JournalTOCs

Peer Community Journal
Number of Followers: 10

This is an Open Access Journal

Open Access journal
ISSN (Online) 2804-3871
Published by Peer Community in (PCI)

[1 journal]

Lenzi, Omar; Grossenbacher, Kurt et al. - Four decades of phenology in an
alpine amphibian: trends, stasis, and climatic drivers
- Abstract: Strong phenological shifts in response to changes in climatic conditions have been reported for many species, including amphibians, which are expected to breed earlier. Phenological shifts in breeding are observed in a wide number of amphibian populations, but less is known about populations living at high elevations, which are predicted to be more sensitive to climate change than lowland populations. The goal of this study is to assess the main factors determining the timing of breeding in an alpine population of the common toad (Bufo bufo) and to describe the observed shifts in its breeding phenology. We modelled the effect of environmental variables on the start and peak dates of the breeding season using 39 years of individual-based data. In addition, we investigated the effect of the lunar cycle, as well as the individual variation in breeding phenology. Finally, to assess the individual heterogeneity in the timing of breeding, we calculated the repeatability of the timing of arrival at the breeding site. Breeding advanced to earlier dates in the first years of the study but the trend continued only until the mid 1990s, and stabilised afterwards. Overall, toads are now breeding on average around 30 days earlier than at the start of the study period. High temperatures and low snow cover in winter and spring, as well as reduced spring precipitation were all associated with earlier breeding. Additionally, we found evidence of males arriving on average before females at the breeding site but no clear and strong effect of the lunar cycle. We only found weak evidence of among-individual variation in shifts in the breeding phenology, as well as a low repeatability of arrival timing. Our findings show that the observed changes in breeding phenology are strongly associated with the environmental conditions. These results contribute to filling a knowledge gap on the effects of climate change on alpine amphibian populations. Moreover, we show that changes in phenology, especially in the mountains, can be hard to predict as local microclimatic conditions do not necessarily reflect the observed global climatic trends.
  PubDate: Tue, 31 Jan 2023 08:10:57 +000
Tezenas, Emilie; Giraud, Tatiana et al. - The fate of recessive
deleterious or overdominant mutations near mating-type loci under partial
selfing
- Abstract: Large regions of suppressed recombination having extended over time occur in many organisms around genes involved in mating compatibility (sex-determining or mating-type genes). The sheltering of deleterious alleles has been proposed to be involved in such expansions. However, the dynamics of deleterious mutations partially linked to genes involved in mating compatibility are not well understood, especially in finite populations. In particular, under what conditions deleterious mutations are likely to be maintained for long enough near mating-compatibility genes remains to be evaluated, especially under selfing, which generally increases the purging rate of deleterious mutations. Using a branching process approximation, we studied the fate of a new deleterious or overdominant mutation in a diploid population, considering a locus carrying two permanently heterozygous mating-type alleles, and a partially linked locus at which the mutation appears. We obtained analytical and numerical results on the probability and purging time of the new mutation. We investigated the impact of recombination between the two loci and of the mating system (outcrossing, intra and inter-tetrad selfing) on the maintenance of the mutation. We found that the presence of a fungal-like mating-type locus (i.e. not preventing diploid selfing) always sheltered the mutation under selfing, i.e. it decreased the purging probability and increased the purging time of the mutations. The sheltering effect was higher in case of automixis (intra-tetrad selfing). This may contribute to explain why evolutionary strata of recombination suppression near the mating-type locus are found mostly in automictic (pseudo-homothallic) fungi. We also showed that rare events of deleterious mutation maintenance during strikingly long evolutionary times could occur, suggesting that deleterious mutations can indeed accumulate near the mating-type locus over evolutionary time scales. In conclusion, our results show that, although selfing purges deleterious mutations, these mutations can be maintained for very long times near a mating-type locus, which may contribute to promote the evolution of recombination suppression in sex-related chromosomes.
