Pedunculate oak ( Quercus robur L.), a long-lived forest tree species, forms symbiotic relationships with ectomycorrhizal (ECM) fungi, which can promote nutrient uptake, stress resilience, and growth. Like other tropical and temperate tree species, pedunculate oak exhibits endogenous rhythmic growth (ERG), a trait conferring the ability to repeatedly alternate root and shoot flushes as well as growth cessation as response to c...

Antagonistic selection between pathogens and their hosts can drive rapid evolutionary change and leave distinct molecular footprints of past and ongoing selection in the genomes of the interacting species. Despite an increasing availability of tools able to identify signatures of selection, the genetic mechanisms underlying coevolutionary interactions and the specific genes involved are still poorly understood, especially in h...

Microbial pathogens can adapt rapidly to changing environments such as the application of pesticides or host resistance. Copy number variations (CNVs) are a major source of adaptive genetic variation for recent adaptation. Here, we analyse how a major fungal pathogen of barley, Rhynchosporium commune , has adapted to the host environment and fungicide applications. We screen the genomes of 125 isolates sampled across a worldwi...

Hyperparasites can affect the evolution of pathosystems by influencing the stability of both pathogen and host populations. However, how pathogens of perennial hosts evolve in the presence of a hyperparasite has rarely been studied. Here, we investigated temporal changes in genetic diversity of the invasive chestnut blight pathogen Cryphonectria parasitica in the presence of its parasitic mycovirus Cryphonectria hypovirus 1 (C...

Grapevine red blotch virus (GRBV) is a recently identified virus that infects grapevine and has a severe impact on the grape industry in North America. Since the first description of the virus 8 years ago, clear progress has been made regarding our understanding of the GRBV pathosystem. However, questions remain regarding the origin of this pathogen and its spread outside North America, especially in Europe. In this study, we...

Convergent evolution leads to identical phenotypic traits in different species or populations. Convergence can be driven by standing variation allowing selection to favour identical alleles in parallel or the same mutations can arise independently. However, the molecular basis of such convergent adaptation remains often poorly resolved. Pesticide resistance in agricultural ecosystems is a hallmark of convergence in phenotypic...

Summary Ectomycorrhizal (ECM) fungi associated with plants constitute one of the most successful symbiotic interactions in forest ecosystems. ECM support trophic exchanges with host plants and are important factors for the survival and stress resilience of trees. However, ECM clades often harbour morpho‐species and cryptic lineages, with weak morphological differentiation. How this relates to intraspecific genome variability a...

Summary Plant pathogens secrete effector proteins to manipulate the host and facilitate infection. Cognate hosts trigger strong defence responses upon detection of these effectors. Consequently, pathogens and hosts undergo rapid coevolutionary arms races driven by adaptive evolution of effectors and receptors. Because of their high rate of turnover, most effectors are thought to be species‐specific and the evolutionary traject...

Host specialization is a key process in ecological divergence and speciation of plant‐associated fungi. The underlying determinants of host specialization are generally poorly understood, especially in endophytes, which constitute one of the most abundant components of the plant microbiome. We addressed the genetic basis of host specialization in two sympatric subspecies of grass‐endophytic fungi from the Epichloë typhina comp...

The genetic and environmental homogeneity in agricultural ecosystems is thought to impose strong and uniform selection pressures. However, the impact of this selection on plant pathogen genomes remains largely unknown. We aimed to identify the proportion of the genome and the specific gene functions under positive selection in populations of the fungal wheat pathogen Zymoseptoria tritici . First, we performed genome scans in f...

Local adaptation plays a key role in the evolutionary trajectory of host–pathogen interactions. However, the genetic architecture of local adaptation in host–pathogen systems is poorly understood. Fungal plant pathogens in agricultural ecosystems provide highly tractable models to quantify phenotypes and map traits to corresponding genomic loci. The outcome of crop–pathogen interactions is thought to be governed largely by gen...

Evolution of fungicide resistance is a major threat to food production in agricultural ecosystems. Fungal pathogens rapidly evolved resistance to all classes of fungicides applied to the field. Resistance to the commonly used azole fungicides is thought to be driven mainly by mutations in a gene ( CYP 51 ) encoding a protein of the ergosterol biosynthesis pathway. However, some fungi gained azole resistance independently of CY...

Hybrid zones allow the measurement of gene flow across the genome, producing insight into the genomic architecture of speciation. Such analysis is particularly powerful when applied to multiple pairs of hybridizing species, as patterns of genomic differentiation can then be related to age of the hybridizing species, providing a view into the build‐up of differentiation over time. We examined 33 809 single nucleotide polymorphi...

Forecasting the ecological effects of climate change on marine species is critical for informing greenhouse gas mitigation targets and developing marine conservation strategies that remain effective and increase species' resilience under changing climate conditions. Highly productive coastal upwelling systems are predicted to experience substantial effects from climate change, making them priorities for ecological forecasting....

Different species of arbuscular mycorrhizal fungi (AMF) alter plant growth and affect plant coexistence and diversity. Effects of within‐AMF species or within‐population variation on plant growth have received less attention. High genetic variation exists within AMF populations. However, it is unknown whether genetic variation contributes to differences in plant growth. In our study, a population of AMF was cultivated under id...