Peer community journal最新文献

{"title":"SEAHORS: Spatial Exploration of ArcHaeological Objects in R Shiny","authors":"A. Royer, Emmanuel Discamps, Sébastien Plutniak, Marc Thomas","doi":"10.24072/pcjournal.289","DOIUrl":"https://doi.org/10.24072/pcjournal.289","url":null,"abstract":"This paper presents SEAHORS, an R shiny application available as an R package, dedicated to the intra-site spatial analysis of piece-plotted archaeological remains. This open-source script generates 2D and 3D scatter and density plots for archaeological objects located with cartesian coordinates. Many different GIS software already exist for this, but they mostly require specific skills and training to be used and are rarely designed for the particular needs of archaeological applications. The goal of SEAHORS is to make the two and three-dimensional intra-site spatial exploration of archaeological data as user-friendly as possible, in order to give the opportunity to researchers not familiar with GIS and R software to utilise such approaches. SEAHORS has an easily accessible interface and can import data from text and Excel files (.csv and .xls/xlsx respectively) without preformatting. The application includes functions to concatenate columns and to merge databases,","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42665692","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":"Multiple hosts, multiple impacts: the role of vertebrate host diversity in shaping mosquito life history and pathogen transmission","authors":"Amélie Vantaux, Nicolas Moiroux, Kounbobr Roch Dabiré, Anna Cohuet, Thierry Lefèvre","doi":"10.24072/pcjournal.288","DOIUrl":"https://doi.org/10.24072/pcjournal.288","url":null,"abstract":"The transmission of malaria parasites from mosquito to human is largely determined by the dietary specialization of Anopheles mosquitoes to feed on humans. Few studies have explored the impact of blood meal sources on the fitness of both the parasite and the mosquito. Our study investigated the effects of 3-4 consecutive blood meals from one of four vertebrate species (human, cattle, sheep, or chicken) on several fitness traits, including mosquito feeding rate, blood meal size, susceptibility to wild isolates of Plasmodium falciparum, survival, fecundity, F1 offspring development time, and size. Our findings revealed no significant effect on parasite development. Similarly, parasite exposure had no overall effects on mosquito fitness. However, blood meal type did have a strong impact on mosquito feeding rate, survival, lifetime fecundity, and offspring size. Specifically, mosquitoes that were fed successive chicken blood meals produced fewer eggs and fewer and smaller F1 adults compared to those fed human blood. Combining our results in a theoretical model, we show a decrease in the vectorial capacity of mosquitoes fed chicken or cow blood and an increase in the capacity of those fed sheep blood compared to those fed human blood. These findings emphasize the importance of considering the diversity of blood meal sources in understanding mosquito ecology and their role in the transmission intensity of malaria parasites.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135268529","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":"Effects of adaptive harvesting on fishing down processes and resilience changes in predator-prey and tritrophic systems","authors":"Eric Tromeur, Nicolas Loeuille","doi":"10.24072/pcjournal.268","DOIUrl":"https://doi.org/10.24072/pcjournal.268","url":null,"abstract":"Many world fisheries display a declining mean trophic level of catches. This “fishing down the food web” is often attributed to reduced densities of high-trophic-level species. We show here that the fishing down pattern can actually emerge from the adaptive harvesting of two- and three-species food webs, where changes in fishing patterns are driven by the relative profitabilities of the harvested species. Shifting fishing patterns from a focus on higher trophic levels to a focus on lower trophic levels can yield abrupt changes in the system, strongly impacting species densities. In predator-prey systems, such regime shifts occur when the predator species is highly valuable relative to the prey, and when the top-down control on the prey is strong. Moreover, we find that when the two species are jointly harvested, high adaptation speeds can reduce the resilience of fisheries. Our results therefore suggest that flexibility in harvesting strategies will not necessarily benefit fisheries but may actually harm their sustainability.