  PubDate: Fri, 27 Jan 2023 10:58:36 +000
Clairet, Colin; Lapalu, Nicolas et al. - Nucleosome patterns in four plant
pathogenic fungi with contrasted genome structures
- Abstract: Fungal pathogens represent a serious threat towards agriculture, health, and environment. Control of fungal diseases on crops necessitates a global understanding of fungal pathogenicity determinants and their expression during infection. Genomes of phytopathogenic fungi are often compartmentalized: the core genome contains housekeeping genes whereas the fast-evolving genome mainly contains transposable elements and species-specific genes. In this study, we analysed nucleosome landscapes of four phytopathogenic fungi with contrasted genome organizations to describe and compare nucleosome repartition patterns in relation with genome structure and gene expression level. We combined MNase-seq and RNA-seq analyses to concomitantly map nucleosome-rich and transcriptionally active regions during fungal growth in axenic culture; we developed the MNase-seq Tool Suite (MSTS) to analyse and visualise data obtained from MNase-seq experiments in combination with other genomic data and notably RNA-seq expression data. We observed different characteristics of nucleosome profiles between species, as well as between genomic regions within the same species. We further linked nucleosome repartition and gene expression. Our findings support that nucleosome positioning and occupancies are subjected to evolution, in relation with underlying genome sequence modifications. Understanding genomic organization and its role in expression regulation is the next gear to understand complex cellular mechanisms and their evolution.
  PubDate: Mon, 23 Jan 2023 12:47:50 +000
Ibanez, Sébastien; Foulquier, Arnaud et al. - The contrasted impacts of
grasshoppers on soil microbial activities in function of primary
production and herbivore diet
- Abstract: Herbivory can have contrasted impacts on soil microbes and nutrient cycling, which has stimulated the development of conceptual frameworks exploring the links between below- and aboveground processes. The “productivity model” predicts that herbivores stimulate microbial activities and accelerate nutrient mineralization in productive ecosystems, while they have an opposite effect in less productive ecosystems. In parallel, the “diet model” predicts that herbivores feeding on conservative plants accelerate nutrient cycling while those feeding on exploitative plants decelerate nutrient cycling, due to changes in litter inputs. Since these two frameworks can lead to conflicting predictions in some cases, experimental evidence combining herbivore diet and plant productivity is required. During two consecutive years, we conducted an experiment controlling the presence of three grasshopper species consuming either grasses, forbs or both in twelve natural and managed alpine grasslands with contrasted productivities. In order to assess the effects of herbivory on soil microbes, we measured their extracellular enzymatic activities, biomass and potential nitrogen mineralization (PNM). Soil and vegetation were also characterized to test how much they modulated the effects of herbivory on microbes. Contrary to the predictions of the diet model, the effects of herbivory on microbial characteristics did not depend on the herbivores diet, but were influenced by primary production, though in a way that differed from the productivity model. The most productive sites were constituted by exploitative plant species which depleted N resources in the soil, and by microbes producing relatively few extracellular enzymes, leading to a lower PNM. Herbivory increased microbial biomass and decreased the production of extracellular enzymes in those sites, possibly through the stimulation of root exudates produced by exploitative species. The least productive sites were characterized by conservative plants, high soil C content, and by microbes having a resource acquisition strategy (more extracellular enzymes, higher PNM). Herbivory decreased microbial biomass and increased the production of extracellular enzymes in those sites. This pattern can be explained by the loss of carbon associated with insect respiration, which increases the resource requirements of microbes and by a lower production of root exudates by conservative species. Therefore, the effects of two years of herbivory on soil microbes were at odds with the productivity model, which focuses instead on longer term effects corresponding to herbivory-induced changes in plant species composition. This highlights the multidimensional feature of the impacts of herbivory on ecosystem functioning, both in space and time.
