Subjects -> AGRICULTURE (Total: 981 journals)
    - AGRICULTURAL ECONOMICS (93 journals)
    - AGRICULTURE (680 journals)
    - CROP PRODUCTION AND SOIL (120 journals)
    - DAIRYING AND DAIRY PRODUCTS (30 journals)
    - POULTRY AND LIVESTOCK (58 journals)

AGRICULTURE (680 journals)            First | 1 2 3 4     

Showing 601 - 263 of 263 Journals sorted by number of followers
Sustainability and Climate Change     Full-text available via subscription   (Followers: 18)
Annals of Arid Zone     Open Access   (Followers: 15)
The Journal of Research, PJTSAU     Open Access   (Followers: 14)
Journal of Sugarcane Research     Open Access   (Followers: 13)
International Journal of Food Science and Agriculture     Open Access   (Followers: 13)
Potato Journal     Open Access   (Followers: 13)
Journal of Cereal Research     Open Access   (Followers: 12)
Peer Community Journal     Open Access   (Followers: 12)
Indian Journal of Extension Education     Open Access   (Followers: 12)
Journal of the Indian Society of Soil Science     Open Access   (Followers: 11)
Future Foods     Open Access   (Followers: 11)
Magazín Ruralidades y Territorialidades     Full-text available via subscription   (Followers: 10)
Indian Journal of Horticulture     Open Access   (Followers: 10)
Journal of the Indian Society of Coastal Agricultural Research     Open Access   (Followers: 10)
Animal - Open Space     Open Access   (Followers: 9)
Indian Journal of Animal Nutrition     Open Access   (Followers: 8)
Agrivet : Jurnal Ilmu-Ilmu Pertanian dan Peternakan / Journal of Agricultural Sciences and Veteriner)     Open Access   (Followers: 5)
Revista Investigaciones Agropecuarias     Open Access   (Followers: 5)
aBIOTECH : An International Journal on Plant Biotechnology and Agricultural Sciences     Hybrid Journal   (Followers: 4)
Sustainability Agri Food and Environmental Research     Open Access   (Followers: 4)
Animal Microbiome     Open Access   (Followers: 3)
Asia-Pacific Journal of Rural Development     Hybrid Journal   (Followers: 2)
CABI Agriculture and Bioscience     Open Access   (Followers: 2)
Animal Diseases     Open Access   (Followers: 2)
Journal of Animal Science and Products     Open Access   (Followers: 2)
Journal of Rural and Community Development     Open Access   (Followers: 1)
Measurement : Food     Open Access   (Followers: 1)
International Journal of Agricultural and Life Sciences     Open Access   (Followers: 1)
Acta Scientiarum Polonorum Technica Agraria     Open Access   (Followers: 1)
Agriscience     Open Access   (Followers: 1)
Journal of Applied Communications     Open Access   (Followers: 1)
Journal of Environmental and Agricultural Studies     Open Access   (Followers: 1)
VITIS : Journal of Grapevine Research     Open Access   (Followers: 1)
Analytical Science Advances     Open Access   (Followers: 1)
Plant Phenomics     Open Access   (Followers: 1)
CSA News     Hybrid Journal   (Followers: 1)
Molecular Horticulture     Open Access   (Followers: 1)
Energy Nexus     Open Access  
International Journal on Food, Agriculture and Natural Resources : IJ-FANRES     Open Access  
Horticultural Studies     Full-text available via subscription  
Reproduction and Breeding     Open Access  
Archiva Zootehnica     Open Access  
Journal of Agriculture and Food Research     Open Access  
Phytopathology Research     Open Access  
Rekayasa     Open Access  
Turkish Journal of Agricultural Engineering Research     Open Access  
Mustafa Kemal Üniversitesi Tarım Bilimleri Dergisi     Open Access  
Viticulture Data Journal     Open Access  
Proceedings of the Vertebrate Pest Conference     Open Access  
Ethiopian Journal of Sciences and Sustainable Development     Open Access  
Nexo Agropecuario     Open Access  
Dissertationen aus dem Julius Kühn-Institut     Open Access  
Berichte aus dem Julius Kühn-Institut     Open Access  
Journal für Kulturpflanzen     Open Access  
Food and Ecological Systems Modelling Journal     Open Access  
Journal of Animal Science, Biology and Bioeconomy     Open Access  
Agrosains : Jurnal Penelitian Agronomi     Open Access  
Agrotechnology Research Journal     Open Access  
PRIMA : Journal of Community Empowering and Services     Open Access  
Dinamika Pertanian     Open Access  

