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Multi-environment GWAS to decipher the response to natural infections in apricot and peach
No full textInternational audienceA great majority of modern apricot and peach varieties remain sensitive to the most problematic pests and diseases. To improve the capacity of varieties to deal with decreased levels of pesticide use, we need a better understanding of resistance and tolerance mechanisms in these crops. To serve this objective, we exposed large and diversified sets of apricot and peach accessions (so-called ‘core-collections’) to natural infections within a multi-environment trial. These core-collections consist in 150 apricot and 206 peach accessions, for which respectively 207,000 and 13,680 SNP data are available, and were observed from 2020 to 2023 at two to three environmentally contrasted locations in South-East of France. Respectively two and five pests and diseases were monitored in apricot and peach. After showing the impact of genetic and GxE effects on phenotypic variance via variance decompositions, we applied several GWAS models to identify associations (i) with conserved effects across environments, (ii), with interactive effects across environments, (iii) with environment-specific effects. We also explored non-additive mechanisms, yielding additional associations. This work led to the identification of 60 high confidence QTLs and 87 candidate genes involving both host-specific and basal resistance mechanisms. Interestingly, candidate regions were enriched for leucine-rich repeat containing receptors (LRR-CRs). We discuss the relevance of environment-dependant QTLs according to the different disease typologies found in this study. This work contributes to the establishment of marker assisted selection strategies to allow for a faster screening of the disease resilience capacity in peach and apricot breeding material
3000 yr-old patterns of mobile pastoralism revealed by multiple isotopes and radiocarbon dating of ancient horses from the Mongolian Altai
No full textInternational audiencePastoral nomadism is of great cultural and economic importance in several regions of the world today. However, documenting ancient patterns of mobility in societies where pastoralism was central is challenging and requires tailored approaches and methodologies.Here we use strontium, oxygen and carbon isotopic analyses of dental enamel, together with a local strontium isoscape, to reconstruct the mobility patterns of seven domestic horses deposited in a Late Bronze Age grave from western Mongolia. Radiocarbon indicates that the animals were deposited within a short period of time, 3000 years ago. The isotope time series obtained from tooth enamel shows that four of the seven horses exhibited a common pattern characterized by a high frequency of mobility, suggesting that in this area (1) cyclical nomadic mobility dates back at least to the Late Bronze Age and (2) the animals belonged to the same herding family, implying that only a small community was involved in the funerary rite of this structure. The data show that the other three horse individuals had a distinct mobility pattern and that one was not from the local area, pointing to flexibility in mobility patterns over time or circulation of animals between herding groups. These results illustrate the power of the isotopic approach to reconstruct animal biographies and effectively address the archaeology of pastoral nomadism and mobility
A single theory for the evolution of sex chromosomes and the two rules of speciation
No full textInternational audienceSex chromosomes are involved in three major empirical patterns: (i) y (or W) chromosomes are often nonrecombining and degenerate; (ii) heterogametic offspring (Xy or ZW) from interspecific crosses are more often sterile or inviable compared with homogametic offspring (Haldane’s rule); and (iii) the X (or Z) has a disproportionately large effect on reproductive isolation between species compared with autosomes (the large X effect). Each observation has received its own tailored explanation involving multiple genetic and evolutionary causes. In this work, we show that these empirical patterns all emerge from a single theory for sex chromosome evolution incorporating the coevolution of cis- and trans-acting regulators of gene expression and leading to systematic misexpression of dosage-compensated genes in heterogametic F1 hybrids, for both young and old sex chromosomes
Analysis of sustainable food supply chains based on social coexistence: An exploratory study of agricultural cooperatives in Asia and Europe
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Hybrid Maximum Principle for Regional Optimal Control Problems with Nonsmooth Interfaces