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"5 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135703152","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 new and almost perfectly accurate approximation of the eigenvalue effective population size of a dioecious population: comparisons with other estimates and detailed proofs","authors":"T. de Meeûs, C. Noûs","doi":"10.24072/pcjournal.280","DOIUrl":"https://doi.org/10.24072/pcjournal.280","url":null,"abstract":"The effective population size is an important concept in population genetics. It corresponds to a measure of the speed at which genetic drift affects a given population. Moreover, this is most of the time the only kind of population size that empirical population genetics can give access to. Dioecious populations are expected to display excesses of heterozygosity as compared to monoecious panmictic populations, as measured by Wright’s FIS. It can be shown that these excesses are negatively correlated with the population size. This is why FIS can be used to estimate the eigenvalue effective population size of dioecious populations. In this paper, we propose a new approximation that provides a very accurate estimate of the eigenvalue effective population size of a dioecious population as a function of the real population size. We then explore the accuracy of different FIS-based methods using the leading eigenvalue of transition matrices or coalescence. It appears that the eigenvalue-based method provides more accurate results in very small populations, probably due to approximations made by the coalescence approach that are less valid in such situations. We also discuss the applicability of this method in the field.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45309480","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":"Soil variation response is mediated by growth trajectories rather than functional traits in a widespread pioneer Neotropical tree","authors":"Sébastien Levionnois, Niklas Tysklind, Eric Nicolini, Bruno Ferry, Valérie Troispoux, Gilles Le Moguedec, Hélène Morel, Clément Stahl, Sabrina Coste, Henri Caron, Patrick Heuret","doi":"10.24072/pcjournal.262","DOIUrl":"https://doi.org/10.24072/pcjournal.262","url":null,"abstract":"1. Trait-environment relationships have been described at the community level across tree species. However, whether interspecific trait-environment relationships are consistent at the intraspecific level is yet unknown. Moreover, we do not know how consistent is the response between organ vs. whole-tree level. 2. We examined phenotypic variability for 16 functional leaf (dimensions, nutrient, chlorophyll) and wood traits (density) across two soil types, Ferralitic Soil (FS) vs. White Sands (WS), on two sites for 70 adult trees of Cecropia obtusa Trécul (Urticaceae) in French Guiana. Cecropia is a widespread pioneer Neotropical genus that generally dominates early successional forest stages. To understand how soil types impact resource use through the processes of growth and branching, we examined the architectural development with a retrospective analysis of growth trajectories. We expect soil types to affect both, functional traits in relation to resource acquisition strategy as already described at the interspecific level, and growth strategies due to resource limitations with reduced growth on poor soils. 3. Functional traits were not involved in the soil response, as only two traits -leaf residual water content and K content-showed significant differences across soil types. Soil effects were stronger on growth trajectories, with WS trees having the slowest growth trajectories and less numerous branches across their lifespan. 4. The analysis of growth trajectories based on architectural analysis improved our ability to characterise the response of trees with soil types. The intraspecific variability is higher for growth trajectories than functional traits for C. obtusa, revealing the complementarity of the architectural approach with the functional approach to gain insights on the way trees manage their resources over their lifetime. Soil-related responses of Cecropia functional traits are not the same as those at the interspecific level, suggesting that the effects of the acting ecological processes are different between the two levels. Apart from soil differences, much variation was found across sites, which calls for further investigation of the factors shaping growth trajectories in tropical forests.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"46 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-05-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135997451","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":"Most diverse, most neglected: weevils (Coleoptera: Curculionoidea) are ubiquitous specialized brood-site pollinators of tropical flora","authors":"J. Haran, G. Kergoat, Bruno A. S. de Medeiros","doi":"10.24072/pcjournal.279","DOIUrl":"https://doi.org/10.24072/pcjournal.279","url":null,"abstract":"In tropical environments, and especially tropical rainforests, a major part of pollination services is provided by diverse insect lineages. Unbeknownst to most, beetles, and more specifically hyper-diverse weevils (Coleoptera: Curculionoidea), play a substantial role there as specialized mutualist brood pollinators. The latter contrasts with a common view where they are only regarded as plant antagonists. This study aims to provide a comprehensive understanding of what is known about plant-weevil brood-site mutualistic interactions, through a review of the known behavioral, morphological and physiological features found in these systems","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-05-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48583192","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":"Symbiotic nutrient cycling enables the long-term survival of Aiptasia in the absence of heterotrophic food sources","authors":"Nils Rädecker, Anders Meibom","doi":"10.24072/pcjournal.281","DOIUrl":"https://doi.org/10.24072/pcjournal.281","url":null,"abstract":"Phototrophic Cnidaria are mixotrophic organisms that can complement their heterotrophic diet with nutrients assimilated by their algal endosymbionts. Metabolic models suggest that the translocation of photosynthates and their derivatives from the algae may be sufficient to cover the metabolic energy demands of the host. However, the importance of heterotrophy to the nutritional budget of these holobionts remains unclear. Here, we report on the long-term survival of the photosymbiotic anemone Aiptasia in the absence of heterotrophic food sources. Following one year of heterotrophic starvation, these anemones remained fully viable but showed an 85 % reduction in biomass compared to their regularly fed counterparts. This shrinking was accompanied by a reduction in host protein content and algal density, indicative of severe nitrogen limitation. Nonetheless, isotopic labeling experiments combined with NanoSIMS imaging revealed that the contribution of algal-derived nutrients to the host metabolism remained unaffected due to an increase in algal photosynthesis and more efficient carbon translocation. Taken together, our results suggest that, on a one- year timescale, heterotrophic feeding is not essential to fulfilling the energy requirements of the holobiont. But, while symbiotic nutrient cycling effectively retains carbon in the holobiont over long time scales, our data suggest that heterotrophic feeding is a critical source of nitrogen required for holobiont growth under oligotrophic conditions.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135183996","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":"Host-symbiont-gene phylogenetic reconciliation","authors":"Hugo Menet, Alexia Nguyen Trung, Vincent Daubin, Eric Tannier","doi":"10.24072/pcjournal.273","DOIUrl":"https://doi.org/10.24072/pcjournal.273","url":null,"abstract":"Motivation Biological systems are made of entities organized at different scales (e.g. macro-organisms, symbionts, genes…) which evolve in interaction. These interactions range from independence or conflict to cooperation and coevolution, which results in them having a common history. The evolution of such systems is approached by phylogenetic reconciliation, which describes the common patterns of diversification between two different levels, e.g. genes and species, or hosts and symbionts for example. The limit to two levels hides the multi-level inter-dependencies that characterize complex systems. Results We present a probabilistic model of evolution of three nested levels of organization which can account for the codivergence of hosts, symbionts and their genes. This model allows gene transfer as well as host switch, gene duplication as well as symbiont diversification inside a host, gene or symbiont loss. It handles the possibility of ghost lineages as well as temporary free-living symbionts. Given three phylogenetic trees, we devise a Monte Carlo algorithm which samples evolutionary scenarios of symbionts and genes according to an approximation of their likelihood in the model. We evaluate the capacity of our method on simulated data, notably its capacity to infer horizontal gene transfers, and its ability to detect hostsymbiont co-evolution by comparing host/symbiont/gene and symbiont/gene models based on their estimated likelihoods. Then we show in a aphid enterobacter system that some reliable transfers detected by our method, are invisible to classic 2-level reconciliation. We finally evaluate different hypotheses on human population histories in the light of their coevolving Helicobacter pylori symbionts, reconciled together with their genes. Availability Implementation is available on GitHub https://github.com/hmenet/TALE. Data are available on Zenodo https://doi.org/10.5281/zenodo.7667342.