Peer community journal最新文献

{"title":"How do monomorphic bacteria evolve? The Mycobacterium tuberculosis complex and the awkward population genetics of extreme clonality","authors":"Christoph Stritt, Sebastien Gagneux","doi":"10.24072/pcjournal.322","DOIUrl":"https://doi.org/10.24072/pcjournal.322","url":null,"abstract":"Exchange of genetic material through sexual reproduction or horizontal gene transfer is ubiquitous in nature. Among the few outliers that rarely recombine and mainly evolve by de novo mutation are a group of deadly bacterial pathogens, including the causative agents of leprosy, plague, typhoid, and tuberculosis. The interplay of evolutionary processes is poorly understood in these organisms. Population genetic methods allowing to infer mutation, recombination, genetic drift, and natural selection make strong assumptions that are difficult to reconcile with clonal reproduction and fully linked genomes consisting mainly of coding regions. In this review, we highlight the challenges of extreme clonality by discussing population genetic inference with the Mycobacterium tuberculosis complex, a group of closely related obligate bacterial pathogens of mammals. We show how uncertainties underlying quantitative models and verbal arguments affect previous conclusions about the way these organisms evolve. A question mark remains behind various quantities of applied and theoretical interest, including mutation rates, the interpretation of nonsynonymous polymorphisms, or the role of genetic bottlenecks. Looking ahead, we discuss how new tools for evolutionary simulations, going beyond the traditional Wright-Fisher framework, promise a more rigorous treatment of basic evolutionary processes in clonal bacteria.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135579666","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":"Validation of a Radio frequency identification system for tracking location of laying hens in a quasi-commercial aviary system","authors":"Sabine G. Gebhardt-Henrich, Alexander Kashev, Matthew B. Petelle, Michael J. Toscano","doi":"10.24072/pcjournal.324","DOIUrl":"https://doi.org/10.24072/pcjournal.324","url":null,"abstract":"Cage-free housing is increasingly chosen in Europe, North America, and Australia as an animal-welfare friendly farm system for laying hens. However, hens are kept in large numbers in those systems which makes checking for health and welfare difficult and individuals cannot be identified. Tracking systems like radio frequency identification allow researchers to monitor these individuals almost continuously. Individual tracking data has revealed substantial individual variation in movement patterns, however, in recent studies, only a subset of animals per flock was tracked. We applied an RFID tracking system to monitor all 1125 laying hens of a flock, which were divided into 5 pens of 225 birds each in a barn with an aviary system. In each pen, 26 antennas were placed on the edges of three tiers and in the litter. For validation purposes, 3 hens in 2 connected pens were fitted with colored backpacks. They were recorded on video and their location throughout the pen was taken from the video and compared with registrations from the RFID system. For 93% of compared transitions, the RFID data matched the observational data regarding the tier or litter whereas the value fell to 39% for specific antennae. When the antennae on the litter were excluded for the validation, the match on tier-level was at least 98% but on antenna-level it remained lower than 50%. The sensitivity of the detection of tiers/litter but not antennae differed among the three hens. We conclude that the RFID tracking system was suitable for studying the movement pattern of individual hens among tiers in an aviary system in a reliable way but tracking birds on the litter needs to be improved.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"20 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135816147","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":"A soft tick vector of Babesia sp. YLG in Yellow-legged gull (Larus michahellis) nests","authors":"Claire Bonsergent, Marion Vittecoq, Carole Leray, Maggy Jouglin, Marie Buysse, Karen D. McCoy, Laurence Malandrin","doi":"10.24072/pcjournal.316","DOIUrl":"https://doi.org/10.24072/pcjournal.316","url":null,"abstract":"Babesia sp. YLG has recently been described in Yellow-legged gull (Larus michahellis) chicks and belongs to the Peircei clade in the new classification of Piroplasms. Here, we studied Babesia sp. YLG vectorial transmission by ticks in the simplified environment of a single seabird breeding colony where the Yellow-legged gull is the sole vertebrate host, Ornithodoros maritimus (syn. Alectorobius maritimus) the sole tick species, and Babesia sp. YLG is the only blood parasite species detected in chicks of the colony. We collected ticks over four years, maintained certain individuals through moulting or oviposition, and dissected fresh ticks to isolate different organs and test for the presence of the parasite using molecular assays. We report the first strong evidence of a Piroplasmidae transmitted by a soft tick. Indeed, Babesia sp. YLG DNA was detected in the salivary glands of nymphs, females and males, a necessary organ to infect for transmission to a new vertebrate host. Parasite DNA was also found in tick ovaries, which could indicate possible transovarial transmission. Our detection of Babesia sp. YLG DNA in several male testes and in endospermatophores, and notably in a parasite-free female (uninfected ovaries and salivary glands), raise the interesting possibility of sexual transmission from infected males to uninfected females. Future work in this system will now need to focus on the degree to which the parasite can be maintained locally by ticks and the epidemiological consequences of infection for both O. maritimus and its avian host.