  PubDate: Mon, 23 Jan 2023 12:43:20 +000
Michel, Elisa; Masson, Estelle et al. - Artisanal and farmer bread making
practices differently shape fungal species community composition in French
sourdoughs
- Abstract: Preserving microbial diversity in food systems is one of the many challenges to be met to achieve food security and quality. Although industrialization led to the selection and spread of specific fermenting microbial strains, there are still ongoing artisanal processes that may allow the conservation of a wider species diversity and genetic diversity. We examined whether the diversity of artisanal practices could lead to an increased level in fungal species diversity for bread making. We used an interdisciplinary participatory research approach including bakers, psycho-sociologists and microbiologists to analyze French bread making practices and describe fungal communities in naturally fermented sourdough of 27 bakers and 12 farmer bakers. Bread making practices were classified in two groups: the farmer-like practice group and the artisanal-like practice group. The well-known bakery yeast, Saccharomyces cerevisiae, was dominant (i.e. with a relative abundance over 50%) in only 24% of sourdoughs while other yeast species, belonging to the Kazachstania genus, were dominant in 54% of sourdoughs. Bread making practices were found to drive the distribution of fungal species across sourdoughs. The most striking bread making practice effect was the occurrence of Kazachstania humilis in sourdoughs made with artisanal-like practices and the occurrence of Kazachstania bulderi in sourdoughs made with farmer-like practices. Phenotypic divergences between sourdough and non-sourdough strains were found for K. humilis but not for K. bulderi. Overall, our results showed that preserving bread making practice diversity allows the preservation of a higher species and phenotypic diversity in microbial communities.
  PubDate: Fri, 20 Jan 2023 07:49:28 +000
Nair, Bharath; Palomo, Ismael Rodríguez et al. - Parchment Glutamine
Index (PQI): A novel method to estimate glutamine deamidation levels in
parchment collagen obtained from low-quality MALDI-TOF data
- Abstract: Parchment was used as a writing material in the Middle Ages and was made using animal skins by liming them with Ca(OH)2. During liming, collagen peptides containing Glutamine (Q) undergo deamidation resulting in a mass shift of 0.984 Da. Assessing the extent of deamidation can inform us about parchment production patterns and quality. In this study, we propose a simple three-step workflow, developed as an R package called MALDIpqi(), to estimate deamidation in parchment derived collagen using low-resolution MALDI-TOF spectra. After pre-processing raw spectra, we used weighted least-squares linear regression to estimate Q deamidation levels from the convoluted isotopic envelope for seven collagen-peptide markers. Finally, we employed a linear mixed effect model to predict the overall deamidation level of a parchment sample termed Parchment Glutamine Index (PQI). To test the robustness of the workflow, we applied MALDIpqi() to previously published ZooMS data generated from almost an entire library of the Cistercian monastery at Orval Abbey, Belgium. In addition to reliably predicting PQI, we observed interesting patterns pertaining to parchment production. MALDIpqi() holds excellent potential for biocodicological and other archaeological studies involving collagen, such as bone, but we also foresee its application in the food and biomedical industry.
  PubDate: Wed, 18 Jan 2023 17:51:48 +000
Vergne, Emilie; Chevreau, Elisabeth et al. - Phenotypic and transcriptomic
analyses reveal major differences between apple and pear scab nonhost
resistance
- Abstract: Nonhost resistance is the outcome of most plant/pathogen interactions, but it has rarely been described in Rosaceous fruit species. Apple (Malus x domestica Borkh.) have a nonhost resistance to Venturia pyrina, the scab species attacking European pear (Pyrus communis L.). Reciprocally, P. communis have a nonhost resistance to Venturia inaequalis, the scab species attacking apple. The major objective of our study was to compare the scab nonhost resistance in apple and in European pear, at the phenotypic and transcriptomic levels. Macro- and microscopic observations after reciprocal scab inoculations indicated that, after a similar germination step, nonhost apple/V. pyrina interaction remained nearly symptomless, whereas more hypersensitive reactions were observed during nonhost pear/V. inaequalis interaction. Comparative transcriptomic analyses of apple and pear nonhost interactions with V. pyrina and V. inaequalis, respectively, revealed differences. Very few differentially expressed genes were detected during apple/V. pyrina interaction, preventing the inferring of underlying molecular mechanisms. On the contrary, numerous genes were differentially expressed during pear/V. inaequalis interaction, allowing a deep deciphering. Pre-invasive defense, such as stomatal closure, could be inferred, as well as several post-invasive defense mechanisms (apoplastic reactive oxygen species accumulation, phytoalexin production and alterations of the epidermis composition). In addition, a comparative analysis between pear scab host and nonhost interactions indicated that, although specificities were observed, two major defense lines seems to be shared in these resistances: cell wall and cuticle potential modifications and phenylpropanoid pathway induction. This first deciphering of the molecular mechanisms underlying a nonhost scab resistance in pear offers new possibilities for the genetic engineering of sustainable scab resistance in this species. Concerning nonhost scab resistance in apple, further analyses must be considered with the aid of tools adapted to this resistance with very few cells engaged.