  First | 1 2 3 4     

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Peer Community Journal
Number of Followers: 12  

  This is an Open Access Journal Open Access journal
ISSN (Online) 2804-3871
Published by Peer Community in (PCI) Homepage  [1 journal]
  • Richter, Daniel J.; Berney, Cédric et al. - EukProt: A database of
           genome-scale predicted proteins across the diversity of eukaryotes

    • Abstract: EukProt is a database of published and publicly available predicted protein sets selected to represent the breadth of eukaryotic diversity, currently including 993 species from all major supergroups as well as orphan taxa. The goal of the database is to provide a single, convenient resource for gene-based research across the spectrum of eukaryotic life, such as phylogenomics and gene family evolution. Each species is placed within the UniEuk taxonomic framework in order to facilitate downstream analyses, and each data set is associated with a unique, persistent identifier to facilitate comparison and replication among analyses. The database is regularly updated, and all versions will be permanently stored and made available via FigShare. The current version has a number of updates, notably ‘The Comparative Set’ (TCS), a reduced taxonomic set with high estimated completeness while maintaining a substantial phylogenetic breadth, which comprises 196 predicted proteomes. A BLAST web server and graphical displays of data set completeness are available at http://evocellbio.com/eukprot/. We invite the community to provide suggestions for new data sets and new annotation features to be included in subsequent versions, with the goal of building a collaborative resource that will promote research to understand eukaryotic diversity and diversification.
      PubDate: Tue, 20 Sep 2022 08:21:51 +000
       
  • Adriaens, Ines; Ouweltjes, Wijbrand et al. - Detecting dairy cows' lying
           behaviour using noisy 3D ultra-wide band positioning data

    • Abstract: In precision livestock farming, technology-based solutions are used to monitor and manage livestock and support decisions based on on-farm available data. In this study, we developed a methodology to monitor the lying behaviour of dairy cows using noisy spatial positioning data, thereby combining time-series segmentation based on statistical changepoints and a machine learning classification algorithm using bagged decision trees. Position data (x, y, z -coordinates) collected with an ultra-wide band positioning system from 30 dairy cows housed in a freestall barn were used. After the data pre-processing and selection, statistical changepoints were detected per cow-day (no. included = 331) in normalized 'distance from the centre of the barn' and (z) time series. Accelerometer-based lying bout data were used as a practical ground truth. For the segmentation, changepoint detection was compared with getting-up or lying-down events as indicated by the accelerometers. For the classification of segments into lying or non-lying behaviour, two data splitting techniques resulting in 2 different training and test sets were implemented to train and evaluate performance: one based on the data collection day and one based on cow identity. In 85.5% of the lying-down or getting-up events a changepoint was detected in a window of 5 minutes. Of the events where no detection had taken place, 86.2% could be associated with either missing data (large gaps) or a very short lying or non-lying bout. Overall classification and lying behaviour prediction performance was above 91% in both independent test sets, with a very high consistency across cow-days. Per cow-day, the average error in the estimation of the lying durations were 7.1% and 7.8% for the cow-identity and time-based data splits respectively. This resulted in sufficient accuracy for automated quantification of lying behaviour in dairy cows, for example for health or welfare monitoring purposes.
      PubDate: Mon, 19 Sep 2022 15:26:45 +000
       
  • Fraïsse, Christelle; Le Moan, Alan et al. - Introgression between highly
           divergent sea squirt genomes: an adaptive breakthrough'

    • Abstract: Human-mediated introductions are reshuffling species distribution on a global scale. Consequently, an increasing number of allopatric taxa are now brought into contact, promoting introgressive hybridization between incompletely isolated species and new adaptive gene transfer. The broadcast spawning marine species, Ciona robusta, has been recently introduced in the native range of its sister taxa, Ciona intestinalis, in the English Channel and North-East Atlantic. These sea squirts are highly divergent, yet hybridization has been reported by crossing experiments and genetic studies in the wild. Here, we examined the consequences of secondary contact between C. intestinalis and C. robusta in the English Channel. We produced genomes phased by transmission to infer the history of divergence and gene flow, and analyzed introgressed genomic tracts. Demographic inference revealed a history of secondary contact with a low overall rate of introgression. Introgressed tracts were short, segregating at low frequency, and scattered throughout the genome, suggesting traces of past contacts during the last 30 ky. However, we also uncovered a hotspot of introgression on chromosome 5, characterized by several hundred kb-long C. robusta haplotypes segregating in C. intestinalis, that introgressed during contemporary times the last 75 years. Although locally more frequent than the baseline level of introgression, C. robusta alleles are not fixed, even in the core region of the introgression hotspot. Still, linkage-disequilibrium patterns and haplotype-based tests suggest this genomic region is under recent positive selection. We further detected in the hotspot an over-representation of candidate SNPs lying on a cytochrome P450 gene with a high copy number of tandem repeats in the introgressed alleles. Cytochromes P450 are a superfamily of enzymes involved in detoxifying exogenous compounds, constituting a promising avenue for functional studies. These findings support that introgression of an adaptive allele is possible between very divergent genomes and that anthropogenic hybridization can provide the raw material for adaptation of native lineages in the Anthropocene.
      PubDate: Tue, 13 Sep 2022 07:15:18 +000
       
