Résumé
Assessing trait responses to environmental gradients requires the simultaneous analysis of the information contained in three tables: L (species distribution across samples), R (environmental characteristics of samples), and Q (species traits). Among the available methods, the so-called fourth-corner and RLQ methods are two appealing alternatives that provide a direct way to test and estimate trait–environment relationships. Both methods are based on the analysis of the fourth-corner matrix, which crosses traits and environmental variables weighted by species abundances. However, they differ greatly in their outputs: RLQ is a multivariate technique that provides ordination scores to summarize the joint structure among the three tables, whereas the fourth-corner method mainly tests for individual trait–environment relationships (i.e., one trait and one environmental variable at a time). Here, we illustrate how the complementarity between these two methods can be exploited to promote new ecological knowledge and to improve the study of trait–environment relationships. After a short description of each method, we apply them to real ecological data to present their different outputs and provide hints about the gain resulting from their combined use.
Auteurs, date et publication :
Auteurs Stéphane Dray , Philippe Choler , Sylvain Dolédec , Pedro R. Peres-Neto , Wilfried Thuiller , Sandrine Pavoine , Cajo J. F. ter Braak
Publication : Ecology
Date : 2025
Volume : 95
Issue : 1
Pages : 14-21
Catégorie(s)
#CNRS #Lautaret #UGARésumé
Biological nitrogen fixation (BNF) is a fundamental part of nitrogen cycling in tropical forests, yet little is known about the contribution made by free-living nitrogen fixers inhabiting the often-extensive forest canopy. We used the acetylene reduction assay, calibrated with 15N2, to measure free-living BNF on forest canopy leaves, vascular epiphytes, bryophytes and canopy soil, as well as on the forest floor in leaf litter and soil. We used a combination of calculated and published component densities to upscale free-living BNF rates to the forest level. We found that bryophytes and leaves situated in the canopy in particular displayed high mass-based rates of free-living BNF. Additionally, we calculated that nearly 2 kg of nitrogen enters the forest ecosystem through free-living BNF every year, 40% of which was fixed by the various canopy components. Our results reveal that in the studied tropical lowland forest a large part of the nitrogen input through free-living BNF stems from the canopy, but also that the total nitrogen inputs by free-living BNF are lower than previously thought and comparable to the inputs of reactive nitrogen by atmospheric deposition.
Auteurs, date et publication :
Auteurs Leandro Van Langenhove , Thomas Depaepe , Lore T. Verryckt , Lucia Fuchslueger , Julian Donald , Celine Leroy , Sruthi M. Krishna Moorthy , Albert Gargallo-Garriga , M.D. Farnon Ellwood , Hans Verbeeck , Dominique Van Der Straeten , Josep Peñuelas , Ivan A. Janssens
Publication : Science of The Total Environment
Date : 2025
Volume : 754
Pages : 142202
Catégorie(s)
#ANR-Citation #CNRS #FORET NouraguesAuteurs, date et publication :
Auteurs James B Barnett , Constantine Michalis , Nicholas E Scott‐Samuel , Innes C Cuthill
Publication : Journal of Evolutionary Biology
Date : 2025
Volume : 34
Issue : 10
Pages : 1531-1540
Catégorie(s)
#CNRS #FORET NouraguesAuteurs, date et publication :
Auteurs Blanka Vlasáková , Blanka Kalinová , Mats HG Gustafsson , Holger Teichert
Publication : Annals of botany
Date : 2025
Volume : 102
Issue : 3
Pages : 295-304
Catégorie(s)
#CNRS #FORET NouraguesRésumé
Many parasites spend part of their life cycle as infectious forms released from an infected host in the external environment, where they may encounter and infect new hosts. The emergence of infectious life stages often occurs once a day to minimize mortality in adverse environments. In bird hosts, intestinal parasites such as coccidia are generally released with feces in the late afternoon. This dynamic is adaptive since it allows avoiding desiccation and ultraviolet (UV) radiation, thus reducing mortality of oocysts in the environment until transmission to the next host. If this circadian rhythm is the result of natural selection to increase oocyst survival, we may hypothesize that oocysts will appear in feces at different times depending on the environment where hosts live. Particularly, in an environment where UV radiation and desiccation are very low, we may expect oocyst circadian release to disappear since the main selective pressure would be relaxed. We sampled different species of birds in tropical and temperate forests in spring and investigated coccidian oocyst output. A strong circadian variation in the prevalence of hosts shedding coccidian oocyst was detected for species caught in the temperate forest with an increase in prevalence in the late afternoon, whereas prevalence of birds shedding oocysts was constant over the course of the day for most species sampled in the tropical rain forest. These results are consistent with the hypothesis that oocysts’ circadian output is maintained by natural selection to increase oocyst survival. We discuss the adaptive significance of diurnal periodicity in parasite output.
