Peer community journal最新文献

{"title":"Telomere length varies with sex, hatching rank and year of birth in the Little Owl, Athene noctua","authors":"François Criscuolo, Inès Fache, Bertrand Scaar, Sandrine Zahn, Josefa Bleu","doi":"10.24072/pcjournal.341","DOIUrl":"https://doi.org/10.24072/pcjournal.341","url":null,"abstract":"Telomeres are non-coding DNA sequences located at the end of linear chromosomes, protecting genome integrity. In numerous taxa, telomeres shorten with age and telomere length (TL) is positively correlated with longevity. Moreover, TL is also affected by environmental stressors and/or resource-demanding situations particularly during early-life. Thus, TL has been used as a physiological marker of individual quality and also as an indicator of population trend in conservation physiology. In this study, we investigated the effects of hatching rank, year of birth (2014 to 2017), sex and nest environment on TL of 137 Little Owls nestlings (Athene noctua). Little Owls’ populations in Europe showed a marked declined in the end of the 20th century. Nowadays, in the studied Alsatian population, the population is increasing. In this study, our results indicated that telomeres are longer in females and, independently of sex, in nestlings with the highest body condition. There was also a negative effect of hatching rank but only for last-hatched nestlings in large clutches of 5 nestlings. We did not find any effect of the environmental covariates on nestlings’ TL. Finally, we found that nestlings’ TL were shorter the last year of the study, while nestlings’ body condition stayed unchanged over the same period. This result is intriguing given the local positive population dynamics and is further discussed in the context of physiological conservation. Future studies should investigate the link between reduced TL and survival prospects in this species.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"17 5","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135391306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of microbial exopolymer producers in sandy and muddy intertidal sediments by compound-specific isotope analysis","authors":"Cédric Hubas, Julie Gaubert-Boussarie, An-Sofie D’Hondt, Bruno Jesus, Dominique Lamy, Vona Meleder, Antoine Prins, Philippe Rosa, Willem Stock, Koen Sabbe","doi":"10.24072/pcjournal.336","DOIUrl":"https://doi.org/10.24072/pcjournal.336","url":null,"abstract":"","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135871977","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Structify-Net: Random Graph generation with controlled size and customized structure","authors":"Remy Cazabet, Salvatore Citraro, Giulio Rossetti","doi":"10.24072/pcjournal.335","DOIUrl":"https://doi.org/10.24072/pcjournal.335","url":null,"abstract":"Network structure is often considered one of the most important features of a network, and various models exist to generate graphs having one of the most studied types of structures, such as blocks/communities or spatial structures. In this article, we introduce a framework for the generation of random graphs with a controlled size —number of nodes, edges— and a customizable structure, beyond blocks and spatial ones, based on node-pair rank and a tunable probability function allowing to control the amount of randomness. We introduce a structure zoo —a collection of original network structures— and conduct experiments on the small-world properties of networks generated by those structures. Finally, we introduce an implementation as a Python library named Structify-net.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135778376","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Influence of endosymbionts on the reproductive fitness of the tick Ornithodoros moubata","authors":"Florian Taraveau, Thomas Pollet, Maxime Duhayon, Laëtitia Gardès, Hélène Jourdan-Pineau","doi":"10.24072/pcjournal.334","DOIUrl":"https://doi.org/10.24072/pcjournal.334","url":null,"abstract":"Over the past decade, many studies have demonstrated the crucial role of the tick microbiome in tick biology. The soft tick Ornithodoros moubata is a hematophagous ectoparasite of Suidae, best known for transmitting the African swine fever virus. Its bacterial microbiota is characterized by a high prevalence of Francisella-like and Rickettsia endosymbionts. The present study aims to better understand the potential influence of these two major members of the tick microbiota on the reproductive fitness of O. moubata. A total of 132 adult female ticks were treated with antibiotics using gentamycin or rifampicin added to the blood meal. Half of the ticks were also supplemented with B vitamins to address the nutritional role of endosymbionts. Over two periods of 50 days, several traits related to the reproductive fitness were monitored to investigate the importance of Francisella and Rickettsia for these traits. It appeared that most of the reproductive parameters considered were not affected. However, antibiotic treatments induced an increase in the tick survival, indicating a potential fitness cost of harboring endosymbionts during the tick reproductive cycle. Similarly, 366 first stage nymphs of O. moubata were exposed to the same treatments for molecular quantification of both endosymbionts. Results from qPCR suggested that the treatments had a bacteriostatic effect on endosymbionts without completely eliminating neither Francisella-like endosymbiont nor Rickettsia.