  • Jaquiéry, Julie; Simon, Jean-Christophe et al. - Masculinization of the
           X-chromosome in aphid soma and gonads

    • Abstract: Males and females share essentially the same genome but differ in their optimal values for many phenotypic traits, which can result in intra-locus conflict between the sexes. Aphids display XX/X0 sex chromosomes and combine unusual X chromosome inheritance with cyclical parthenogenesis. Theoretical and empirical works support the hypothesis that the large excess of male-biased genes observed on the aphid X chromosome compared to autosomes evolved in response to sexual conflicts, by restricting the products of sexually antagonistic alleles to the sex they benefits. However, whether such masculinization of the X affects all tissues (as expected if it evolved in response to sexual conflicts) or is limited to specific tissues remains an open question. Here, we measured gene expression in three different somatic and gonadic tissues of males, sexual females and parthenogenetic females of the pea aphid. We observed a masculinization of the X in each of the studied tissues, with male-biased genes being 2.5 to 3.5 more frequent on the X than expected. We also tested the hypothesis that gene duplication can facilitate the attenuation of conflicts by allowing gene copies to neo- or sub-functionalize and reach sex-specific optima. As predicted, X-linked copies of duplicated genes having their other copies on autosomes were more frequently male-biased (40.5% of the genes) than duplicated autosomal genes (6.6%) or X-linked single-copy genes (32.5%). These results highlight a peculiar pattern of expression of X-linked genes in aphids at the tissue level and provide further support for sex-biased expression as a mechanism to attenuate intra-locus sexual conflicts.
      PubDate: Wed, 07 Sep 2022 11:40:17 +000
       
  • De Meeûs, Thierry; Noûs, Camille - A simple procedure to detect, test
           for the presence of stuttering, and cure stuttered data with spreadsheet
           programs

    • Abstract: Microsatellites are powerful markers for empirical population genetics, but may be affected by amplification problems like stuttering that produces heterozygote deficits between alleles with one repeat difference. In this paper, we present a simple procedure that aims at detecting stuttering for each locus overall subsamples and only requires the use of a spreadsheet interactive application on any operating system. We compare the performances of this procedure with the one of MicroChecker on simulations of dioecious pangamic populations, monoecious selfing populations and clonal populations with or without stuttering, and on real data of vectors and parasites. We also propose a cure for loci affected and compare the results with those expected without stuttering. In sexual populations (dioecious or selfers), the new procedure appeared more than three times more efficient than MicroChecker. Cure was able to restore Wright's FIS of stuttered data to the expected value, and particularly so in selfing simulations. In clones, lack of segregation artificially increased false stuttering detection, and only highly significant stuttering tests and loci strongly deviating from others, could be usefully cured, in which case FIS estimate could be much improved. In doubt, and whenever possible, removal of affected and not curable loci may help to shift population genetics parameter estimates towards more reliable values.
      PubDate: Tue, 30 Aug 2022 14:49:14 +000
       
  • Dupraz, Marlène; Leroy, Chloé et al. - Within and among population
           differences in cuticular hydrocarbons in the seabird tick Ixodes uriae