Auteurs, date et publication :
Auteurs Clotilde Biard , Karine Monceau , Maria Teixeira , Sébastien Motreuil , Soline Bettencourt-Amarante , Lucie Develay , Jérôme Moreau
Publication : Parasitology
Date : 2025
Volume : 149
Issue : 4
Pages : 469-481
Catégorie(s)
#ANR-Citation #CNRS #FORET NouraguesRésumé
Background: EGFR mutations cause inconsistent response to EGFR tyrosine-kinase inhibitors (TKI). To better understand these features, we reviewed all cases of EGFR-mutated non-small-cell lung cancer collected in the Biomarkers France database.
Patients and methods: Of 17 664 patients, 1837 (11%) with EGFR-mutated non-small-cell lung cancer were retrospectively analyzed for clinical and molecular characteristics. Results were correlated with survival and treatment response for the 848 stage IV patients.
Results: EGFR exon 18, 19, 20 and 21 mutations were found in 102 (5.5%), 931 (51%), 102 (5.5%) and 702 (38%) patients, respectively. Over 50% of exon 18 and 20 mutated patients were smokers. The median follow-up was 51.7 months. EGFR mutation type was prognostic of overall survival (OS) versus wild-type {exon 19: hazard ratio (HR)=0.51 [95% confidence interval (CI): 0.41-0.64], P < 0.0001; exon 21: HR = 0.76 (95% CI: 0.61-0.95), P = 0.002; exon 20: HR = 1.56 (95% CI: 1.02-2.38), P = 0.004}. EGFR mutation type was prognostic of progression-free survival versus wild-type [exon 19: HR = 0.62 (95% CI: 0.49-0.78), P < 0.0001; exon 20: HR = 1.46 (95% CI: 0.96-2.21), P = 0.07]. First-line treatment choice did not influence OS in multivariate analysis. First-line TKI predicted improved progression-free survival versus chemotherapy [HR = 0.67 (95% CI: 0.53-0.85), P = 0.001]. OS was longer for del19 versus L858R, which was associated with better OS compared with other exon 21 mutations, including L861Q. TKI improved survival in patients with exon 18 mutations, while chemotherapy was more beneficial for exon 20-mutated patients.
Conclusion: EGFR mutation type can inform the most appropriate treatment. Therapeutic schedule had no impact on OS in our study, although TKI should be prescribed in first-line considering the risk of missing the opportunity to use this treatment.
Auteurs, date et publication :
Auteurs C. Leduc , J. P. Merlio , B. Besse , H. Blons , D. Debieuvre , P. P. Bringuier , I. Monnet , I. Rouquette , S. Fraboulet-Moreau , A. Lemoine , D. Pouessel , J. Mosser , F. Vaylet , A. Langlais , P. Missy , F. Morin , D. Moro-Sibilot , J. Cadranel , F. Barlesi , M. Beau-Faller
Publication : Annals of Oncology: Official Journal of the European Society for Medical Oncology
Date : 2017
Volume : 28
Issue : 11
Pages : 2715-2724
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
Abstract
Introduction
Patients with stage IV non–small-cell lung cancer (NSCLC) and BRAF V600 mutations may benefit from targeted therapies. Chemotherapy outcomes are little known in this population.
Methods
The French Cooperative Thoracic Intergroup (IFCT) Biomarkers France study was a national prospective cohort study aiming to describe the molecular characteristics and clinical outcome of all consecutive NSCLC patients (N = 17,664) screened for molecular alterations. We used this data set to set up a case–control analysis. Cases had stage IV BRAF-mutated (BRAF-MT) NSCLC, whereas controls had NSCLC that was wild-type for EGFR, KRAS, HER2, BRAF, PIK3CA and ALK. Each case was matched for sex, age at diagnosis and smoking status to two controls randomly selected.