  PubDate: Tue, 17 Jan 2023 11:10:12 +000
Abu-Awad, Diala; Waller, Donald - Conditions for maintaining and eroding
pseudo-overdominance and its contribution to inbreeding depression
- Abstract: Classical models that ignore linkage predict that deleterious recessive mutations should purge or fix within inbred populations, yet inbred populations often retain moderate to high segregating load. True overdominance could generate balancing selection strong enough to sustain inbreeding depression even within inbred populations, but this is considered rare. However, arrays of deleterious recessives linked in repulsion could generate appreciable pseudo-overdominance that would also sustain segregating load. We used simulations to explore how long pseudo-overdominant (POD) zones persist once created (e.g., by hybridization between populations fixed for alternative mildly deleterious mutations). Balanced haplotype loads, tight linkage, and moderate to strong cumulative selective effects all serve to maintain POD zones. Tight linkage is key, suggesting that such regions are most likely to arise and persist in low recombination regions (like inversions). Selection and drift unbalance the load, eventually eliminating POD zones, but this process is quite slow under strong pseudo-overdominance. Background selection accelerates the loss of weak POD zones but reinforces strong ones in inbred populations by disfavoring homozygotes. Models and empirical studies of POD dynamics within populations help us understand how POD zones may allow the load to persist, greatly affecting load dynamics and mating systems evolution
  PubDate: Tue, 17 Jan 2023 09:13:10 +000
Depeux, Charlotte; Branger, Angèle et al. - Deleterious effects of
thermal and water stresses on life history and physiology: a case study on
woodlouse
- Abstract: We tested independently the influences of increasing temperature and decreasing moisture on life history and physiological traits in the arthropod Armadillidium vulgare. Both increasing temperature and decreasing moisture led reproductive success to decrease. While the density of immune cells decreased and the β-galactosidase activity increased with increasing temperature and decreasing moisture, which suggests a negative impact of these stressors on individual performance, increased temperature and decreased moisture affected differently the other biomarkers conjuring different underlying mechanisms depending on the stress applied. Our findings demonstrate overall a negative impact of high temperature and low moisture on woodlouse welfare. Changing temperature or moisture had slightly different effects, illustrating the need to test further the respective role of each of these key components of climate change on organisms to predict more reliably the future of our ecosystems.
  PubDate: Mon, 16 Jan 2023 12:53:52 +000
De Sanctis, Bianca; Schneemann, Hilde et al. - How does the mode of
evolutionary divergence affect reproductive isolation'
- Abstract: When divergent populations interbreed, the outcome will be affected by the genomic and phenotypic differences that they have accumulated. In this way, the mode of evolutionary divergence between populations may have predictable consequences for the fitness of their hybrids, and so for the progress of speciation. To investigate these connections, we present a new analysis of hybridization under Fisher's geometric model, making few assumptions about the allelic effects that differentiate the hybridizing populations. Results show that the strength and form of postzygotic reproductive isolation (RI) depend on just two properties of the evolutionary changes, which we call the "total amount" and "net effect" of change, and whose difference quantifies the similarity of the changes at different loci, or their tendency to act in the same phenotypic direction. It follows from our results that identical patterns of RI can arise in different ways, since different evolutionary histories can lead to the same total amount and net effect of change. Nevertheless, we show how these estimable quantities do contain some information about the history of divergence, and that — thanks to Haldane's Sieve — the dominance and additive effects contain complementary information.
