Peer community journal最新文献

{"title":"Data stochasticity and model parametrisation impact the performance of species distribution models: insights from a simulation study","authors":"Charlotte Lambert, Auriane Virgili","doi":"10.24072/pcjournal.263","DOIUrl":"https://doi.org/10.24072/pcjournal.263","url":null,"abstract":"Species distribution models (SDM) are widely used to describe and explain how species relate to their environment and predict their spatial distributions. As such, they are the cornerstone of most of spatial planning efforts worldwide. SDM can be implemented with a wide array of data types (presence-only, presence-absence, count...), which can either be point- or areal-based, and use a wide array of environmental conditions as predictor variables. The choice of the sampling type as well as the resolution of environmental conditions to be used are recognized as of crucial importance, yet we lack any quantification of the effects these decisions may have on SDM reliability. In the present work, we fill this gap with an unprecedented simulation procedure. We simulated 100 possible distributions of two different virtual species in two different regions. Species distribution were modelled using either segment- or areal-based sampling and five different spatial resolutions of environmental conditions. The SDM performances were inspected by statistical metrics, model composition, shapes of relationships and prediction quality. We provided clear evidence of stochasticity in the modelling process (particularly in the shapes of relationships): two dataset from the same survey, species and region could yield different results. Sampling type had stronger effects than spatial resolution on the final model relevance. The effect of coarsening the resolution was directly related to the resistance of the spatial features to changes of scale: SDM failed to adequately identify spatial distributions when the spatial features targeted by the species were diluted by resolution coarsening. These results have important implications for the SDM community, backing up some commonly accepted choices, but also by highlighting some up-to-now unexpected features of SDM (stochasticity). As a whole, this work calls for carefully weighted decisions in implementing models, and for caution in interpreting results.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"16 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135742564","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":"Different approaches to processing environmental DNA samples in turbid waters have distinct effects for fish, bacterial and archaea communities","authors":"Rachel Turba, Glory H. Thai, David K. Jacobs","doi":"10.24072/pcjournal.256","DOIUrl":"https://doi.org/10.24072/pcjournal.256","url":null,"abstract":"Coastal lagoons are an important habitat for endemic and threatened species in California that have suffered impacts from urbanization and increased drought. Environmental DNA has been promoted as a way to aid in the monitoring of biological communities, but much remains to be understood on the biases introduced by different protocols meant to overcome challenges presented by unique systems under study. Turbid water is one methodologic challenge to eDNA recovery in these systems as it quickly clogs filters, preventing timely processing of samples. We investigated biases in community composition produced by two solutions to overcome slow filtration due to turbidity: freezing of water prior to filtration (for storage purposes and long-term processing), and use of sediment (as opposed to water samples). Bias assessments of community composition in downstream eDNA analysis was conducted for two sets of primers, 12S (fish) and 16S (bacteria and archaea). Our results show that freezing water prior to filtration had different effects on community composition for each primer, especially for the 16S, when using a filter of larger pore size (3 μm). Nevertheless, pre-freezing water samples can still be a viable alternative for storage and processing of turbid water samples when focusing on fish communities (12S). The use of sediment samples as an alternative to processing water samples should be done with caution, and at minimum the number of biological replicates and/or volume sampled should be increased.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-04-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135904763","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 helper strategy in vector-transmission of plant viruses","authors":"Jérémy Di Mattia, J. Zeddam, M. Uzest, S. Blanc","doi":"10.24072/pcjournal.258","DOIUrl":"https://doi.org/10.24072/pcjournal.258","url":null,"abstract":"An intriguing aspect of vector-transmission of plant viruses is the frequent involvement of a helper component (HC). HCs are virus-encoded non-structural proteins produced in infected plant cells that are mandatory for the transmission success. Over five decades, all data collected on HCs from unrelated viral species transmitted by distinct vector species were consistent with a unique mode of action designated “the bridge hypothesis”: the HC has two functional domains, one binding the virus particle and the other binding a putative receptor in the vector, creating a reversible molecular bridge be-tween the two. This hypothesis appeared fully satisfactory as HCs were reported solely in viruses transmitted non-circulatively – i.e. the virus particle binds externally to the mouthpart of its vector, and can later be released therefrom and inoculated. Recently, however, HCs have also been reported in viruses transmitted circulatively, where the virus particles are internalized in gut cells and cycle","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47696871","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":"Population genetics of Glossina fuscipes fuscipes from southern Chad","authors":"S. Ravel, Mahamat Hisséne Mahamat, A. Ségard, R. Argilés-Herrero, J. Bouyer, J. Rayaissé, P. Solano, Brahim Guihini Mollo, M. Peka, Justin Darnas, A. Bélem, Wilfrid Yoni, C. Noûs, T. de Meeûs","doi":"10.24072/pcjournal.257","DOIUrl":"https://doi.org/10.24072/pcjournal.257","url":null,"abstract":"In