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"24 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135883688","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"COVFlow: phylodynamics analyses of viruses from selected SARS-CoV-2 genome sequences","authors":"Gonché Danesh, Corentin Boennec, Laura Verdurme, Mathilde Roussel, Sabine Trombert-Paolantoni, Benoit Visseaux, Stéphanie Haim-Boukobza, Samuel Alizon","doi":"10.24072/pcjournal.333","DOIUrl":"https://doi.org/10.24072/pcjournal.333","url":null,"abstract":"Phylodynamic analyses can generate important and timely data to optimise public health response to SARS-CoV-2 outbreaks and epidemics. However, their implementation is hampered by the massive amount of sequence data and the difficulty to parameterise dedicated software packages. We introduce the COVFlow pipeline, accessible at https://gitlab.in2p3.fr/ete/CoV-flow, which allows a user to select sequences from the Global Initiative on Sharing Avian Influenza Data (GISAID) database according to user-specified criteria, to perform basic phylogenetic analyses, and to produce an XML file to be run in the Beast2 software package. We illustrate the potential of this tool by studying two sets of sequences from the Delta variant in two French regions. This pipeline can facilitate the use of virus sequence data at the local level, for instance, to track the dynamics of a particular lineage or variant in a region of interest.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"76 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136114333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SNP discovery by exome capture and resequencing in a pea genetic resource collection","authors":"Grégoire Aubert, Jonathan Kreplak, Magalie Leveugle, Hervé Duborjal, Anthony Klein, Karen Boucherot, Emilie Vieille, Marianne Chabert-Martinello, Corinne Cruaud, Virginie Bourion, Isabelle Lejeune-Hénaut, Marie-Laure Pilet-Nayel, Yanis Bouchenak-Khelladi, Nicolas Francillonne, Nadim Tayeh, Jean-Philippe Pichon, Nathalie Rivière, Judith Burstin","doi":"10.24072/pcjournal.332","DOIUrl":"https://doi.org/10.24072/pcjournal.332","url":null,"abstract":"Pea is a major pulse crop in temperate regions and a model plant in genetics. Large genetic marker resources are needed to assess the genetic diversity in the species genepool and to provide selection tools for breeders. In this study, we used second-generation sequencing to perform an exome-capture protocol using a diverse pea germplasm collection, and produced a resource of over 2 million Single Nucleotide Polymorphisms. This dataset was then used to characterize the genetic diversity present in the panel and compute phylogenetic and structure analyses. The development of this resource paves the way for Genome-wide association studies and the development of powerful genotyping tools.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"57 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135858683","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The evolutionary dynamics of plastic foraging and its ecological consequences: a resource-consumer model","authors":"Léo Ledru, Jimmy Garnier, Océane Guillot, Erwan Faou, Camille Noûs, Sébastien Ibanez","doi":"10.24072/pcjournal.330","DOIUrl":"https://doi.org/10.24072/pcjournal.330","url":null,"abstract":"Phenotypic plasticity has important ecological and evolutionary consequences. In particular, behavioural phenotypic plasticity such as plastic foraging (PF) by consumers, may enhance community stability. Yet little is known about the ecological conditions that favor the evolution of PF, and how the evolutionary dynamics of PF may modulate its effects on community stability. In order to address these questions, we constructed an eco-evolutionary model in which resource and consumer niche traits underwent evolutionary diversification. Consumers could either forage randomly, only as a function of resources abundance, or plastically, as a function of resource abundance, suitability and consumption by competitors. PF evolved when the niche breadth of consumers with respect to resource use was large enough and when the ecological conditions allowed substantial functional diversification. In turn, PF promoted further diversification of the niche traits in both guilds. This suggests that phenotypic plasticity can influence the evolutionary dynamics at the community-level. Faced with a sudden environmental change, PF promoted community stability directly and also indirectly through its effects on functional diversity. However, other disturbances such as persistent environmental change and increases in mortality, caused the evolutionary regression of the PF behaviour, due to its costs. The causal relationships between PF, community stability and diversity are therefore intricate, and their outcome depends on the nature of the environmental disturbance, in contrast to simpler models claiming a direct positive relationship between PF and stability.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136013097","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Integrating biodiversity assessments into local conservation planning: the importance of assessing suitable data sources","authors":"Thibaut Ferraille, Christian Kerbiriou, Charlotte Bigard, Fabien Claireau, John D. Thompson","doi":"10.24072/pcjournal.331","DOIUrl":"https://doi.org/10.24072/pcjournal.331","url":null,"abstract":"Strategic Environmental Assessment (SEA) of land-use planning is a fundamental tool to minimize environmental impacts of artificialization. In this context, Systematic Conservation Planning (SCP) tools based on Species Distribution Models (SDM) are frequently used for the elaboration of spatially exhaustive biodiversity diagnostics. Despite the paradigm of “garbage in - garbage out” that emphasises the importance of testing the suitability of data for SDM and priority conservation areas, the assessment of database sources remains relatively rare. In addition, the lack of practical recommendations for the use of open-access databases by SEA stakeholders remains a problem. The