceived effort. Here, we propose a model in which fatigue and pain reduce physical and cognitive capacity, requiring greater effort to compensate; this increased effort is in turn perceived and feeds back onto fatigue and pain, creating a self-sustaining loop. Recent literature suggests that both physical and mental fatigue, along with pain, increase perceived effort by impacting available resources and the motivation to engage and persist in cognitive and physical tasks. This modulation can have direct consequences on patient engagement and adherence to rehabilitation. When effort is perceived as disproportionate, even for an objectively simple task, it may lead to reduced participation or even withdrawal from rehabilitation. Conversely, a better understanding of the perception of effort could pave the way for personalized interventions that consider not only patients' actual capacities but also their subjective experiences. It is therefore urgent to consider the perception of effort as a clinical indicator in its own right, one that sits at the intersection of body, brain and lived experience. By integrating this dimension, research could better explain why some patients disengage from post-stroke care despite good recovery potential, and clinical practice could refine its motivational strategies and therapeutic adherence models. The stakes are twofold: to improve understanding of the mechanisms underlying effort perception, and to harness it as a lever for optimizing post-stroke care trajectories.

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  Section: Animal Science ; Topics: Agricultural sciences, Physiology

  Is homeostatic efficiency a positive aspect of health and well-being?

  Colditz, Ian  

  10.24072/pcjournal.808 - Peer Community Journal, Volume 6 (2026), article no. e102

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  It has been recognized for more than a century that health entails strength and vitality and is more than the absence of disease. In the 1930s, the capacity of regulatory processes to maintain homeostasis in the face of environmental challenges was proposed as a measure of vitality. More recently, this same capacity has been described as resilience. With growing interest in breeding and managing animals for a better (positive) quality of life it is timely to re-examine vitality and resilience through the lens of homeostatic efficiency. The starting point for considering the impact of environmental perturbations is the nature of the animal – environment relationship. This discussion paper examines the relationship from an ecological perspective that emphasizes the subjective character of environmental perception. The ecological viewpoint recognizes that environmental perturbations provide opportunities as well as challenges to the animal. Processes facilitating acquisition of competence to master environmental perturbations – the attribute described as agency - are described. The characteristic that Walter Cannon and colleagues called homeostatic efficiency is compared with present day concepts of resilience and vitality. The relevance of the term homeostatic efficiency is appraised from the contemporary perspectives of homeorhesis and allostasis. It is suggested that homeostatic efficiency retains utility to describe proficiency of the animal in capturing opportunities and minimizing challenges in everyday life, as well as resilience in adversity. In accord with the biopsychosocial model of health, homeostatic efficiency is a system property of organismal regulation that integrates physiological, immune, cognitive, affective, behavioural, microbiome and social processes. Analyses of deviations from trajectories in outcomes of organismal regulation including milk yield, body weight, egg weight, fibre diameter, and feed intake have attracted attention recently as indicators of resilience. It is suggested that both resilience and vitality influence these outcomes. Better characterization of vitality could help clarify concepts and management of positive health and well-being in animals. A multidisciplinary collaboration to develop complementary definitions of the closely related concepts of vitality, resilience, thriving, flourishing, vigour, physiological reserve, and functional capacity would assist this endeavour.

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  Section: Genomics ; Topics: Genetics/genomics, Biophysics and computational biology, Systems biology

  NetSyn: prokaryotic genomic context exploration of protein families

  Stam, Mark;   Langlois, Jordan; Chevalier, Céline; Mainguy, Jean; Reboul, Guillaume;   Bastard, Karine;   Médigue, Claudine;   Vallenet, David  

  10.24072/pcjournal.805 - Peer Community Journal, Volume 6 (2026), article no. e101

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  Background. The growing availability of large prokaryotic genomic datasets presents an opportunity to discover new metabolic pathways and enzymatic reactions useful for industrial or synthetic biological applications. Efforts to identify new enzyme functions in this vast number of sequences cannot be achieved without bioinformatics tools and the development of new strategies. Standard methods for assigning a biological function to a gene are based on sequence similarity. However, complementary approaches rely on mining databases to identify conserved gene clusters (e.g., syntenies). In prokaryotic genomes, genes involved in the same pathway are frequently encoded in a single locus with an operonic organisation. This genomic context conservation is considered as a reliable indicator of functional relationships, and is therefore a promising approach for improving gene function prediction. Methods. Here we present NetSyn (Network Synteny), a tool to group protein sequences based on the conservation of their genomic context rather than solely on sequence similarity. From a list of protein sequence identifiers, NetSyn searches for the corresponding genome entries to  retrieve neighbouring genes. Corresponding protein sequences are grouped into families to define homology relationships and compute a synteny conservation score between the different extracted genomic contexts. A network is then created in which the nodes represent the input proteins and the edges indicate that two proteins share a conserved synteny. Finally, the network is partitioned into clusters grouping proteins with similar genomic contexts, using a community detection algorithm. Results. As a proof of concept, we used NetSyn on two different datasets. The first one is the BKACE protein family (formerly named DUF849) which has previously been divided into isofunctional sub-families. NetSyn was able to go a step further by providing additional sub-families beyond those already described. The second dataset corresponds to a set of non-homologous proteins belonging to three different glycoside hydrolase (GH) families. These GHs are known to work cooperatively in Polysaccharide-Utilization Loci (PUL) and are therefore grouped together in the same genomic contexts. NetSyn was able to identify a locus grouping 3 GHs, involved in the degradation of xyloglucan, in 162 prokaryotic genomes. Discussion. By highlighting conserved synteny in distantly related prokaryotic species, NetSyn enables functional links between proteins to be established beyond sequence similarity alone. We showed that NetSyn is efficient for exploring large prokaryotic protein families, enabling the definition of isofunctional groups and the identification of functional interactions between non-homologous enzymes. These features enable the prediction of new genomic structures that have not yet been experimentally characterised. Finally, NetSyn is also useful for pinpointing annotation errors that have been propagated across databases, and for suggesting annotations for proteins lacking functional prediction. NetSyn is freely available at https://github.com/labgem/netsyn.