Biology subjects

Zwaan, B.

Publications and source records attributed to Zwaan, B..

7 recordsLinked to original sources

bioRxiv2026

Non-triazole agricultural fungicides indirectly select for triazole resistance in the human pathogen Aspergillus fumigatus

The intensification of agriculture relies on chemical fungicides to manage crop disease1,2, leading to the evolution of resistance in plant pathogens.3 Fungicides have long half-lives, allowing them to remain active well beyond their intended targets and affect downstream ecosystems and agricultural practices. The saprophytic fungus Aspergillus fumigatus is an airborne ubiquitous fungus and an important human pathogen causing severe life-threatening invasive fungal disease.4 Selection pressure from agricultural triazoles, demethylase inhibitors (DMIs), has led to cross-resistance to clinical triazoles, as they share the same target gene, cyp51A.5,6 In the Netherlands7,8, most triazole resistance arises from two cyp51A haplotypes, the TR34 and TR46.9,10 Genomic surveys of A. fumigatus have shown that these triazole-resistance alleles often co-occur with resistance alleles to non-DMI classes, these include some of the dominant fungicide classes used in Europe such as quinone outside inhibitors (QoIs), and succinate dehydrogenase inhibitors (SDHIs).11 Hypothesizing that agricultural environments with non-DMI fungicides can indirectly select for triazole resistance, we used grass mesocosms to compete A. fumigatus isolates. We found that already at low concentrations, commonly found in agricultural residues, DMI, SDHI, and QoI fungicides can each independently increase the proportions of triazole resistant alleles. We show that the resistance alleles for each class are not intrinsically cross-resistant, indicating that their co-occurrences in allelic combinations produce this multi-resistance selection. Consistent with our mesocosms results, environmental samples contained high phenotypic (>20%) triazole resistance in heaps with only non-DMI fungicides. This work provides the first experimental and field evidence of selection for triazole resistance by non-triazole fungicides via genomic hitch-hiking. We thus predict that when novel fungicides are used in the same selective environment, novel resistance alleles will most likely be selected in isolates that have already accumulated resistance alleles to other fungicide classes. Because of linked resistance alleles, tackling selection and spread of environmental triazole resistance will require consideration of all fungicide classes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/728463v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@259848org.highwire.dtl.DTLVardef@30bfdeorg.highwire.dtl.DTLVardef@84bb35org.highwire.dtl.DTLVardef@1eb39d_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LITriazole-resistance alleles often co-occur with resistance alleles to non-DMI fungicide classes such as SDHI and QoI. C_LIO_LIDMI, SDHI, and QoI all independently increase the proportions of triazole resistant alleles at low concentrations (0.1 mg/kg) commonly found in agricultural residues. C_LIO_LIThe DMI resistance allele TR46 has a high fitness only under fungicide selective conditions, whereas TR34 maintains its fitness also under fungicide free conditions. C_LIO_LIBeneficial alleles for one fungicide class increase in frequency and hitch-hike with resistance alleles to other fungicide classes. C_LIO_LIResistance alleles to novel fungicide classes will more likely be selected in isolates that already accumulated other fungicide resistance alleles. C_LI

microbiology↗

bioRxiv2024

Genomic prediction in insects: a case study on wing morphology traits in the jewel wasp Nasonia vitripennis

BackgroundBiological control is a sustainable strategy to combat agricultural pests. Yet, due to legislation, importing non-native biocontrol agents is increasingly restricted. Thus, selective breeding of biocontrol traits of native species is suggested to enhance performance of existing biocontrol agents. Genomic prediction is a new alternative to exploit genetic variation for improving biocontrol efficacy. This study aims to establish proof-of-principle for genomic prediction in insect biocontrol agents, using wing morphology traits in the parasitoid Nasonia vitripennis Walker (Pteromalidae) as a model. MethodsWe performed genomic prediction using a Genomic Best Linear Unbiased Prediction (GBLUP) model, using a total of 1,230 individuals with 8,639 SNPs generated by genotyping-by-sequencing (GBS). We used individuals from two generations from the outbred HVRx population, 717 individuals from generation G169 and 513 from generation G172. To assess genomic prediction accuracy, we used across- generation validation: forward validation for G172 from G169, backward in time validation for G169 from G172, and also 5-fold cross-validation, randomly using one fifth of the population as validiation and the others as training groups. ResultsFor size-related traits, including tibia length, wing length, width, and second moment wing area, the accuracy of genomic prediction was close to zero in both across-generation validations, but much higher in 5-fold cross-validation (ranging 0.54-0.68). For the shape-related trait wing aspect ratio, a high accuracy was found for all three validation strategies, with 0.47 for across-generation forward validation, 0.65 for across-generation backward validation, and 0.54 for 5-fold cross-validation. ConclusionPromising accuracies were observed for all traits in 5-fold cross-validation, but not in the across-generation validations. Overall, applying genomic selection in insect biocontrol agents with a relative small effective population size seems promising. However, factors such as the biology of insects, the techniques of phenotyping, and costs of large-scale genotyping still challenge the application of genomic selection to biocontrol agents.

genetics↗

bioRxiv2024

Uncovering large effect loci and epistasis for lifespan in standing genetic variation in the fruit fly Drosophila melanogaster