    • Abstract: The hydrophobic layer of the arthropod cuticle acts to maintain water balance, but can also serve to transmit chemical signals via cuticular hydrocarbons (CHC), essential mediators of arthropod behavior. CHC signatures typically vary qualitatively among species, but also quantitatively among populations within a species, and have been used as taxonomic tools to differentiate species or populations in a variety of taxa. Most work in this area to date has focused on insects, with little known for other arthropod groups such as ticks. The worldwide distribution and extensive host-range of the seabird tick Ixodes uriae make it a good model to study the factors influencing CHC composition. Genetically differentiated host-races of I. uriae have evolved across the distribution of this species but the factors promoting sympatric population divergence are still unknown. To test for a potential role of host-associated CHC in population isolation, we collected I. uriae specimens from two of its seabird hosts, the Atlantic puffin (Fratercula arctica) and the common guillemot (Uria aalge) in different colonies in Iceland. Using gas-chromatography and mass-spectrometry, we detected a complex cuticular mixture of 22 hydrocarbons, including n-alkanes, methyl-alkanes and alkenes ranging from 17 to 33 carbons in length. We found that each population had a distinct CHC profile. The host group explained the greatest amount of population divergence, with long-chain hydrocarbons being more abundant in puffin tick populations compared to guillemot tick populations. Future work will now be required to test whether the different CHC signals reinforce assortative mating, thereby playing a role in generating I. uriae population divergence patterns, and to evaluate diverse hypotheses on the origin of distinct population signatures.
      PubDate: Tue, 30 Aug 2022 14:47:38 +000
       
  • Sauve, Drew; Hudecki, Jane et al. - Improving species conservation plans
           under IUCN’s One Plan Approach using quantitative genetic methods

    • Abstract: Human activities are resulting in altered environmental conditions that are impacting the demography and evolution of species globally. If we wish to prevent anthropogenic extinction and extirpation, we need to improve our ability to restore wild populations. Ex situ populations can be an important tool for species conservation. However, it is difficult to prevent deviations from an optimal breeding design and altered environments in captivity seem likely to lead to evolutionary or plasticity-induced phenotypic change that could make reintroduction more difficult. Quantitative genetic analysis can help disentangle the causes of phenotypic change in ex situ populations. Consequently, quantitative genetics can improve the management of these populations and the success of in situ population management actions that they support. In this review we outline methods that could be used to improve the management of in situ and ex situ populations in a One Plan Approach. We discuss how quantitative genetic models can help measure genetic variation, phenotypic plasticity, and social effects on phenotypes. Finally, we discuss how phenotypic change can be predicted using measurements of additive genetic variance and selection. While previous work has highlighted the value of ex situ populations for the field of quantitative genetics, we argue that quantitative genetics can, in turn, offer opportunities to improve management and consequently conservation of populations of species at risk. We show that quantitative genetic analyses are a tool that could be incorporated into and improve ex situ management practices.
      PubDate: Tue, 30 Aug 2022 12:46:07 +000
       
  • Coulson, Tim; Felmy, Anja et al. - Density dependent environments can
           select for extremes of body size

    • Abstract: Body size variation is an enigma. We do not understand why species achieve the sizes they do, and this means we also do not understand the circumstances under which gigantism or dwarfism is selected. We develop size-structured integral projection models to explore evolution of body size and life history speed. We make few assumptions and keep models simple: all functions remain constant across models except for the one that describes development of body size with age. We set sexual maturity to occur when size attains 80% of the asymptotic size, which is typical of a large mammal, and allow negative density dependence to only affect either reproduction or juvenile survival. Fitness -- the quantity that is maximized by adaptive evolution -- is carrying capacity in our models, and we are consequently interested in how it changes with size at sexual maturity, and how this association varies with development rate. The simple models generate complex dynamics while providing insight into the circumstances when extremes of body size evolve. The direction of selection leading to either gigantism or dwarfism crucially depends on the proportion of the population that is sexually mature, which in turn depends on how the development function determines the survivorship schedule. The developmental trajectories consequently interact with size-specific survival or reproductive rates to determine the best life history and the optimal body size emerges from that interaction. These dynamics result in trade-offs between different components of the life history, with the form of the trade-off that emerges depending upon where in the life history density dependence operates most strongly. Empirical application of the approach we develop has potential to help explain the enigma of body size variation across the tree of life.
      PubDate: Tue, 30 Aug 2022 12:44:50 +000
       
  • Shivani; Huchard, Elise et al. - The effect of dominance rank on female
           reproductive success in social mammals