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135814494","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":"DRomics, a workflow to exploit dose-response omics data in ecotoxicology","authors":"Marie Laure Delignette-Muller, Aurélie Siberchicot, Floriane Larras, Elise Billoir","doi":"10.24072/pcjournal.325","DOIUrl":"https://doi.org/10.24072/pcjournal.325","url":null,"abstract":"Omics technologies has opened new possibilities to assess environmental risks and to understand the mode(s) of action of pollutants. Coupled to dose-response experimental designs, they allow a non-targeted assessment of organism responses at the molecular level along an exposure gradient. However, describing the dose-response relationships on such high-throughput data is no easy task. In a first part, we review the software available for this purpose, and their main features. We set out arguments on some statistical and modeling choices we have made while developing the R package DRomics and its positioning compared to others tools. The DRomics main analysis workflow is made available through a web interface, namely a shiny app named DRomics-shiny. Next, we present the new functionalities recently implemented. DRomics has been augmented especially to be able to handle varied omics data considering the nature of the measured signal (e.g. counts of reads in RNAseq) and the way data were collected (e.g. batch effect, situation with no experimental replicates). Another important upgrade is the development of tools to ease the biological interpretation of results. Various functions are proposed to visualize, summarize and compare the responses, for different biological groups (defined from biological annotation), optionally at different experimental levels (e.g. measurements at several omics level or in different experimental conditions). A new shiny app named DRomicsInterpreter-shiny is dedicated to the biological interpretation of results. The institutional web page https://lbbe.univ-lyon1.fr/fr/dromics gathers links to all resources related to DRomics, including the two shiny applications.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"23 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135814352","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 abundance and diversity of populations of the Pseudomonas syringae and Soft Rot Pectobacteriaceae species complexes throughout the Durance River catchment from its French Alps sources to its delta","authors":"C.E. Morris, C. Lacroix, C. Chandeysson, C. Guilbaud, C. Monteil, S. Piry, E. Rochelle Newall, S. Fiorini, F. Van Gijsegem, M.A. Barny, O. Berge","doi":"10.24072/pcjournal.317","DOIUrl":"https://doi.org/10.24072/pcjournal.317","url":null,"abstract":"Rivers, creeks, streams are integrators of biological, chemical and physical processes occurring in a catchment linking land cover from the headwaters to the outlet. The dynamics of human and animal pathogens in catchments have been widely studied in a large variety of contexts allowing the optimization of disease risk reduction. In parallel, there is an emerging awareness that crop pathogens might also be disseminated via surface waters especially when they are used for irrigation. However, there are no studies on the extent to which potential plant pathogens are present – nor about their dynamics - along the full course of a catchment. Here we have compared the seasonal dynamics of populations of the Pseudomonas syringae (Psy) and the Soft Rot Pectobacteriaceae (SRP) species complexes along a 270 km stretch of the Durance River from the upstream alpine reaches to the downstream agricultural production areas at the confluence with the Rhone River at Avignon. Among 168 samples collected at 21 sites in fall, winter, spring and summer of 2016 and 2017, Psy strains were detected at all sampling sites and in 156 of the samples at population densities up to 105 bacteria L-1. In contrast, SRP strains were detected in 98 of the samples, mostly from the southern part of the river, at population densities that did not exceed 3 ´ 104 bacteria L-1. Among the biological and chemical parameters that were characterized at each sampling site, temperature was the only factor that explained a significant amount of the variability in population size for both species complexes. Psy densities decreased with increasing temperature whereas SRP densities increased with increasing temperature. River-borne populations of SRP were composed mainly of Pectobacterium versatile and P. aquaticum that have little known epidemiological importance. Only a few strains of Pectobacterium and Dickeya species reputed for their epidemiological impact were observed. In contrast, Psy populations at all sites were dominated by a genetic lineage of phylogroup 2 known from other studies for its broad host range and its geographic and habitat ubiquity. Our observations suggest that surveillance of river water for SRP could be leveraged to signal diagnostic and management reactions to avoid disease outbreaks. In contrast, the constant presence of Psy throughout the catchment in absence of regular and widespread disease outbreaks due to this group of bacteria suggests that surveillance should focus on future changes in land use, river water conditions and agronomic practices that could destabilize the mechanisms currently holding Psy outbreaks in check.