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135380588","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":"Co-obligate symbioses have repeatedly evolved across aphids, but partner identity and nutritional contributions vary across lineages","authors":"Alejandro Manzano-Marín, Armelle Coeur d’acier, Anne-Laure Clamens, Corinne Cruaud, Valérie Barbe, Emmanuelle Jousselin","doi":"10.24072/pcjournal.278","DOIUrl":"https://doi.org/10.24072/pcjournal.278","url":null,"abstract":"Aphids are a large family of phloem-sap feeders. They typically rely on a single bacterial endosymbiont, Buchnera aphidicola, to supply them with essential nutrients lacking in their diet. This association with Buchnera was described in model aphid species from the Aphidinae subfamily and has been assumed to be representative of most aphids. However, in two lineages, Buchnera has lost some essential symbiotic functions and is now complemented by additional symbionts. Though these cases break our view of aphids harbouring a single obligate endosymbiont, we know little about the extent, nature, and evolution of these associations across aphid subfamilies. Here, using metagenomics on 25 aphid species from nine subfamilies, re-assembly and re-annotation of 20 aphid symbionts previously sequenced, and 16S rRNA amplicon sequencing on 223 aphid samples (147 species from 12 subfamilies), we show that dual symbioses have evolved anew at least six times. We also show that these secondary co-obligate symbionts have typically evolved from facultative symbiotic taxa. Genome-based metabolic inference confirms interdependencies between Buchnera and its partners for the production of essential nutrients but shows contributions vary across pairs of co-obligate associates. Fluorescent in situ hybridisation microscopy shows a common bacteriocyte localisation of two newly acquired symbionts. Lastly, patterns of Buchnera genome evolution reveal that small losses affecting a few key genes can be the onset of these dual systems, while large gene losses can occur without any co-obligate symbiont acquisition. Hence, the Buchnera-aphid association, often thought of as exclusive, seems more flexible, with a few metabolic losses having recurrently promoted the establishment of a new co-obligate symbiotic partner.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"51 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135813106","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":"Domestication of different varieties in the cheese-making fungus Geotrichum candidum","authors":"Bastien Bennetot, Jean-Philippe Vernadet, Vincent Perkins, Sophie Hautefeuille, Ricardo C. Rodríguez de la Vega, Samuel O’Donnell, Alodie Snirc, Cécile Grondin, Marie-Hélène Lessard, Anne-Claire Peron, Steve Labrie, Sophie Landaud, Tatiana Giraud, Jeanne Ropars","doi":"10.24072/pcjournal.266","DOIUrl":"https://doi.org/10.24072/pcjournal.266","url":null,"abstract":"Domestication is an excellent model for studying adaptation processes, involving recent adaptation and diversification, convergence following adaptation to similar conditions, as well as degeneration of unused functions. Geotrichum candidum is a fungus used for cheese making and is also found in other environments such as soil and plants. By analyzing whole-genome data from 98 strains, we found that all strains isolated from cheese formed a monophyletic clade. Within the cheese clade, we identified three genetically differentiated populations and we detected footprints of recombination and admixture. The genetic diversity in the cheese clade was similar as that in the wild clade, suggesting the lack of strong bottlenecks. Commercial starter strains were scattered across the cheese clade, thus not constituting a single clonal lineage. The cheese populations were phenotypically differentiated from other populations, with a slower growth on all media, even cheese, a prominent production of typical cheese volatiles and a lower proteolytic activity. One of the cheese clusters encompassed all soft goat cheese strains, suggesting an effect of cheese-making practices on differentiation. Another of the cheese populations seemed to represent a more advanced stage of domestication, with stronger phenotypic differentiation from the wild clade, harboring much lower genetic diversity, and phenotypes more typical of cheese fungi, with denser and fluffier colonies and a greater ability of excluding cheese spoiler fungi. Cheese populations lacked two beta lactamase-like genes present in the wild clade, involved in xenobiotic clearance, and displayed higher contents of transposable elements, likely due to relaxed selection. Our findings suggest the existence of genuine domestication in G. candidum, which led to diversification into different varieties with contrasted phenotypes. Some of the traits acquired by cheese strains indicate convergence with other, distantly related fungi used for cheese maturation.","PeriodicalId":74413,"journal":{"name":"Peer community journal","volume":"2 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135960926","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}