No full textInternational audienceWe consider a general Mayer optimal control problem whose controlled dynamics is defined regionally, and, additionally, we suppose that the interface between two regions is nonsmooth in the sense that it is described by a locally Lipschitz continuous function. Our objective is to derive a hybrid maximum principle in this setting. Doing so, we consider a sequence of mollifiers which allows us to approximate uniformly the interface between two regions by a sequence of smooth functions. This makes possible to apply the hybrid maximum principle on a sequence of approximated optimal control problems involving the smooth interface in place of the nonsmooth one. By passing to the limit as the approximation parameter tends to zero, we obtain the desired necessary optimality conditions in the form of a nonsmooth hybrid maximum principle. Our approach relies on the derivation of subgradients of a locally Lipschitz continuous function via mollifiers
Predicting the global economic costs of biological invasions by tetrapods
No full textInternational audienceHighlights: • Global economic costs of invasive tetrapods conservatively sum to >US$55 billion. • Costs are predicted by species traits — longevity, female maturation age, diet and invasion pathway. • Directionality of predictions can differ between ecto- and endothermic invaders. • Significant discrepancies exist between databases documenting ecological and economic impacts. • Profiling of life history traits can help to identify and mitigate future costs.Abstract: Globalisation has accelerated rates of biological invasions worldwide, leading to widespread environmental perturbations that often translate into rapidly expanding socio-economic costs. Although such monetary costs can be estimated from the observed effects of invasions, the pathways that lead invasive species to become economically impactful remain poorly understood. Here, we implement the first global-scale test of the hypothesis that adaptive traits that influence demographic resilience predict economic costs, using invasive terrestrial vertebrates as models given their well-catalogued impacts and characteristics. Our results reveal that total global costs of invasive tetrapods are conservatively in the tens of billions of dollars, with the vast majority due to damage costs from invasive mammals. These monetary impacts are predicted by longevity, female maturation age, diet and invasion pathway traits, although the directionality in the association between impacts and these drivers varied across classes. Alarmingly, costs remain unknown for >90 % of recorded established alien tetrapods worldwide, and across the majority of invaded countries. These huge socio-economic costs demonstrate the necessity of mitigating tetrapod invasions and filling knowledge gaps. Effective identification of traits predictive of costs among and within these groups can facilitate the prioritisation of resources to efficiently target the most damaging existing and emerging invasive tetrapod species
Resource extraction and land-use choice in a two-player two-period game
No full textLand use is an important driver for irrigation but rarely included in models of renewable resource economics. We set up a dynamic twoperiod model in which farmers decide on both land-use and water-use, while extracting from a common groundwater resource. We compute the Nash feedback equilibrium and the common property optimal solution, for symmetric and heterogeneous players. We first study the case where only water is a decision variable and then the case where water and land-use are decision variables, characterizing the intensive and extensive margins. We show that under Nash, in contrast to the optimal policy, more water is extracted than optimal, but more importantly, greater surfaces are irrigated and more water is extracted in the first period than in the second, showing the effect of strategic competition. We show in an example how regulating land-use may be a Pareto-improving policy and that not regulating it increases the difference between optimal and Nash gains, questionning the Gisser-Sanchez effect
Transcriptomic data reveal divergent paths of chitinase evolution underlying dietary convergence in anteaters and pangolins
No full textData and Resource Availability: Raw RNAseq Illumina reads have been submitted to the Short Read Archive (SRA) of the National Center for Biotechnology Information (NCBI) and are available under BioProject number PRJNA909065. Transcriptome assemblies, phylogenetic datasets, corresponding trees, and other supplementary materials are available from: https://doi.org/10.5281/zenodo.7355329.International audienceAnt-eating mammals represent a textbook example of convergent evolution. Among them, anteaters and pangolins exhibit the most extreme convergent phenotypes with complete tooth loss, elongated skulls, protruding tongues, and hypertrophied salivary glands producing large amounts of saliva. However, comparative genomic analyses have shown that anteaters and pangolins differ in their chitinase acidic gene (CHIA) repertoires, which potentially degrade the chitinous exoskeletons of ingested ants and termites. While the southern tamandua (Tamandua