Subsaharan Africa, tsetse flies (genus Glossina ) are vectors of trypanosomes causing Human African Trypanosomiasis (HAT) and Animal African Trypanosomosis (AAT). Some foci of HAT persist in Southern Chad, where a program of tsetse control was started against","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47550212","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":"MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes","authors":"Bertrand Néron, Rémi Denise, Charles Coluzzi, Marie Touchon, Eduardo P.C. Rocha, Sophie S. Abby","doi":"10.24072/pcjournal.250","DOIUrl":"https://doi.org/10.24072/pcjournal.250","url":null,"abstract":"Complex cellular functions are usually encoded by a set of genes in one or a few organized genetic loci in microbial genomes. Macromolecular System Finder (MacSyFinder) is a program that uses these properties to model and then annotate cellular functions in microbial genomes. This is done by integrating the identification of each individual gene at the level of the molecular system. We hereby present a major release of MacSyFinder (version 2) coded in Python 3. The code was improved and rationalized to facilitate future maintainability. Several new features were added to allow more flexible modelling of the systems. We introduce a more intuitive and comprehensive search engine to identify all the best candidate systems and sub-optimal ones that respect the models’ constraints. We also introduce the novel macsydata companion tool that enables the easy installation and broad distribution of the models developed for MacSyFinder (macsy-models) from GitHub repositories. Finally, we have updated and improved MacSyFinder popular models: TXSScan to identify protein secretion systems, TFFscan to identify type IV filaments, CONJscan to identify conjugative systems, and CasFinder to identify CRISPR associated proteins. MacSyFinder and the updated models are available at: https://github.com/gem-pasteur/macsyfinder and https://github.com/macsy-models.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"60 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136046489","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":"Extrinsic mortality and senescence: a guide for the perplexed","authors":"Charlotte de Vries, Matthias Galipaud, Hanna Kokko","doi":"10.24072/pcjournal.253","DOIUrl":"https://doi.org/10.24072/pcjournal.253","url":null,"abstract":"Do environments or species traits that lower the mortality of individuals create selection for delaying senescence? Reading the literature creates an impression that mathematically oriented biologists cannot agree on the validity of George Williams' prediction (who claimed 'yes'). The abundance of models and opinions may bewilder those that are new to the field. Here we provide heuristics as well as simple models that outline when the Williams prediction holds, why there is a ‘null model’ where extrinsic mortality does not change the evolution of senescence at all, and why it is also possible to expect the opposite of William’s prediction, where increased extrinsic mortality favours slower senescence. We hope to offer intuition by quantifying how much delaying the ‘placement’ of an offspring into the population reduces its expected contribution to the gene pool of the future. Our first example shows why sometimes increased extrinsic mortality has no effect (the null result), and why density dependence can change that. Thereafter, a model with ten different choices for population regulation shows that high extrinsic mortality favours fast life histories (Williams) if increasing density harms the production of juveniles or their chances to recruit into the population. If instead increasing density harms the survival of older individuals in a population, then high extrinsic mortality favours slow life histories (anti-Williams). We discuss the possibility that empirically found Williams-like patterns provide indirect evidence for population regulation operating via harming the production or fitness prospects of juveniles, as opposed to the survival of established breeders.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136046492","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":"Performance and limitations of linkage-disequilibrium-based methods for inferring the genomic landscape of recombination and detecting hotspots: a simulation study","authors":"Marie Raynaud, Pierre-Alexandre Gagnaire, Nicolas Galtier","doi":"10.24072/pcjournal.254","DOIUrl":"https://doi.org/10.24072/pcjournal.254","url":null,"abstract":"Knowledge of recombination rate variation along the genome provides important insights into genome and phenotypic evolution. Population genomic approaches offer an attractive way to infer the population-scaled recombination rate ρ=4Ner using the linkage disequilibrium information contained in DNA sequence polymorphism data. Such methods have been used in a broad range of plant and animal species to build genome-wide recombination maps. However, the reliability of these inferences has only been assessed under a restrictive set of conditions. Here, we evaluate the ability of one of the most widely used coalescent-based programs, LDhelmet, to infer a genomic landscape of recombination with the biological characteristics of a human-like landscape including hotspots. Using simulations, we specifically assessed the impact of methodological (sample size, phasing errors, block penalty) and evolutionary parameters (effective population size (Ne), demographic history, mutation to recombination rate ratio) on inferred map quality. We report reasonably good correlations between simulated and inferred landscapes, but point to limitations when it comes to detecting recombination hotspots. False positive and false negative hotspots considerably confound fine-scale patterns of inferred recombination under a wide range of conditions, particularly when Ne is small and the mutation/recombination rate ratio is low, to the extent that maps inferred from populations sharing the same recombination landscape appear uncorrelated. We thus address a message of caution for the users of these approaches, at least for genomes with complex recombination landscapes such as in humans.