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"339 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136154061","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":"Implementing a rapid geographic range expansion - the role of behavior changes","authors":"Corina Logan, Kelsey McCune, Christa LeGrande-Rolls, Zara Marfori, Josephine Hubbard, Dieter Lukas","doi":"10.24072/pcjournal.320","DOIUrl":"https://doi.org/10.24072/pcjournal.320","url":null,"abstract":"It is generally thought that behavioral flexibility, the ability to change behavior when circumstances change, plays an important role in the ability of species to rapidly expand their geographic range. Great-tailed grackles (Quiscalus mexicanus) are a social, polygamous species that is rapidly expanding its geographic range by settling in new areas and habitats. They are behaviorally flexible and highly associated with human-modified environments, eating a variety of human foods in addition to foraging on insects and on the ground for other natural food items. They offer an opportunity to assess the role of behavior change over the course of their expansion. We compared behavior in wild-caught grackles from two populations across their range (an older population in the middle of the northern expansion front: Tempe, Arizona, and a more recent population on the northern edge of the expansion front: Woodland, California) to investigate whether certain behaviors (flexibility, innovativeness, exploration, and persistence) have higher averages and variances in the newer or older population. We found that grackles in the edge population had a higher flexibility variance (measured by reversal learning) and a higher persistence average (they participated in a larger proportion of trials), and that there were no population differences in average levels of flexibility, innovativeness (number of loci solved on a multiaccess box), or exploration (latency to approach a novel environment). Our results elucidated that individuals differentially expressing a particular behavior in an edge population could facilitate the rapid geographic range expansion of great-tailed grackles, and we found no support for the importance of several traits that were hypothesized to be involved in such an expansion. Our findings highlight the value of population studies and of breaking down cognitive concepts into direct measures of individual abilities to better understand how species might adapt to novel circumstances.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"14 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136310938","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 demographic history of the wild crop relative Brachypodium distachyon is shaped by distinct past and present ecological niches","authors":"Nikolaos Minadakis, Hefin Williams, Robert Horvath, Danka Caković, Christoph Stritt, Michael Thieme, Yann Bourgeois, Anne C. Roulin","doi":"10.24072/pcjournal.319","DOIUrl":"https://doi.org/10.24072/pcjournal.319","url":null,"abstract":"Closely related to economically important crops, the grass Brachypodium distachyon has been originally established as a pivotal species for grass genomics but more recently flourished as a model for developmental biology. Grasses encompass more than 10,000 species and cover more than 40% of the world land area from tropical to temperate regions. Given that grasses also supply about a fifth of the world's dietary protein as cereal grains, unlocking the sources of phenotypic variation in B. distachyon is hence of prime interest in fundamental and applied research in agronomy, ecology and evolution. We present here the B. distachyon diversity panel, which encompasses 332 fully sequenced accessions covering the whole species distribution from Spain to Iraq. By combining population genetics, niche modeling and landscape genomics, we suggest that B. distachyon recolonized Europe and the Middle East following the last glacial maximum. Consequently, the species faced new environmental conditions which led to clear associations between bioclimatic variables and genetic factors as well as footprints of positive selection in the genome. Altogether, this genomic resource offers a powerful alternative to Arabidopsis thaliana to investigate the genetic bases of adaptation and phenotypic plasticity in plants and more specifically in monocots.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"71 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136308966","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":"General encoding of canonical k-mers","authors":"Roland Wittler","doi":"10.24072/pcjournal.323","DOIUrl":"https://doi.org/10.24072/pcjournal.323","url":null,"abstract":"To index or compare sequences efficiently, often k-mers, i.e., substrings of fixed length k, are used. For efficient indexing or storage, k-mers are often encoded as integers, e.g., applying some bijective mapping between all possible σk k-mers and the interval [0, σk −1], where σ is the alphabet size. In many applications, e.g., when the reading direction of a DNA-sequence is ambiguous, canonical k-mers are considered, i.e., the lexicographically smaller of a given k-mer and its reverse (or reverse complement) is chosen as a representative. In naive encodings, canonical k-mers are not evenly distributed within the interval [0, σk −1]. We present a minimal encoding of canonical k-mers on alphabets of arbitrary size, i.e., a mapping to the interval [0, σk/2−1]. The approach is introduced for canonicalization under reversal and extended to canonicalization under reverse complementation. We further present a space and time efficient bit-based implementation for the DNA alphabet.