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Four new species of Cichlidogyrus (Platyhelminthes, Monopisthocotyla, Dactylogyridae) from Lake Victoria haplochromine cichlid fishes, with the redescription of C. bifurcatus and C. longipenis
No full textInternational audienceAfrican cichlids are model systems for evolutionary studies and host-parasite interactions, because of their adaptive radiations and because they harbour many species of monogenean parasites with high host-specificity. Five locations were sampled in southern Lake Victoria: gill-infecting monogeneans were surveyed from 18 cichlid species belonging to this radiation superflock and two others representing two older and distantly related lineages. We found one species of Gyrodactylidae, Gyrodactylus sturmbaueri Vanhove, Snoeks, Volckaert & Huyse, 2011, and seven species of Dactylogyridae. Four are described herein: Cichlidogyrus pseudodossoui n. sp., Cichlidogyrus nyanza n. sp., Cichlidogyrus furu n. sp., and Cichlidogyrus vetusmolendarius n. sp. Another Cichlidogyrus species is reported but not formally described (low number of specimens, morphological similarity with C. furu n. sp.). Two other species are redescribed: C. bifurcatus Paperna, 1960 and C. longipenis Paperna & Thurston, 1969. Our results confirm that the monogenean fauna of Victorian littoral cichlids displays lower species richness and lower host-specificity than that of Lake Tanganyika littoral cichlids. In C. furu n. sp., hooks V are clearly longer than the others, highlighting the need to re-evaluate the current classification system that considers hook pairs III–VII as rather uniform. Some morphological features of C. bifurcatus, C. longipenis, and C. nyanza n. sp. suggest that these are closely related to congeners that infect other haplochromines. Morphological traits indicate that representatives of Cichlidogyrus colonised Lake Victoria haplochromines or their ancestors at least twice, which is in line with the Lake Victoria superflock being colonised by two cichlid tribes (Haplochromini and Oreochromini)
Identification of Resistance QTLs to Black Leaf Streak Disease (Due to Pseudocercospora fijiensis) in Diploid Bananas (Musa acuminata)
No full textThe following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/horticulturae10060608/s1, Figure S1: Location of the recombinations detected on each parent (KNO and IDN110) on the physical map of DH Pahang reference genome version 4 [37]; Figure S2: Manhattan plots of KNO (a.) and IDN110 (b.) for the 16 phenotypic variables; Table S1: For all hybrids, BLUP values of the phenotypic variables and genotypes for the 2084 non-redundant markers; Table S2: List of the genes or putative genes identified in the four main QTLs of IDN110.International audienceBlack Leaf Streak Disease (BLSD), caused by the fungus Pseudocercospora fijiensis, is a recent pandemic and the most economically and environmentally important leaf disease of banana. To assist breeding of varieties with durable resistance to the rapidly evolving P. fijiensis, we used a diploid genitor 'IDN 110' with partial resistance to BLSD to search for QTLs. We assessed diploid progeny of 73 hybrids between 'IDN 110' and the diploid cultivar 'Khai Nai On', which is susceptible to BLSD. Hybrids were phenotyped with artificial inoculation under controlled conditions. This method allowed us to focus on resistance in the early stages of the interaction already identified as strongly influencing BLSD epidemiology. Progeny were genotyped by sequencing. As both parents are heterozygous for large reciprocal translocations, the distribution of recombination was assessed and revealed regions with low recombination rates. Fourteen non-overlapping QTLs of resistance to BLSD were identified of which four main QTLs from the 'IDN110' parent, located on chromosomes 06, 07, 08, and 09, were shown to be of interest for marker-assisted selection. Genes that underline those four QTLs are discussed in the light of previous literature
Reassessing the alternative ecosystem states proposition in the African savanna‐forest domain
No full textInternational audienceEcologists are being challenged to predict how ecosystems will respond to climate changes. According to the Multi-Colored World (MCW) hypothesis, climate impacts may not manifest because consumers such as fire and herbivory can override the influence of climate on ecosystem state. One MCW interpretation is that climate determinism fails because alternative ecosystem states (AES) are possible at some locations in climate space. We evaluated theoretical and empirical evidence for the proposition that forest and savanna are AES in Africa. We found that maps which infer where AES zones are located were contradictory. Moreover, data from longitudinal and experimental studies provide inconclusive evidence for AES. That is, although the forest-savanna AES proposition is theoretically sound, the existing evidence is not yet convincing. We conclude by making the case that the AES proposition has such fundamental consequences for designing management actions to mitigate and adapt to climate change in the savanna-forest domain that it needs a more robust evidence base before it is used to prescribe management actions