  PubDate: Mon, 16 Jan 2023 08:22:45 +000
Hullot, Manon; Merceron, Gildas et al. - Spatio-temporal diversity of
dietary preferences and stress sensibilities of early and middle Miocene
Rhinocerotidae from Eurasia: impact of climate changes
- Abstract: Major climatic and ecological changes are documented in terrestrial ecosystems during the Miocene epoch. The Rhinocerotidae are a very interesting clade to investigate the impact of these changes on ecology, as they are abundant and diverse in the fossil record throughout the Miocene. Here, we explored the spatio-temporal evolution of rhinocerotids’ paleoecology during the early and middle Miocene of Europe and Pakistan. We studied the dental texture microwear (proxy for diet) and enamel hypoplasia (stress indicator) of 19 species belonging to four sub-tribes and an unnamed clade of Rhinocerotidae, and coming from nine Eurasian localities ranging from Mammal Neogene zone (MN) 2 to MN7/8. Our results suggest clear differences in the feeding ecology and thus niche partitioning at Kumbi 4 (MN2, Pakistan), Sansan (MN6, France), and Villefranche d’Astarac (MN7/8, France), while overlap of the interpreted diets and subtle variations are discussed for Béon 1 (MN4, France) and Gračanica (MN5/6, Bosnia-Herzegovina). All rhinocerotids studied were interpreted as browsers or mixed-feeders, and none had a grazer nor frugivore diet. The prevalence of hypoplasia was moderate (∼10%) to high (> 20%) at all localities but Kumbi 4 (∼6%), and documented quite well the local conditions. For instance, the high prevalence at the close to Miocene Climatic Optimum locality of Béon 1 (∼26%) has been correlated with periodical droughts, while the moderate ones (∼10%) at Sansan and Devínska Nová Ves Spalte (Slovakia) both dated from the MN6 (i.e., by the middle Miocene Climatic Transition, ca. 13.9 Mya) were linked to the persistence of sub-tropical local conditions. Besides locality, species and tooth locus were also important factors of variation for the prevalence of hypoplasia. The very large hippo-like Brachypotherium brachypus was one of the most affected species at all concerned localities (but Sansan), whereas early-diverging elasmotheriines were very little affected, suggesting an influence of phylogeny and/or diet in stress susceptibility.
  PubDate: Wed, 11 Jan 2023 09:38:21 +000
Mahood, Adam L.; Joseph, Maxwell B. et al. - Ten simple rules for working
with high resolution remote sensing data
- Abstract: Researchers in Earth and environmental science can extract incredible value from high- resolution (sub-meter, sub-hourly or hyper-spectral) remote sensing data, but these data can be difficult to use. Correct, appropriate and competent use of such data requires skills from remote sensing and the data sciences that are rarely taught together. In practice, many researchers teach themselves how to use high-resolution remote sensing data with ad hoc trial and error processes, often resulting in wasted effort and resources. In order to implement a consistent strategy, we outline ten rules with examples from Earth and environmental science to help academic researchers and professionals in industry work more effectively and competently with high-resolution data.
  PubDate: Wed, 11 Jan 2023 09:37:23 +000
Lamonica, Dominique; Charles, Sandrine et al. - Chemical effects on
ecological interactions within a model-experiment loop
- Abstract: We propose in this paper a method to assess the effects of a contaminant on a micro-ecosystem, integrating the population dynamics and the interactions between species. For that, we developed a dynamic model to describe the functioning of a microcosm exposed to a contaminant and to discriminate direct and indirect effects. Then, we get back from modelling to experimentation in order to identify which of the collected data have really been necessary and sufficient to estimate model parameters in order to propose a more efficient experimental design for further investigations. We illustrated our approach using a 2-L laboratory microcosm involving three species (the duckweed Lemna minor, the microalgae Pseudokirchneriella subcapitata and the daphnids Daphnia magna) exposed to cadmium contamination. We modelled the dynamics of the three species and their interactions using a mechanistic model based on coupled ordinary differential equations. The main processes occurring in this three-species microcosm were thus formalized, including growth and settling of algae, growth of duckweeds, interspecific competition between algae and duckweeds, growth, survival and grazing of daphnids, as well as cadmium effects. We estimated model parameters by Bayesian inference, using simultaneously all the data issued from multiple laboratory experiments specifically conducted for this study. Cadmium concentrations ranged between 0 and 50 μg.L-1 . For all parameters of our model, we obtained biologically realistic values and reasonable uncertainties. The cascade of cadmium effects, both direct and indirect, was identified. Critical effect concentrations were provided for the life history traits of each species. An example of experimental design adapted to this kind a microcosm was also proposed. This approach appears promising when studying contaminant effects on ecosystem functioning.