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136308887","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":"Combining several indicators to assess the effectiveness of tailor-made health plans in pig farms","authors":"Pierre Levallois, Mily Leblanc-Maridor, Annalisa Scollo, Paolo Ferrari, Catherine Belloc, Christine Fourichon","doi":"10.24072/pcjournal.318","DOIUrl":"https://doi.org/10.24072/pcjournal.318","url":null,"abstract":"A tailor-made health plan is a set of recommendations for a farmer to achieve and maintain a high health and welfare status. Tailored to each farm, it is intended to be an effective way of triggering change. This study aimed to assess the effectiveness of tailor-made health plans in pig farms, designed in various situations after a systematic biosecurity and herd health audit. An intervention study was carried out in 20 farrow-to-finish pig farms. An initial standardized audit and discussion between the farm veterinarian and the farmer resulted in a specific plan. Compliance with recommendations was monitored during 8 months. Changes in health, performances and antimicrobial use were monitored. We defined two categories of plans: i) 14 plans targeting a given health disorder present in a farm; ii) 17 plans to improve prevention, not targeting a specific health disorder (a farm could have both types of plans). A small number of priority recommendations were made per farm. In 18 farms, farmers implemented 1 to 4 recommendations (none in 2 farms). Of the 17 non-disorder-specific plans, 11 were considered effective ( > 50% recommendations implemented), 3 intermediate (at least one but less than half of the recommendations implemented) and 3 ineffective (no implementation). Of the 14 disorder-specific plans, 9 were followed with full or good compliance ( > 50% recommendations implemented), 2 with intermediate compliance (1 recommendation implemented out of 2) and 3 with no compliance (no recommendation implemented). When at least one recommendation was implemented, change in clinical, performance and antimicrobial use indicators was assessed if a biological association with the disorder was deemed plausible and if their initial value showed room for improvement. Improvement was evidenced 4/9, 1/6 and 1/6 times for these indicators, respectively. Independently, veterinarians concluded that 8/14 plans were effective. Overall, tailor-made health plans were effective in triggering changes in farm management. Three key points were identified for future assessments of the effectiveness of tailor-made health plans. Compliance should be the first indicator of assessment. Outcome indicators and their monitoring periods should be adapted to each farm and to the targeted health disorder. Indicators should be combined to have a holistic description of the evolution of a health disorder. Further research is needed to identify how to select indicators to combine and how to combine them, according to health disorders.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"17 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136312831","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":"Provision of essential resources as a persistence strategy in food webs","authors":"Michael Raatz","doi":"10.24072/pcjournal.315","DOIUrl":"https://doi.org/10.24072/pcjournal.315","url":null,"abstract":"Pairwise interactions in food webs, including those between predator and prey are often modulated by a third species. Such higher-order interactions are important structural components of natural food webs that can increase the stability of communities against perturbations and ensure continued ecosystem functioning. Particularly the flux of rare organic and inorganic compounds that are essential to species in the community can create higher-order interactions. Even though many such compounds exist, their effect on structuring communities is little understood. In this study, I perform invasion analyses on a general food web model that depicts apparent and exploitative competition. Introducing the provision of essential resources by a prey species to either its competitor or its predator as a higher-order interaction, I find that this mechanism can ensure the focal prey’s persistence. Larger dietary essentiality, i.e. a stronger dependence of the predator or the competitor on the essential resource can increase the invasion growth rate of the focal prey to positive values, thus promoting its persistence when it would go extinct for low essentiality. This research shows that essential resources and the higher-order interactions created by them should be considered in community ecology.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"31 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135827574","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}