Revisiting superiority and stability metrics of cultivar performances using genomic data: derivations of new estimators
No full textAll the code and data used in this study can be found in the repository: https://github.com/TheRocinante-lab/Publications/GEmetrics.A Correction to this paper has been published: https://doi.org/10.1186/s13007-024-01231-1. The original article has been corrected.International audienceThe selection of highly productive genotypes with stable performance across environments is a major challenge of plant breeding programs due to genotype-by-environment (GE) interactions. Over the years, different metrics have been proposed that aim at characterizing the superiority and/or stability of genotype performance across environments. However, these metrics are traditionally estimated using phenotypic values only and are not well suited to an unbalanced design in which genotypes are not observed in all environments. The objective of this research was to propose and evaluate new estimators of the following GE metrics: Ecovalence, Environmental Variance, Finlay–Wilkinson regression coefficient, and Lin–Binns superiority measure. Drawing from a multi-environment genomic prediction model, we derived the best linear unbiased prediction for each GE metric. These derivations included both a squared expectation and a variance term. To assess the effectiveness of our new estimators, we conducted simulations that varied in traits and environment parameters. In our results, new estimators consistently outperformed traditional phenotype-based estimators in terms of accuracy. By incorporating a variance term into our new estimators, in addition to the squared expectation term, we were able to improve the precision of our estimates, particularly for Ecovalence in situations where heritability was low and/or sparseness was high. All methods are implemented in a new R-package: GEmetrics. These genomic-based estimators enable estimating GE metrics in unbalanced designs and predicting GE metrics for new genotypes, which should help improve the selection efficiency of high-performance and stable genotypes across environments
Rubber-Based Agroforestry Systems Associated with Food Crops: A Solution for Sustainable Rubber and Food Production?
No full textThe following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/agriculture14071038/s1, Table S1: All 415 references extracted from the zotero library.International audienceAgroforestry is often seen as a sustainable land-use system for agricultural production providing ecosystem services. Intercropping with food crops leads to equal or higher productivity than monoculture and results in food production for industry and subsistence. Low rubber price and low labor productivity in smallholdings have led to a dramatic conversion of rubber plantations to more profitable crops. The literature analysis performed in this paper aimed at better understanding the ins and outs that could make rubber-based agroforestry more attractive for farmers. A comprehensive search of references was conducted in March 2023 using several international databases and search engines. A Zotero library was set up consisting of 415 scientific references. Each reference was carefully read and tagged in several categories: cropping system, country, main tree species, intercrop type, intercrop product, level of product use, discipline of the study, research topic, and intercrop species. Of the 232 journal articles, 141 studies were carried out on rubber agroforestry. Since 2011, the number of studies per year has increased. Studies on rubber-based agroforestry systems are performed in most rubber-producing countries, in particular in Indonesia, Thailand, China, and Brazil. These studies focus more or less equally on perennials (forest species and fruit trees), annual intercrops, and mixed plantations. Of the 47 annual crops associated with rubber in the literature, 20 studies dealt with rice, maize, banana, and cassava. Agronomy is the main discipline in the literature followed by socio-economy and then ecology. Only four papers are devoted to plant physiology and breeding. The Discussion Section has attempted to analyze the evolution of rubber agroforestry research, progress in the selection of food crop varieties adapted to agroforestry systems, and to draw some recommendations for rubber-based agroforestry systems associated with food crops