    • Abstract: Life in social groups, while potentially providing social benefits, inevitably leads to conflict among group members. In many social mammals, such conflicts lead to the formation of dominance hierarchies, where high-ranking individuals consistently outcompete other group members. Given that competition is a fundamental tenet of the theory of natural selection, it is generally assumed that high-ranking individuals have higher reproductive success than lower-ranking individuals. Previous reviews have indicated large variation across populations on the potential effect of dominance rank on reproductive success in female mammals. Here, we perform a meta-analysis based on 444 effect sizes from 187 studies on 86 mammal species to investigate how life-history, ecology and sociality modulate the relationship between female dominance rank and fitness. As predicted, we found that (1) dominance rank is generally positively associated with reproductive success, independent of the approach different studies have taken to answer this question; and that (2) the relationship between rank and reproductive success is conditional on life-history mechanisms, with higher effects of dominance rank on reproductive output than on survival, particularly in species with high reproductive investment. Contrary to our predictions, (3) the fitness benefits to high-ranking females appear consistent across ecological conditions rather than increasing when resources decrease. Instead, we found that the social environment consistently mitigates rank differences on reproductive success by modulating female competition, with, as predicted, (4) dominant females showing higher reproductive success than subordinates in two different types of societies: first, effect sizes are highest when females live in cooperatively breeding groups composed of a single dominant female and one or more subordinate females; second, they are also elevated when females form differentiated relationships which occurs when groups are composed of unrelated females. Our findings indicate that obtaining a high ranking position in a social group consistently provides female mammals with fitness benefits, even though future studies might show lower effects given various biases in the literature we were able to access, including, but not restricted to, a publication bias. They further draw a complex landscape of the level of social inequality across mammalian societies, reflected by variation in the benefits of social dominance, which appears to be shaped by reproductive and social competition more than by ecological competition.
      PubDate: Tue, 30 Aug 2022 08:01:32 +000
       
  • Martínez-Batlle, José-Ramón - Fire and forest loss in the Dominican
           Republic during the 21st Century

    • Abstract: Forest loss is an environmental issue that threatens ecosystems in the Dominican Republic (the DR). Although shifting agriculture by slash-and-burn methods is thought to be the main driver of forest loss in the DR, empirical evidence of this relationship is still lacking. Since remotely sensed data on fire occurrence is a suitable proxy for estimating the spread of shifting agriculture, here I explore the association between forest loss and fire during the first 18 years of the 21st Century using zonal statistics and spatial autoregressive models on different spatio-temporal layouts. First, I found that both forest loss and fire were spatially autocorrelated and statistically associated with each other at a country scale over the study period, particularly in the western and central part of the DR. However, no statistical association between forest loss and fire was found in the eastern portion, a region that hosts a large international tourism hub. Second, deforestation and fire showed a joint cyclical variation pattern of approximately four years up to 2013, and from 2014 onwards deforestation alone followed a worrying upward trend, while at the same time fire activity declined significantly. Third, I found no significant differences in forest loss patterns between the deforested area of small (<1 ha) and large (>1 ha) clearings of forest. I propose these findings hold potential to inform land management policies that help reduce forest loss, particularly in protected areas, mountain areas, and the vicinity of tourism hubs.
      PubDate: Tue, 30 Aug 2022 08:00:12 +000
       
  • Orjuela, Julie; Comte, Aurore et al. - CulebrONT: a streamlined long reads
           multi-assembler pipeline for prokaryotic and eukaryotic genomes

    • Abstract: Using long reads provides higher contiguity and better genome assemblies. However, producing such high quality sequences from raw reads requires to chain a growing set of tools, and determining the best workflow is a complex task.
      To tackle this challenge, we developed CulebrONT, an open-source, scalable, modular and traceable Snakemake pipeline for assembling long reads data. CulebrONT enables to perform tests on multiple samples and multiple long reads assemblers in parallel, and can optionally perform, downstream circularization and polishing. It further provides a range of assembly quality metrics summarized in a final user-friendly report. CulebrONT alleviates the difficulties of assembly pipelines development, and allow users to identify the best assembly options.
      PubDate: Mon, 22 Aug 2022 15:34:48 +000
       
  • Mahringer, David; Zmarz, Pawel et al. - Functional correlates of immediate
           early gene expression in mouse visual cortex

    • Abstract: During visual development, response properties of layer 2/3 neurons in visual cortex are shaped by experience. Both visual and visuomotor experience are necessary to coordinate the integration of bottom-up visual input and top-down motor-related input. Whether visual and visuomotor experience engage different plasticity mechanisms, possibly associated with the two separate input pathways, is still unclear. To begin addressing this, we measured the expression level of three different immediate early genes (IEG) (c-fos, egr1 or Arc) and neuronal activity in layer 2/3 neurons of visual cortex before and after a mouse’s first visual exposure in life, and subsequent visuomotor learning. We found that expression levels of all three IEGs correlated positively with neuronal activity, but that first visual and first visuomotor exposure resulted in differential changes in IEG expression patterns. In addition, IEG expression levels differed depending on whether neurons exhibited primarily visually driven or motor-related activity. Neurons with strong motor-related activity preferentially expressed EGR1, while neurons that developed strong visually driven activity preferentially expressed Arc. Our findings are consistent with the interpretation that bottom-up visual input and top-down motor-related input are associated with different IEG expression patterns and hence possibly also with different plasticity pathways.
      PubDate: Fri, 29 Jul 2022 13:58:30 +000
       