  PubDate: Wed, 04 Jan 2023 14:51:38 +000
Trichogramma+evanescens&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2023&rft.volume=">van Oudenhove, Louise; Cazier, Aurélie et al. - Non-target effects of ten
essential oils on the egg parasitoid Trichogramma evanescens
- Abstract: Essential oils (EOs) are increasingly used as biopesticides due to their insecticidal potential. This study addresses their non-target effects on a biological control agent: the egg parasitoid Trichogramma evanescens. In particular, we tested whether EOs affected parasitoid fitness either directly, by decreasing pre-imaginal survival, or indirectly, by disrupting parasitoids' orientation abilities. The effect of Anise, Fennel, Sweet orange, Basil, Coriander, Oregano, Peppermint, Mugwort, Rosemary and Thyme EOs were studied on five strains of T. evanescens. Specific experimental setups were developed, and data obtained from image analysis were interpreted with phenomenological models fitted with Bayesian inference. Results highlight the fumigant toxicity of EOs on parasitoid development. Anise, Fennel, Basil, Coriander, Oregano, Peppermint and Thyme EOs are particularly toxic and drastically reduce the emergence rate of T. evanescens. Most EOs also affect parasitoid behavior: (i) Basil, Coriander, Oregano, Peppermint, Mugwort and Thyme EOs are highly repellent for naive female parasitoids; (ii) Anise and Fennel EOs can have repellent or attractive effects depending on strains; and (iii) Sweet orange, Oregano and Rosemary EOs have no detectable impact on orientation behavior. This study shows that EOs fumigation have non-target effects on egg parasitoids. This highlights the need to cautiously precise the deployment framework of biopesticides in an agroecological perspective.
  PubDate: Mon, 02 Jan 2023 10:32:50 +000
Cottereau, Romain; Ortiz, Katia et al. - Can growth in captivity alter the
calcaneal microanatomy of a wild ungulate'
- Abstract: Reduced mobility associated with captivity induces changes in biomechanical stress on the skeleton of domesticated animals. Due to bone plasticity, bone’s morphology and internal structure can respond to these new biomechanical stresses over individuals’ lifetime. In a context where documenting early process of animal domestication is challenging, this study will test the hypothesis that change in mobility patterns during a wild ungulate’s life will alter the internal structure of its limb bones and provide a proof of concept for the application of this knowledge in Zooarchaeology. Using the calcaneus as a phenotypic marker through qualitative and quantitative 3D microanatomical analyses, we relied on a comparative study across wild boars (Sus scrofa) populations from controlled experimental conditions with different mobility patterns (natural habitat, large pen, and stall) and archaeological specimens collected from middle and late Mesolithic as surrogate for the norm of reaction in European wild boar phenotype before the spread of agriculture and domestic pigs. Results provide evidence for compressive and tensile forces as the main elements affecting the variation in the cortical thickness along the calcaneus. Furthermore, changes in the internal structure of the calcaneus between mobility patterns are observed but their intensity is not directly associated with the degree of mobility restriction and only weakly impacted by the size or weight of the individuals. Despite having greater bone volume, the calcaneus of the Mesolithic wild boars displays a very similar microanatomy compared to the present-day hunted or captive wild boars. These results suggest that calcaneal microanatomy is more affected by population differences than by locomotor variation. For all these reasons, this preliminary study doesn’t support the use of microanatomy of the calcaneus as an indicator of change in locomotor behaviour induced by captivity in the archaeological record.