The interplay of facilitation and competition drives the emergence of multistability in dryland plant communities
No full textInternational audienceWithin communities, species are wrapped in a set of feedbacks with each other and with their environment. When such feedbacks are strong enough they can generate alternative stable states. So far, research on alternative stable states has mostly focused on systems with a small number of species and a limited diversity of interaction types. Here, we analyze a spatial model of plant community dynamics in stressed ecosystems such as drylands, where each species is characterized by a strategy, and the different species interact through facilitation and competition for space and resources, such as water. We identify three different types of multistability emerging from the interplay of competition and facilitation. Under low‐stress levels, plant communities organize in small groups of coexisting species, maintained by space, competition and facilitation (“cliques”). Under higher stress levels, positive feedback from facilitation lead to the dominance of a single facilitating species (“mutual exclusion states”). At the highest stress levels, the single facilitating species left in the system coexists with the desert state. By linking community ecology and alternative stable states theory using a spatial plant community model for stressed ecosystems, our study contributes to highlight the importance of positive feedback loops for the stability of ecological communities
DisCoM-KD: Cross-Modal Knowledge Distillation via Disentanglement Representation and Adversarial Learning
No full textInternational audienceCross-modal knowledge distillation (CMKD) refers to the scenario in which a learning framework must handle training and test data that exhibit a modality mismatch, more precisely, training and test data do not cover the same set of data modalities. Traditional approaches for CMKD are based on a teacher/student paradigm where a teacher is trained on multi-modal data with the aim to successively distill knowledge from a multi-modal teacher to a single-modal student. Despite the widespread adoption of such paradigm, recent research has highlighted its inherent limitations in the context of cross-modal knowledge transfer.Taking a step beyond the teacher/student paradigm, here we introduce a new framework for cross-modal knowledge distillation, named DisCoM-KD (Disentanglement-learning based Cross-Modal Knowledge Distillation), that explicitly models different types of per-modality information with the aim to transfer knowledge from multi-modal data to a single-modal classifier. To this end, DisCoM-KD effectively combines disentanglement representation learning with adversarial domain adaptation to simultaneously extract, foreach modality, domain-invariant, domain-informative and domain-irrelevant features according to a specific downstream task. Unlike the traditional teacher/student paradigm, our framework simultaneously learns all single-modal classifiers, eliminating the need to learn each student model separately as well as the teacher classifier. We evaluated DisCoM-KD on three standard multi-modal benchmarks and compared its behaviourwith recent SOTA knowledge distillation frameworks. The findings clearly demonstrate the effectiveness of DisCoM-KD over competitors considering mismatch scenarios involving both overlapping and non-overlapping modalities. These results offer insights to reconsider the traditional paradigm for distilling information from multi-modal data to single-modal neural networks
The competition between endogeneous phospholipids and proteins from pea protein ingredients rules their interfacial properties
No full textInternational audienceSustainable incentives foster the use of plant-based ingredients as emulsifiers, but their functionality, for instance in terms of solubility, is far from optimal. The underlying reasons encompass a lack of characterization of the physicochemical properties of such ingredients. Thus, we comprehensively analyzed the composition of pea and lupin protein isolates and concentrates and highlighted a large part of non-proteinaceous compounds, notably lipids, constituting 3.8 to 11.7 wt.% (d.m.) of the powders. Over half of these lipids were phospholipids, which may have a pivotal impact regarding interfacial properties. A high-pressure homogenization (HPH) treatment was applied to aqueous suspensions of the ingredients. It broke down undispersed powder grains, enhanced protein solubility and released endogenous submicron lipid structures [1]. The interplay between these endogenous lipids and proteins was investigated regarding emulsifying and interfacial properties. Oil-in-water emulsions (10 wt.