  • Fuandila, Nurul Novelia; Gosselin-Grenet, Anne-Sophie et al. - Structural
           variation turnovers and defective genomes: key drivers for the in vitro
           evolution of the large double-stranded DNA koi herpesvirus (KHV)

    • Abstract: Structural variations (SVs) constitute a significant source of genetic variability in virus genomes. Yet knowledge about SV variability and contribution to the evolutionary process in large double-stranded (ds)DNA viruses is limited. Cyprinid herpesvirus 3 (CyHV-3), also commonly known as koi herpesvirus (KHV), has the largest dsDNA genome within herpesviruses. This virus has become one of the biggest threats to common carp and koi farming, resulting in high morbidity and mortalities of fishes, serious environmental damage, and severe economic losses. A previous study analyzing CyHV-3 virulence evolution during serial passages onto carp cell cultures suggested that CyHV-3 evolves, at least in vitro, through an assembly of haplotypes that alternatively become dominant or under-represented. The present study investigates the SV diversity and dynamics in CyHV-3 genome during 99 serial passages in cell culture using, for the first time, ultra-deep whole-genome and amplicon-based sequencing. The results indicate that KHV polymorphism mostly involves SVs. These SVs display a wide distribution along the genome and exhibit high turnover dynamics with a clear bias towards inversion and deletion events. Analysis of the pathogenesis-associated ORF150 region in ten intermediate cell passages highlighted mainly deletion, inversion and insertion variations that deeply altered the structure of ORF150. Our findings indicate that SV turnovers and defective genomes represent key drivers in the viral population dynamics and in vitro evolution of KHV. Thus, the present study can contribute to the basic research needed to design safe live-attenuated vaccines, classically obtained by viral attenuation after serial passages in cell culture. 
      PubDate: Fri, 29 Jul 2022 13:57:57 +000
       
  • Le Trionnaire, Gaël; Hudaverdian, Sylvie et al. - Dopamine pathway
           characterization during the reproductive mode switch in the pea aphid

    • Abstract: Aphids are major pests of most of the crops worldwide. Such a success is largely explained by the remarkable plasticity of their reproductive mode. They reproduce efficiently by viviparous parthenogenesis during spring and summer generating important damage on crops. At the end of the summer, viviparous parthenogenetic females perceive the photoperiod shortening and transduce this signal to their embryos that change their reproductive fate to produce sexual individuals: oviparous females and males. After mating, those females lay cold-resistant eggs. Earlier studies showed that some transcripts coding for key components of dopamine pathway were regulated between long days and short days conditions suggesting that dopamine might be involved in the transduction of seasonal cues prior to reproductive mode switch. In this study, we aimed at going deeper into the characterization of the expression dynamics of this pathway but also in the analysis of its functional role in this context in the pea aphid Acyrthosiphon pisum. We first analysed the level of expression of ten genes of this pathway in embryos and larval heads of aphids reared under long days (asexual producers) or short days (sexual producers) conditions. We then performed in situ hybridization experiments to localize in embryos the ddc and pale transcripts that are coding for two key enzymes in dopamine synthesis. Finally, Using CRISPR-Cas9 mutagenesis in eggs produced after the mating of sexual individuals, we targeted the ddc gene. We could observe strong melanization defaults in ddc mutated eggs, which confidently mimicked the Drosophila ddc phenotype. Nevertheless, such a lethal phenotype did not allow us to validate the involvement of dopamine as a signaling pathway necessary to trigger the reproductive mode switch in embryos.
      PubDate: Mon, 25 Jul 2022 08:23:12 +000
       
  • Seah, Brandon Kwee Boon; Singh, Aditi et al. - Karyorelict ciliates use an
           ambiguous genetic code with context-dependent stop/sense codons

    • Abstract: In ambiguous stop/sense genetic codes, the stop codon(s) not only terminate translation but can also encode amino acids. Such codes have evolved at least four times in eukaryotes, twice among ciliates (Condylostoma magnum and Parduczia sp.). These have appeared to be isolated cases whose next closest relatives use conventional stop codons. However, little genomic data have been published for the Karyorelictea, the ciliate class that contains Parduczia sp., and previous studies may have overlooked ambiguous codes because of their apparent rarity. We therefore analyzed single-cell transcriptomes from four of the six karyorelict families to determine their genetic codes. Reassignment of canonical stops to sense codons was inferred from codon frequencies in conserved protein domains, while the actual stop codon was predicted from full-length transcripts with intact 3’-untranslated regions (3’-UTRs). We found that all available karyorelicts use the Parduczia code, where canonical stops UAA and UAG are reassigned to glutamine, and UGA encodes either tryptophan or stop. Furthermore, a small minority of transcripts may use an ambiguous stop-UAA instead of stop-UGA. Given the ubiquity of karyorelicts in marine coastal sediments, ambiguous genetic codes are not mere marginal curiosities but a defining feature of a globally distributed and diverse group of eukaryotes.
      PubDate: Tue, 19 Jul 2022 14:10:29 +000
       