  PubDate: Mon, 02 Jan 2023 10:29:54 +000
Botrytis+cinerea+strains+infecting+grapevine+and+tomato+display+contrasted+repertoires+of+accessory+chromosomes,+transposons+and+small+RNAs&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2022&rft.volume=">Simon, Adeline; Mercier, Alex et al. - Botrytis cinerea strains infecting
grapevine and tomato display contrasted repertoires of accessory
chromosomes, transposons and small RNAs
- Abstract: The fungus Botrytis cinerea is a polyphagous pathogen that encompasses multiple host-specialized lineages. While several secreted proteins, secondary metabolites and retrotransposons-derived small RNAs have been characterized as virulence factors, their roles in host specialization remain unknown. The aim of this study was to identify the genomic correlates of host-specialization in populations of B. cinerea associated with grapevine and tomato. Using PacBio sequencing, we produced complete assemblies of the genomes of strains Sl3 and Vv3 that represent the French populations T and G1 of B. cinerea, specialized on tomato and grapevine, respectively. Both assemblies revealed 16 core chromosomes that were highly syntenic with chromosomes of the reference strain B05.10. The main sources of variation in gene content were the subtelomeric regions and the accessory chromosomes, especially the chromosome BCIN19 of Vv3 that was absent in Sl3 and B05.10. The repertoires and density of transposable elements were clearly different between the genomes of Sl3 and Vv3 with a larger number of subfamilies (26) and a greater genome coverage in Vv3 (7.7%) than in Sl3 (14 subfamilies, 4.5% coverage). An Helitron-like element was found in almost all subtelomeric regions of the Vv3 genome, in particular in the flanking regions of a highly duplicated gene encoding a Telomere-Linked Helicase, while both features were absent from the Sl3 and B05.10 genomes. Different retrotransposons in the Sl3 and the Vv3 strains resulted in the synthesis of distinct sets of small RNAs. Finally, extending the study to additional strains indicated that the accessory chromosome BCIN19 and the small RNAs producing retrotransposons Copia_4 and Gypsy_7 are common features of the G1 population that are scarcely if ever found in strains isolated from other populations. This research reveals that accessory chromosomes, repertoires of transposons and their derived small RNAs differ between populations of B. cinerea specialized on different hosts. The genomic data characterized in our study pave the way for further studies aiming at investigating the molecular mechanisms underpinning host specialization in a polyphagous pathogen.
  PubDate: Tue, 20 Dec 2022 07:50:41 +000
Myzus+persicae+are+shaped+by+identities+of+the+host+plant+and+the+virus&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2022&rft.volume=">Chesnais, Quentin; Golyaev, Victor et al. - Transcriptome responses of the
aphid vector Myzus persicae are shaped by identities of the host plant and
the virus
- Abstract: Background: Numerous studies have documented modifications in vector orientation behavior, settling and feeding behavior, and/or fecundity and survival due to virus infection in host plants. These alterations are often expected to enhance virus transmission, which has led to the hypothesis that such effects are vector manipulations by the virus. However, until now, the gene expression changes correlating with these effects and indicative of modified vector pathways and mechanisms are mostly unknown.Results: Transcriptome profiling of Myzus persicae aphids feeding on turnip yellows virus (TuYV) and cauliflower mosaic virus (CaMV) infected Arabidopsis thaliana and Camelina sativa revealed a substantial proportion of commonly deregulated genes, amongst them many with general functions in plant-virus-aphid interactions. We identified also aphid genes specifically deregulated by CaMV or TuYV infection, which might be related to the viral transmission mode. Furthermore, we observed strong host-specific differences in the gene expression patterns with plant virus infection causing more deregulations of aphid genes on A. thaliana than on C. sativa, likely related to the differences in susceptibility of the plant hosts to these viruses. Finally, stress-related aphid genes were downregulated in M. persicae on both infected plants, regardless of the virus.Conclusions: TuYV, relying on the circulative persistent mode of transmission, tended to affect developmental genes. This could increase the proportion of alate aphids, but also affect their locomotion, neuronal activity, and lifespan. CaMV, using the non-circulative non-persistent mode of transmission, had a strong impact on feeding-related genes and in particular those related to salivary proteins. In general, these transcriptome alterations targeted pathways that seem to be particularly adapted to the transmission mode of the corresponding virus and could be evidence of vector manipulation by the virus.