% oil) were prepared using HPH to reach droplet diameters around 2.5 µm. Protein surface load, composition measurements, and microscopic investigations suggested the formation of different interfacial films and an inner competition between proteins and phospholipids for interfacial adsorption. Therefore, we conducted complementary dilatational interfacial rheology analyses, using our commercial pea isolate on the one hand, and purified pea proteins and lipids on the other hand. Oscillatory deformations of the oil-water interface were analyzed by Lissajous plots (Figure 1), which substantiated the interactions between proteins and lipids by deciphering their respective contributions. The formation of mixed interfacial films according to the protein-to-lipid ratio was demonstrated, with notably a prevalent influence of pea lipids on the rheological signature of the mixed films. Atomic force microscopy confirmed the formation of mixed interfacial films where lipid domains coexisted with protein aggregates. These insights are key to understand the interactions between plant proteins and endogenous lipids in emulsions, and thereby to facilitate food products’ rational formulation with such complex ingredient
Endogenous lipids: disregarded co-passengers shaping the emulsifying and interfacial properties of pea and lupin protein ingredients
No full textInternational audienceSustainable incentives foster the use of plant-based ingredients to stabilize emulsions, which display promising technological properties. Yet, their functionality, for instance in terms of solubility, is far from optimal. The underlying reasons remain unclear, partly because comprehensive characterization of the physicochemical properties of such ingredients is lacking.In-depth analysis of the composition of pea and lupin protein isolates and concentrates revealed a large part of non-proteinaceous compounds, notably lipids, constituting 3.8 to 11.7 wt.% (d.m.) of the powders. Over half of these lipids were phospholipids, which may have a pivotal impact regarding interfacial properties. A high-pressure homogenization (HPH) treatment was applied to aqueous suspensions of the ingredients. It broke down undispersed powder grains, enhanced protein solubility and released endogenous submicron lipid structures. The interplay between these endogenous lipids and proteins was investigated regarding emulsifying and interfacial properties. Oil-in-water emulsions (10 wt.% oil) were prepared using HPH to reach droplet diameters around 2.5 µm. Protein surface load, composition measurements, and detailed microscopic investigations suggested the formation of different interfacial films and an inner competition between proteins and phospholipids for interfacial adsorption. Dilatational interfacial rheology assays were performed to further explore this competition and the associated interfacial structures (oil-water interface). Kinetic adsorption studies revealed the dynamic architecture of the interfaces evolving through time. While proteins initially prevailed at the interface, phospholipids played a crucial role in reaching high surface pressures (around 20 mN/m). Oscillatory deformations of the interface were conducted and analyzed by Lissajous plots (Figure) providing insights into complex structural arrangements within the film. Atomic force microscopy images confirmed the formation of mixed interfacial films where lipid domains coexisted with protein aggregates.These new insights are key to understanding the interactions of phospholipids with proteins to stabilize food emulsions and facilitate food product’s rational formulation with such sustainable, yet complex ingredient
Guilty or scapegoat? Land consolidation and the hedgerow decline
No full textLand consolidation is a standard policy tool to reduce land fragmentation through the spatial redistribution of property rights; however, the risk of adverse effects on the landscape raises concerns about its environmental sustainability. This study investigates the landscape impacts of consolidation on the hedgerow network of Lower Normandy, France. Implementing a staggered difference-in-differences strategy on a longitudinal survey (1972-2010), we show that consolidation led to a significant reduction in hedgerow density of -14.3m/ha (standard error: 2.33), accounting for 13.7% of the overall decline observed in consolidated areas. Our results also suggest a diminishing impact over time of consolidation and time since consolidation, an increasing impact with higher initial hedgerow density, no spillover effect, and a negative impact on network connectivity. Our findings confirm that land consolidation has significantly contributed to the decline of hedgerows, but they challenge prevailing beliefs about its share of responsibility among other factors of landscape changes