  • Ledru, Léo; Garnier, Jimmy et al. - Mutualists construct the ecological
           conditions that trigger the transition from parasitism

    • Abstract: The evolution of mutualism between hosts and initially parasitic symbionts represents a major transition in evolution. Although vertical transmission of symbionts during host reproduction and partner control both favour the stability of mutualism, these mechanisms require specifically evolved features that may be absent in the first place. Therefore, the first steps of the transition from parasitism to mutualism may suffer from the cost of mutualism at the organismic level. We hypothesize that spatial structure can lead to the formation of higher selection levels favouring mutualism. This resembles the evolution of altruism, with the additional requirement that the offspring of mutualistic hosts and symbionts must co-occur often enough. Using a spatially explicit agent-based model we demonstrate that, starting from a parasitic system with global dispersal, the joint evolution of mutualistic effort and local dispersal of hosts and symbionts leads to a stable coexistence between parasites and mutualists. The evolution of local dispersal mimics vertical transmission and triggers the formation of mutualistic clusters, counteracting the organismic selection level of parasites that maintain global dispersal. The transition occurs when mutualistic symbionts increase the density of hosts, which strengthens competition between hosts and disfavours hosts inhabiting areas dominated by parasitic symbionts: mutualists construct the ecological conditions that allow their own spread. Therefore, the transition to mutualism may come from an eco-evolutionary feedback loop involving spatially structured population dynamics.
      PubDate: Tue, 19 Jul 2022 09:10:20 +000
       
  • Cataglyphis+hispanica:+stepping+stones+towards+genomic+studies+of+hybridogenesis+and+thermal+adaptation+in+desert+ants&rft.title=Peer+Community+Journal&rft.issn=2804-3871&rft.date=2022&rft.volume=">Darras, Hugo; De Souza Araujo, Natalia et al. - Chromosome-level genome
           assembly and annotation of two lineages of the ant Cataglyphis hispanica:
           stepping stones towards genomic studies of hybridogenesis and thermal
           adaptation in desert ants

    • Abstract: Cataglyphis are thermophilic ants that forage during the day when temperatures are highest and sometimes close to their critical thermal limit. Several Cataglyphis species have evolved unusual reproductive systems such as facultative queen parthenogenesis or social hybridogenesis, which have not yet been investigated in detail at the molecular level. We generated high-quality genome assemblies for two hybridogenetic lineages of the Iberian ant Cataglyphis hispanica using long-read Nanopore sequencing and exploited chromosome conformation capture (3C) sequencing to assemble contigs into 26 and 27 chromosomes, respectively. Further karyotype analyses confirm this difference in chromosome numbers between lineages; however, they also suggest it may not be fixed among lineages. We obtained transcriptomic data to assist gene annotation and built custom repeat libraries for each of the two assemblies. Comparative analyses with 19 other published ant genomes were also conducted. These new genomic resources pave the way for exploring the genetic mechanisms underlying the remarkable thermal adaptation and the molecular mechanisms associated with transitions between different genetic systems characteristic of the ant genus Cataglyphis.
      PubDate: Mon, 18 Jul 2022 11:44:10 +000
       
  • Arnould, Olivier; Capron, Marie et al. - Mechanical characterisation of
           the developing cell wall layers of tension wood fibres by Atomic Force
           Microscopy

    • Abstract: Trees generate mechanical stresses at periphery of stem and branches to improve their strength and to control the orientation of their axes. This key factor in the biomechanical design of trees, named “maturation stress”, occurs in wood fibres during cellular maturation when their secondary cell wall thickens. In this study, the spatial and temporal stiffening kinetics of the different cell wall layers were recorded during fibre maturation on a sample of poplar tension wood using atomic force microscopy. The thickening of the different layers was also recorded. The stiffening of the CML, S1 and S2-layers was initially synchronous with the thickening of the S2-layer and continued a little after the S2-layer reached its final thickness as the G-layer began to develop. In contrast, the global stiffness of the G-layer, which initially increased with its thickening, was close to stable long before it reached its final maximum thickness. A limited radial gradient of stiffness was observed in the G-layer, but it decreased sharply on the lumen side, where the new sub-layers are deposited during cell wall thickening. Although very similar at the ultrastructural and biochemical levels, the stiffening kinetics of the poplar G-layer appears to be very different from that described in maturing bast fibres.
      PubDate: Wed, 13 Jul 2022 09:26:58 +000
       