tetradactyla) harbors four functional CHIA paralogs (CHIA1-4), Asian pangolins (Manis spp.) have only one functional paralog (CHIA5). Here, we performed a comparative transcriptomic analysis of salivary glands in 33 placental species, including 16 novel transcriptomes from ant-eating species and close relatives. Our results suggest that salivary glands play an important role in adaptation to an insect-based diet, as expression of different CHIA paralogs is observed in insectivorous species. Furthermore, convergently-evolved pangolins and anteaters express different chitinases in their digestive tracts. In the Malayan pangolin, CHIA5 is overexpressed in all major digestive organs, whereas in the southern tamandua, all four functional paralogs are expressed, at very high levels for CHIA1 and CHIA2 in the pancreas, and for CHIA3 and CHIA4 in the salivary glands, stomach, liver, and pancreas. Overall, our results demonstrate that divergent molecular mechanisms within the chitinase acidic gene family underlie convergent adaptation to the ant-eating diet in pangolins and anteaters. This study highlights the role of historical contingency and molecular tinkering of the chitin-digestive enzyme toolkit in this classic example of convergent evolution
Life cycle of the root-knot nematode Meloidogyne javanica in papaya and histological analyses of root infection and gall development
No full textPapaya (Carica papaya L.) is susceptible to attacks by root-knot nematodes (RKN), which lead to significant production losses. Understanding the life cycle of RKN in papaya is essential for developing effective control strategies and screening for natural resistance in papaya cultivars. In this study, the development of the RKN Meloidogyne javanica was assessed in the susceptible papaya variety Solo8 over a period of 35 days, using microscopic observation of inoculated roots stained with fuchsin. By 9 days after inoculation (DAI), second-stage juveniles (J2s) were observed migrating through the root cortex and feeding within the vascular cylinder. At 16 DAI, galls containing enlarged J2s had formed within the stele, where feeding sites were established. Young females began appearing within the galls at 26 DAI, and mature pear-shaped females with egg masses were present by 35 DAI. Remarkably, some egg masses were deposited within the cortex, where a new generation of J2s hatched inside the root. Histological cross-sections of galls revealed that feeding sites initiated around the nematode head within the stele by 9 DAI, with four to eight multinucleated giant cells (GCs) present at these sites. These GCs, located within xylem and protophloem elements, were progressively encased by additional cell layers from adjacent vascular and cortical tissues as the nematode developed within the gall at 16, 26, and 35 DAI. The GCs reached maximum size by 16 DAI. Cytoplasmic analysis showed that GCs were rich in proteins, as evidenced by Naphtol Blue Black staining, and that their cell walls were strongly stained for polysaccharides using PAS. This study offers comprehensive histological insights into nematode development within papaya roots, underscoring that screening papaya genotypes for RKN resistance should consider egg mass production within the root tissue
Co-circulation of multiple pathogens and population-scale consequences
No full textInternational audienceMultiple infections, or ‘co-infections’, occur when a single host is infected by different pathogen species, or genotypes. This is known to affect symptom expression and pathogen multiplication in many pathosystems. However, the population-scale consequences remain poorly explored.Rice grown in Burkina Faso is affected by multiple pests, of which the rice yellow mottle virus (RYMV) and the bacteria Xanthomonas oryzae (Xo) are known to interact in experimental co-infections. In addition, several lineages of the RYMV co-circulate locally, and were evidenced as mixed infections. In this project, we aimed to investigate the evolutionary consequences of multiple infections (both within and between species) and their role in maintaining viral genetic diversity, for the RYMV in Burkina Faso.To this end, a stratified random sampling was performed in two sites, during two consecutive years (2021 and 2022). Molecular detection applied jointly to RYMV and Xo revealed a much higher frequency of samples co-infected by the two pathogens, than inferred from the observations of the two types of specific symptoms on the same plants. We then characterised the genetic diversity of RYMV in collected samples revealing a locally high diversity within fields, and significant structuration between the two sites. In addition, we found some evidence for an association of some RYMV lineages with the presence of Xo, suggesting reciprocal influence of co-infecting pathogens on the genetic structuration of other pathogen species. Further research could confirm such consequences of multiple infections on the evolution of viral populations