Latest Articles
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Section: Ecology ; Topics: Ecology
A Julia toolkit for species distribution data
10.24072/pcjournal.589 - Peer Community Journal, Volume 5 (2025), article no. e101
Get full text PDF(1) Species distribution modeling requires to handle varied types of data, and benefits from an integrated approach to programming. (2) We introduce SpeciesDistributionToolkit, a Julia package aiming to facilitate the production of species distribution models. It covers various steps of the data collection and analysis process, extending to the development of interfaces for integration of additional functionalities. (3) By relying on semantic versioning and strong design choices on modularity, we expect that this package will lead to improved reproducibility and long-term maintainability. (4) We illustrate the functionalities of the package through several case studies, accompanied by reproducible code.
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Section: Microbiology ; Topics: Microbiology, Computer sciences
EnVhogDB: an extended view of the viral protein families on Earth through a vast collection of HMM profiles
10.24072/pcjournal.627 - Peer Community Journal, Volume 5 (2025), article no. e100
Get full text PDFOver the last twenty years, hundreds of metagenomic studies have generated millions of viral genomic sequences from a wide variety of ecosystems. Despite this, the overall genetic diversity of viruses remains elusive, both in terms of the number of protein families they encode and the diversity of these families. Indeed, even if it is recognized that the organization of the viral protein sequence space requires sensitive homology detection methods, such methods have never been applied at a large scale. To produce a more realistic and comprehensive view of the protein diversity in the viral world, we have (i) collected thousands of viromes and identified viral contigs and proteins within them, (ii) retrieved viral proteins available in different public databases, and (iii) applied sensitive similarity searches to cluster all these proteins into families and (iv) annotated the protein clusters produced. More than 46 million deduplicated proteins were clustered into less than 2.3 million protein families. After further removing genomic sequences likely of cellular origin using an iterative procedure, the remaining 2,203,457 clusters were coined enVhogs (for environmental Viral homologous groups). Their multiple sequence alignments have been transformed into HMMs to constitute the EnVhog database. Even if only a small proportion of enVhogs were annotated (15.9 %), they encompass almost half of the protein dataset (44.8 %). Applied to the annotation of four recently published viromes from diverse environments (sulfuric soil, grassland, surface seawater and human gut), enVhog HMMs doubled the number of viral sequences characterized, and increased by 54%-74% the number of proteins functionally annotated. EnVhogDB, the largest comprehensive compilation of viral protein information to date, is a resource that will thus further help to determine the functions of proteins encoded in newly sequenced viral genomes, and help to improve the accuracy of viral sequence detection tools. EnVhog database is available at http://envhog.u-ga.fr/envhog.
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Section: Nutrition ; Topics: Psychological and cognitive sciences
Sustainable diets: Links between knowledge, motivations and eating practices.
10.24072/pcjournal.622 - Peer Community Journal, Volume 5 (2025), article no. e99
Get full text PDFTo preserve the planet's ecosystems and ensure the well-being of its inhabitants, the adoption of more sustainable diets is necessary. At present, however, consumer dietary practices often remain unsustainable. One main barrier to adopting sustainable diets is the lack of both knowledge and motivation. The primary objective of this study was to examine whether a link exists between knowledge about sustainable diets and sustainable eating practices, and whether this link is mediated by motivations. Additionally, we compared the respective roles of objective and subjective knowledge about sustainable diets. To this end, 273 participants aged 20 to 60 years responded to questionnaires about their motivations concerning sustainable food choices, as well as their objective and subjective knowledge about sustainable diets, and their self-reported sustainable eating practices. A PLS-SEM model was used to analyze the relationships among these variables, demonstrating good reliability of the indicators, internal consistency, convergent and discriminant validity, and no multicollinearity. The predictive power of this model was found to be satisfactory, with 18% of the variance explained for motivations and 34% for practices. Our results indicate a significant link between knowledge about sustainable diets and sustainable eating practices, with motivations acting as a crucial mediator in this relationship. This finding was confirmed for both objective and subjective knowledge. Subjective knowledge was thus also revealed to have a direct effect on sustainable eating practices. These findings suggest that the manner in which individuals perceive their own knowledge about sustainable diets may have a greater impact on their practices than their actual knowledge, and that motivations play a central role in shaping sustainable behaviors.
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Section: Ecology ; Topics: Ecology, Environmental sciences, Population biology
Long term trend and short-term dynamics of a willow ptarmigan population
10.24072/pcjournal.590 - Peer Community Journal, Volume 5 (2025), article no. e98
Get full text PDFWillow ptarmigan Lagopus lagopus is abundant in Arctic and tundra regions, but rapid climate warming has raised concerns about possible declines as has been observed in several bird species. In this study, we used a hierarchical state-space model to analyze data from a 139 km line transects in mid-Sweden over 48 years. Adult numbers and breeding success were analyzed separately, and we included covariates on vole abundance, numbers of snow-free days in autumn and spring, and the last day of frost in May. We assessed long-term trends in the adult population and estimated the effects of breeding success and weather variation on short-term changes. The estimates of adult density did not show any trend for the period 1976 to 2023, and the dynamics were characterized by a strong direct negative density dependence indicating a stationary process. A number of possible mechanisms have been suggested for how a warmer climate affects willow ptarmigan population dynamics, but our results do not support the hypothesis that lack of snow in autumn and spring increases the vulnerability of willow ptarmigan to predation and leads to population decline. Breeding success is an important driver of changes in, but independent of, adult density. In addition to predation, we propose that climate conditions and emerging vegetation during egg formation and laying are important. We suggest that our results can be explained by a diverse predator assemblage that makes it difficult for the population to escape top-down control, resulting in short-term fluctuations at lower densities.
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