aim of this study is to explore the quality of data sources that can be used in SEA to assess priority conservation areas in SEA. The study used data for nine taxonomic groups (commonly used in inventories for environmental impact assessment) and three databases available to SEA stakeholders. Three local administrative entities in very different socio-ecological contexts were used to examine three main issues : (i) the suitability of local versus regional or country databases for assessing conservation priorities, (ii) differences among taxonomic groups or territories in terms of the suitability of databases, (iii) the importance of the quality of databases for the application of SDM to assess priority conservation areas. Our study provides several clear messages for potential users of open-access databases. First, the need for prudence in the interpretation of biodiversity maps. Second, the collection of individual databases at the country scale is necessary to complete local data and ensure the suitability of SDM in a local context. Third, a data driven approach can lead to the use of notably different species communities to identify priority conservation areas when compared to the community in the original database. Finally, we propose a workflow to guide SEA stakeholders through the process of data rationalization and use in conservation planning.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"63 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135141360","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods","authors":"Olivier Rué, Monika Coton, Eric Dugat-Bony, Kate Howell, Françoise Irlinger, Jean-Luc Legras, Valentin Loux, Elisa Michel, Jérôme Mounier, Cécile Neuvéglise, Delphine Sicard","doi":"10.24072/pcjournal.321","DOIUrl":"https://doi.org/10.24072/pcjournal.321","url":null,"abstract":"Next generation sequencing offers several ways to study microbial communities. For agri-food sciences, identifying species in diverse food ecosystems is key for both food sustainability and food security. The aim of this study was to compare metabarcoding pipelines and markers to determine fungal diversity in food ecosystems, from Illumina short reads. We built mock communities combining the most representative fungal species in fermented meat, cheese, wine and bread. Four barcodes (ITS1, ITS2, D1/D2 and RPB2) were tested for each mock and on real fermented products. We created a database, including all mock species sequences for each barcode to compensate for the lack of curated data in available databases. Four bioinformatics tools (DADA2, QIIME, FROGS and a combination of DADA2 and FROGS) were compared. Our results clearly showed that the combined DADA2 and FROGS tool gave the most accurate results. Most mock community species were not identified by the RPB2 barcode due to unsuccessful barcode amplification. When comparing the three rDNA markers, ITS markers performed better than D1/D2, as they are better represented in public databases and have better specificity to distinguish species. Between ITS1 and ITS2, differences in the best marker were observed according to the studied ecosystem. While ITS2 is best suited to characterize cheese, wine and fermented meat communities, ITS1 performs better for sourdough bread communities. Our results also emphasized the need for a dedicated database and enriched fungal-specific public databases with novel barcode sequences for 118 major species in food ecosystems.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135435013","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Chikungunya intra-vector dynamics in Aedes albopictus from Lyon (France) upon exposure to a human viremia-like dose range reveals vector barrier’s permissiveness and supports local epidemic potential","authors":"Barbara Viginier, Lucie Cappuccio, Céline Garnier, Edwige Martin, Carine Maisse, Claire Valiente Moro, Guillaume Minard, Albin Fontaine, Sébastian Lequime, Maxime Ratinier, Frédérick Arnaud, Vincent Raquin","doi":"10.24072/pcjournal.326","DOIUrl":"https://doi.org/10.24072/pcjournal.326","url":null,"abstract":"Arbovirus emergence and epidemic potential, as approximated by the vectorial capacity formula, depends on host and vector parameters, including the vector’s intrinsic ability to replicate then transmit the pathogen known as vector competence. Vector competence is a complex, time-dependent, quantitative phenotype influenced by biotic and abiotic factors. A combination of experimental and modelling approaches is required to assess arbovirus intra-vector dynamics and estimate epidemic potential. In this study, we measured infection, dissemination, and transmission dynamics of chikungunya virus (CHIKV) in a field-derived Aedes albopictus population (Lyon, France) after oral exposure to a range of virus doses spanning human viraemia. Statistical modelling indicates rapid and efficient CHIKV progression in the vector mainly due to an absence of a dissemination barrier, with 100% of the infected mosquitoes ultimately exhibiting a disseminated infection, regardless of the virus dose. Transmission rate data revealed a time-dependent, but overall weak, transmission barrier, with individuals transmitting as soon as 2 days post-exposure (dpe) and >50% infectious mosquitoes at 6 dpe for the highest dose. Based on these experimental intra-vector dynamics data, epidemiological simulations conducted with an agent-based model showed that even at low mosquito biting rates, CHIKV could trigger outbreaks locally. Together, this reveals the epidemic potential of CHIKV upon transmission by Aedes albopictus in mainland France.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"54 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134977963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}