  • Friggens, N.C.; Adriaens, I. et al. - Resilience: reference measures based
           on longer-term consequences are needed to unlock the potential of
           precision livestock farming technologies for quantifying this trait

    • Abstract: Climate change, with its increasing frequency of environmental disturbances puts pressures on the livestock sector. To deal with these pressures, more complex traits such as resilience must be considered in our management strategies and in our breeding programs. Resilient animals respond well to environmental challenges, and have a decreased probability of needing assistance to overcome them. This paper discusses the need for operational measures of resilience that can be deployed at large scale across different farm types and livestock species. Such measures are needed to provide more precise phenotypes of resilience for use in farm management, but also for use in animal breeding. Any measure of response and recovery reflects both the animals resilience and the perceived size of the environmental disturbance, which can vary over time, depending on multiple animal and farm-related contexts. Therefore, and because universal definitions of resilience are too broad to be operational, we argue that resilience should be seen as a latent construct that cannot be directly measured and selected for. This leads to the following two points: (1) any postulated operational measure of resilience to a disturbance should be constructed from a sufficient number of indicators that each individually capture different facets of the resilience, such that when combined they better reflect the full resilience response; and (2) any postulated operational measure of resilience will have to be validated against reference measures that are the accumulated consequences of good resilience (e.g. productive lifespan or ability to re-calve). In a dairy cow case study, a practical resilience definition for dairy cattle was proposed and tested based on a scoring system containing several categories. In general terms and within a given parity, a cow receives plus points for each calving, and for a shorter calving interval, fewer inseminations and a higher milk production compared to her herd peers. She will receive minus points in case the number of inseminations increases, for each curative treatment day, and if her milk production is lower compared to her herd peers. By using readily available farm data, we were able to assess a practical lifetime resilience score, based on which cows can then be ranked within the herd. Cows that reach a next parity were shown to have a higher rank than cows that are culled before the next parity. To examine the usefulness of such a score, this resilience ranking was linked to two precision livestock technology-derived measures, related to milk yield deviations and accelerometer-derived deviations. Higher resilience ranking cows had fewer drops in milk yield and a more stable activity pattern during the lactation. This case study, taking the operational approach to quantifying and defining resilience, shows the promise of a data-driven approach for identifying resilience measures when applied within a biologically logical framework.
      PubDate: Wed, 13 Jul 2022 09:25:47 +000
       
  • Capdevielle Dulac, Claire; Benoist, Romain et al. - Spontaneous
           parthenogenesis in the parasitoid wasp Cotesia typhae: low frequency
           anomaly or evolving process'

    • Abstract: Hymenopterans are haplodiploids and unlike most other Arthropods they do not possess sexual chromosomes. Sex determination typically happens via the ploidy of individuals: haploids become males and diploids become females. Arrhenotoky is believed to be the ancestral reproduction mode in Hymenopterans, with haploid males produced parthenogenetically, and diploid females produced sexually. However, a number of transitions towards thelytoky (diploid females produced parthenogenetically) have appeared in Hymenopterans, and in most cases populations or species are either totally arrhenotokous or totally thelytokous. Here we present the case of Cotesia typhae (Fernandez-Triana), a Braconidae that produces parthenogenetic females at a low frequency. The phenotyping of two laboratory strains and one natural population showed that this frequency is variable, and that this rare thelytokous phenomenon also happens in the wild. Moreover, mated females from one of the laboratory strains produce a few parthenogenetic daughters among a majority of sexual daughters. The analysis of daughters of heterozygous virgin females allowed us to show that a mechanism similar to automixis with central fusion is very likely at play in C. typhae. This mechanism allows some parts of the genome to remain heterozygous, especially at the chromosomes’ centromeres, which can be advantageous depending on the sex determination system involved. Lastly, in most species, the origin of thelytoky is either bacterial or genetic, and an antibiotic treatment as well as PCR experiments did not demonstrate a bacterial cause in C. typhae. The unusual case of low parthenogenetic frequency described in this species constitutes another example of the fascinating diversity of sex determination systems in Arthropods.
      PubDate: Wed, 22 Jun 2022 09:50:13 +000
       
 
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