Results
Overall, 83 cases with BRAF mutant disease (66.3% V600E) were matched to 166 controls. Five cases received tyrosine kinase inhibition in the first-line and 16 in the second-line. All others were treated with standard chemotherapy. There was no significant difference in first-line and second-line progression-free survival (PFS) between the groups, as well as in the disease control rate, BRAF mutation was not found to be prognostic of overall survival. We found no significant difference in outcome between the treatment types used in first-line or second-line in patients with BRAF-MT disease compared with controls nor between BRAF V600E or non-V600E compared with controls.
Conclusions
BRAF mutation is not a strong prognostic factor in NSCLC. Although taxan-based therapy shows poorest PFS in first-line, no chemotherapy regimen was associated with prognosis.
Auteurs, date et publication :
Auteurs Sébastien Couraud , Fabrice Barlesi , Clara Fontaine-Deraluelle , Didier Debieuvre , Jean-Philippe Merlio , Lionel Moreau , Michèle Beau-Faller , Rémi Veillon , Jean Mosser , Faraj Al Freijat , Pierre-Paul Bringuier , Hervé Léna , L'Houcine Ouafik , Virginie Westeel , Alain Morel , Clarisse Audigier-Valette , Pascale Missy , Alexandra Langlais , Franck Morin , Pierre-Jean Souquet
Publication : European Journal of Cancer
Date : 2019
Volume : 116
Pages : 86-97
Catégorie(s)
#CNRS #EcoGenO #Université de RennesRésumé
The holobiont concept defines a given organism and its associated symbionts as a potential level of selection over evolutionary time. In clonal plants, recent experiments demonstrated vertical transmission of part of the microbiota from one ramet (i.e., potentially autonomous individual) to another within the clonal network (i.e., connections by modified stems present in ∼35% of all plants). Because of this heritability, and potentially reciprocal exchange of microbes between generations of ramets, we propose to extend the existing holobiont framework to the concept of meta-holobiont. A meta-holobiont is a network of holobionts that can exchange biomolecules and microbiota across generations, thus impacting the fitness of both biological scales: holobionts and meta-holobionts. Specifically, meta-holobiont dynamics can result in sharing, specialization, and division of labor across plant clonal generations. This paper, which coins the meta-holobiont concept, is expected to stimulate discussion and to be applied beyond the context of networked clonal plants (e.g., to social insects).
Auteurs, date et publication :
Auteurs Nathan Vannier , Cendrine Mony , Anne-Kristel Bittebiere , Kevin R. Theis , Eugene Rosenberg , Philippe Vandenkoornhuyse
Publication : mSystems
Date : 2019
Volume : 4
Issue : 2
Catégorie(s)
#CNRS #EcoGenO #Université de RennesAuteurs, date et publication :
Auteurs Blanka Vlasáková , Mats HG Gustafsson
Publication : Nordic Journal of Botany
Date : 2025
Volume : 29
Issue : 2
Pages : 178-181
Catégorie(s)
#CNRS #FORET NouraguesRésumé
BackgroundLitter decomposition is a fundamental process of biogeochemical cycles, and there is a strong consensus that litter mixture interactions are one of the factors driving the decomposition process. A better understanding of how climate change can alter interactions between species and the litter decomposition process could facilitate projections of ecosystem functioning into the future.MethodsA 24-month litterbag decomposition experiment was carried out in a Mediterranean forest to analyze the effects of climate and species diversity changes on litter mixture interactions and the decomposition process.ResultsIn the control plot, synergistic interactions increased with time and species diversity in litter mixtures, leading to more efficient litter decomposition. Drier conditions obtained in the field with a rain exclusion device decreased decomposition rates, resulting in three-fold less synergistic interactions and five-fold more antagonistic interactions during the decomposition process. Furthermore, synergistic interactions were better preserved in the drought conditions with increasing number of species.ConclusionsOur findings underline how a longer drought season could strongly affect the relationship between biodiversity and ecosystem functioning. Drier climate led to slower mass loss rates and a strong shift in the litter mixture interactions, with fewer synergistic interactions and more antagonistic interactions.
Auteurs, date et publication :
Auteurs Mathieu Santonja , Catherine Fernandez , Thierry Gauquelin , Virginie Baldy
Publication : Plant and Soil
Date : 2015
Volume : 393
Issue : 1-2
Pages : 69-82