  PubDate: Fri, 16 Dec 2022 16:05:30 +000
Billotte, Jackie - A pipeline for assessing the quality of images and
metadata from crowd-sourced databases
- Abstract: Crowd-sourced biodiversity databases provide easy access to data and images for ecological education and research. One concern with using publicly sourced databases; however, is the quality of their images, taxonomic descriptions, and geographical metadata. The method presented in this paper attempts to address this concern using a suite of pipelines to evaluate taxonomic consistency, how well geo-tagging fits known distributions, and the image quality of crowd-sourced data acquired from iNaturalist, a crowd-sourced biodiversity database. Additionally, it provides researchers that use these datasets to report a quantifiable assessment of the taxonomic consistency. The pipeline allows users to analyze multiple images from iNaturalist and their associated metadata; to determine the level of taxonomic identification (family, genera, species) for each occurrence; whether the taxonomy label for an image matches accepted nesting of families, genera, and species; and whether geo-tags match the distribution of the taxon described using occurrence data from the Global Biodiversity Infrastructure Facility (GBIF) as a reference. Additionally, image quality is assessed using BRISQUE, an algorithm that allows for image quality evaluation without a reference photo. Entries from the order Araneae (spiders) are used as a case study. Overall, the results suggest that iNaturalist can provide large metadata and image sets for research. Given the inevitability of some low-quality observations, this pipeline provides a valuable resource for researchers and educators to evaluate the quality of iNaturalist and other crowd-sourced data.
  PubDate: Tue, 13 Dec 2022 15:16:34 +000
Jelavić, Stanislav; Thygesen, Lisbeth G. et al. - Soot and charcoal as
reservoirs of extracellular DNA
- Abstract: The vast potential of using sediment adsorbed DNA as a window to past and present biodiversity rely on the ability of solid surfaces to adsorb environmental DNA. However, a comprehensive insight into DNA adsorption at surfaces in general is lacking. Soot and charcoal are carbonaceous materials widespread in the environment where they readily can come in contact with extracellular DNA shed from organisms. Using batch adsorption, we measured DNA adsorption capacity at soot and charcoal as a function of solution composition, time and DNA length. We observed that the adsorption capacity for DNA is highest at low pH, that it increases with solution concentration and cation valency and that the activation energy for DNA adsorption at both soot and charcoal is ~50 kJmol-1, suggesting strong binding. We demonstrate how the interaction between DNA and soot and charcoal partly occurs via terminal base pairs, suggesting that, besides electrostatic forces, hydrophobic interactions play an important role in binding. The large adsorption capacities and strong binding of DNA to soot and charcoal are features important for eDNA research and provide a motivation for use of carbonaceous materials from, e.g., anthropogenic pollution or wildfire as sources of biodiversity information.
  PubDate: Mon, 12 Dec 2022 15:15:43 +000
Dobigny, Gauthier; Morand, Serge - Zoonotic emergence at the
animal-environment-human interface: the forgotten urban socio-ecosystems
- Abstract: Zoonotic emergence requires spillover from animals to humans, hence animal-human interactions. A lot has been emphasized on human intrusion into wild habitats (e.g., deforestation, hunting) and the development of agricultural and farming activities. However, the highly human-modified urban and peri-urban socio-ecosystems are also of great concern due to huge amounts of pet, domesticated and wild animals (e.g., birds, rodents and bats) that live in very close contact to very dense human populations. This adds to the existence of wet wildlife markets, urban parks and wastelands, zoos and even labs, where spillover from wildlife to humans may also occur. Furthermore, cities are transport hubs that form hotspots of import/export of living resources including animals, thus potentially promoting rapid and wide-scale spread of reservoir and vectors, hence pathogens, as well as pathogen admixture through viral recombination or bacterial plasmid exchanges. Finally, cities are deeply modified environments where living organisms, including reservoirs, vectors and pathogens, undergo strong selective pressures, thus opening the gate to evolutionary novelties, hence potential new infectious threats. As such, we believe urban socio-ecosystems should be paid more attention in terms of drivers of zoonotic emergence in humans needing adapted surveillance and mitigation. Accordingly, we propose and discuss several avenues of research and examples of actions that could be tested or generalized (e.g., focus on hotspots of emergence risks like informal settlements, wet markets or transport hubs; development of participative surveillance programs; shift towards inter-sectoral academic courses; massive investment into education and community information) in order to operationalize effective zoonotic surveillance. We advocate that this would allow ones to add emergence-preventive and early warning to usual outbreaks response strategies, thus significantly improving our collective ability to prevent zoonotic emergence and subsequent pandemics.
  PubDate: Fri, 09 Dec 2022 16:54:14 +000