Lifespan is a heritable trait with a polygenic architecture. Experimental evolution in combination with re-sequencing has often been used to identify candidate loci for lifespan in Drosophila melanogaster. Previous experiments showed that Drosophila populations experimentally evolved to increase late-life reproduction showed a correlated responses in development time, body size, but also lifespan. Subsequent whole genome sequencing allowed for the identification of candidate loci that correlated to lifespan differentiation. However, it remains difficult to assess whether candidate loci affect lifespan and to what extent such loci pleiotropically underpin multiple traits. Furthermore, recent studies indicate that lifespan effects of loci are often context dependent, but genotype-by-genotype interactions remain understudied. Therefore, here, we report on a study where we genotyped 3210 individuals for 32 candidate loci that emerged from our evolve and re-sequence experiment and tested, (1) whether these loci significantly affected lifespan, (2) the effect size of each locus, and, (3) how these loci mutually interact, i.e. determine the level of epistasis in moulding lifespan. Of the 32 loci, six showed significant main effect associations, of which three loci showed effects of 6.6 days difference in lifespan or larger, while the overall average lifespan was 41.7 days. Eight additional significant pairwise interactions between loci were found, of which four (single) main effects and one three-way interaction was significant. Lastly, we found that alleles that increased lifespan did not necessarily have higher frequencies in populations that showed increased lifespan, indicating that lifespan itself had not been the major target of selection. Our study indicates that individual genotyping following an evolve and re-sequencing study is essential to understand the mechanistic basis of polygenetic adaptation.

evolutionary biology↗

bioRxiv2024

Shifts and rebound in microbial community function following repeated introduction of a novel species

Natural microbial communities continually encounter novel species that may successfully establish or simply be transient, yet both outcomes can alter the resident community composition and function. Preserving natural microbial communities and innovating synthetic ones requires insight on the immediate and long-term impact of species introductions on both composition and function. For instance, it remains unclear whether there are gradual and long-term impacts from repeated invasions where the introduced species fails to establish - so-called failed invaders. To investigate the persistent impacts by failed invaders, we present an experimental test of community stability over multiple generations against repeated novel species introduction. We propagated a natural microbial community from a traditional fermented milk beverage for approximately 100 generations, with or without, repeated introduction of Escherichia coli at each transfer. Community function was determined by metabolic profiling, and we observed alterations therein immediately after E. coli introduction, followed by recovery, or rebound once ceased. In contrast to this proxy of community function, changes in the bacterial community composition were never detected. Our results evidence that community composition and function do not necessarily respond in parallel to an introduced species, potentially due to genotypic changes below species level detection or metabolic plasticity. Our work shows an ability for functional recovery in microbial communities and contributes insight on long-term community stability to sustained disturbances.

ecology↗

bioRxiv2018

Adaptation to developmental diet influences the response to selection on age at reproduction in the fruit fly

Experimental evolution (EE) is a powerful tool for addressing how environmental factors influence life-history evolution. While in nature different selection pressures experienced across the lifespan shape life histories, EE studies typically apply selection pressures one at a time. Here we assess the consequences of adaptation to three different developmental diets in combination with classical selection for early or late reproduction in the fruit fly Drosophila melanogaster. We find that the response to each selection pressure is similar to that observed when they are applied independently, but the overall magnitude of the response depends on the selection regime experienced in the other life stage. For example, adaptation to increased age at reproduction increased lifespan across all diets, however, the extent of the increase was dependent on the dietary selection regime. Similarly, adaptation to a lower calorie developmental diet led to faster development and decreased adult weight, but the magnitude of the response was dependent on the age-at-reproduction selection regime. Given that multiple selection pressures are prevalent in nature, our findings suggest that trade-offs should be considered not only among traits within an organism, but also among adaptive responses to different - sometimes conflicting - selection pressures, including across life stages.

evolutionary biology↗

bioRxiv2018

Epigenetic selection and the DNA methylation signatures of adverse prenatal environments

Maternal adversity is associated with long-term physiological changes in offspring. These are believed to be mediated through epigenetic mechanisms, including DNA methylation (DNAm). Changes in DNAm are often interpreted as damage or as part of plastic responses of the embryo. We propose that selection on stochastic DNAm differences generated during epigenetic reprogramming after fertilization contributes to the effects of maternal adversity on DNAm. Using a mathematical model of epigenetic reprogramming in the early embryo we predict that this \"epigenetic selection\" will generate a characteristic reduction in variance of DNAm at selected loci in populations exposed to maternal adversity. We tested this prediction using DNAm data from a human cohort prenatally exposed to the Dutch Famine and confirmed the reduction in DNAm variance, suggesting that epigenetic selection may have occurred. Epigenetic selection should be considered as a possible mechanism linking adversity in pregnancy to offspring health and may have implications for the likely effectiveness of intervention strategies.

epidemiology↗

bioRxiv2018

Genomic analysis of European Drosophila melanogaster populations on a dense spatial scale reveals longitudinal population structure and continent-wide selection

Genetic variation is the fuel of evolution, with standing genetic variation especially important for short-term evolution and local adaptation. To date, studies of spatio-temporal patterns of genetic variation in natural populations have been challenging, as comprehensive sampling is logistically difficult, and sequencing of entire populations costly. Here, we address these issues using a collaborative approach, sequencing 48 pooled population samples from 32 locations, and perform the first continent-wide genomic analysis of genetic variation in European Drosophila melanogaster. Our analyses uncover longitudinal population structure, provide evidence for continent-wide selective sweeps, identify candidate genes for local climate adaptation, and document clines in chromosomal inversion and transposable element frequencies. We also characterise variation among populations in the composition of the fly microbiome, and identify five new DNA viruses in our samples.

evolutionary biology↗