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"133 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136195782","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":"Best organic farming expansion scenarios for pest control: a modeling approach","authors":"Thomas Delattre, Mohamed-Mahmoud Memah, Pierre Franck, Pierre Valsesia, Claire Lavigne","doi":"10.24072/pcjournal.251","DOIUrl":"https://doi.org/10.24072/pcjournal.251","url":null,"abstract":"Organic Farming (OF) has been expanding recently in response to growing consumer demand and as a response to environmental concerns. The area under OF is expected to further increase in the future. The effect of OF expansion on pest densities in organic and conventional crops remains difficult to predict because OF expansion impacts Conservation Biological Control (CBC), which depends on the surrounding landscape (i.e. both the crop mosaic and semi-natural habitats). In order to understand and forecast how pests and their biological control may vary during OF expansion, we modeled the effect of spatial changes in farming practices on population dynamics of a pest and its natural enemy. We investigated the impact on pest density and on predator to pest ratio of three contrasted scenarios aiming at 50% organic fields through the progressive conversion of conventional fields. Scenarios were 1) conversion of Isolated conventional fields first (IP), 2) conversion of conventional fields within Groups of conventional fields first (GP), and 3) Random conversion of conventional field (RD). We coupled a neutral spatially explicit landscape model to a predator-prey model to simulate pest dynamics in interaction with natural enemy predators. The three OF expansion scenarios were applied to nine landscape contexts differing in their proportion and fragmentation of semi-natural habitat. We further investigated if the ranking of scenarios was robust to pest control methods in OF fields and pest and predator dispersal abilities. We found that organic farming expansion affected more predator densities than pest densities for most combinations of landscape contexts and OF expansion scenarios. The impact of OF expansion on final pest and predator densities was also stronger in organic than conventional fields and in landscapes with large proportions of highly fragmented semi-natural habitats. Based on pest densities and the predator to pest ratio, our results suggest that a progressive organic conversion with a focus on isolated conventional fields (scenario IP) could help promote CBC. Careful landscape planning of OF expansion appeared most necessary when pest management was substantially less efficient in organic than in conventional crops, and in landscapes with low proportion of semi-natural habitats.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135795664","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":"Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species","authors":"A. Wallner, A. Klonowska, Ludivine Guigard, E. King, I. Rimbault, E. Ngonkeu, Phuong Nguyen, G. Béna, L. Moulin","doi":"10.24072/pcjournal.252","DOIUrl":"https://doi.org/10.24072/pcjournal.252","url":null,"abstract":"Beyond being a reliable nutrient provider, some bacteria will perceive the plant as a potential host and undertake root colonization leading to mutualistic or parasitic interactions. Bacteria of the Burkholderia and Paraburkholderia genera are frequently found in the rhizosphere of rice. While the latter are often described as plant growth promoting species, Burkholderia are often studied for their human opportunistic traits. Here, we used root exudate stimulation on three Burkholderia and three Paraburkholderia strains isolated from rice roots to characterize their preliminary adaptation to the rice host at the transcriptomic level. Instead of the awaited genus-dependent adaptation, we observed a strongly species-specific response for all tested strains. While all bacteria originate from the rice environment, there are great disparities in their levels of adaptation following the sensing of root exudates. We further report the shared major functions that were differentially regulated in this early step of bacterial adaptation to plant colonization, including amino acids and putrescine metabolism, the Entner-Doudoroff (ED) pathway as well as cyclic diguanylate monophosphate (c-di-GMP) cycling.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43279662","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":"African army ants at the forefront of virome surveillance in a remote tropical forest","authors":"Matthieu Fritz, Bérénice Reggiardo, Denis Filloux, Lisa Claude, Emmanuel Fernandez, Frédéric Mahé, Simona Kraberger, Joy M. Custer, Pierre Becquart, Telstar Ndong Mebaley, Linda Bohou Kombila, Léadisaelle H. Lenguiya, Larson Boundenga, Illich M. Mombo, Gael D. Maganga, Fabien R. Niama, Jean-Sylvain Koumba, Mylène Ogliastro, Michel Yvon, Darren P. Martin, Stéphane Blanc, Arvind Varsani, Eric Leroy, Philippe Roumagnac","doi":"10.24072/pcjournal.249","DOIUrl":"https://doi.org/10.24072/pcjournal.249","url":null,"abstract":"In this study, we used a predator-enabled metagenomics strategy to sample the virome of a remote and difficult-to-access densely forested African tropical region. Specifically, we focused our study on the use of army ants of the genus Dorylus that are obligate collective foragers and group predators that attack and overwhelm a broad array of animal prey. Using 209 army ant samples collected from 29 colonies and the virion-associated nucleic acid-based metagenomics approach, we showed that a broad diversity of bacterial, plant, invertebrate and vertebrate viral sequences were accumulated by army ants: including sequences from 157 different viral genera in 56 viral families. This suggests that using predators and scavengers such as army ants to sample broad swathes of tropical forest viromes can shed light on the composition and the structure of viral populations of these complex and inaccessible ecosystems.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"371 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135956416","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}