Biology subjects

Walser, J.-C.

Publications and source records attributed to Walser, J.-C..

18 recordsLinked to original sources

bioRxiv2025

Stool Dynamics and the Developing Gut Microbiome During Infancy

The infant gut microbiome is a dynamic ecosystem that plays a crucial role in early development, influences immune system maturation, and overall health. Recent insights reveal that the gut microbiota undergoes changes across the 24-h day, raising the possibility that it may act as "zeitgeber", helping to regulate the hosts sleep-wake organisation. Despite its importance, timing factors influencing microbiome composition are poorly understood, limiting its use as a health predictor. This study investigates the relationship between stool dynamics (interval since last defecation, collection time of the sample), sleep pressure (interval since last sleep), meal timing and the composition of the gut microbiome. Stool samples from 198 healthy infants, aged 3 to 31 months, were analysed to assess microbial diversity, richness evenness, and abundance. Our findings reveal that longer intervals since the last bowel movement are associated with increased microbial diversity, evenness, and richness. Stool timing is associated with shifts in microbial composition, especially in younger infants, indicating that diurnal microbial fluctuations may become more stable as infants mature. We found that longer periods of wakefulness were associated with increased microbial diversity in early infancy, although this effect appeared to diminish with age. Feeding schedules appeared to have a limited effect on the gut microbiome. Longer fasting before sampling showed no significant associations with most microbial parameters, except for a positive association with microbial richness. At the phylum level, results indicate that infant gut microbial composition is influenced by behaviour and physiology. Longer intervals between bowel movements were associated with shifts in bacterial abundance, with Proteobacteria decreasing and Actinobacteria increasing. Stool timing and meal timing also affected microbial diversity: later sampling times showed higher Actinobacteria levels, and longer fasting was associated with reduced Bacteroidetes. Sleep pressure showed a trend effect with Firmicutes displaying a slight decrease in infants who had been awake longer. Our findings underscore the importance of time-based factors on infant gut microbiome composition.

systems biology↗

bioRxiv2025

Rhythms of Early Life: Gut Microbiota Rhythmicity and Circadian Maturation in infants

BackgroundThe human gut microbiota undergoes daily fluctuations, yet its interaction with sleep-wake patterns during infancy remains largely uncharted. This study aims to elucidate the relationship between gut microbiota rhythmicity and the development of sleep patterns in infants over the first year of life. We continuously monitored 162 healthy infants across multiple days at 3, 6, and 12 months of age using ankle actigraphy and 24-hour diaries. The Circadian Function Index (CFI) was computed as a proxy for sleep-wake rhythm maturation. Stool samples were collected to profile gut microbiota taxa composition via 16S rRNA gene amplicon sequencing, and microbial oscillations were assessed through sine and cosine fitting to detect 24-hour patterns. ResultsOur findings revealed that the relative abundance of bacterial taxa exhibited rhythmic patterns, with 26 zOTUs (1.74%) following a sine pattern and 100 zOTUs (6.69%) displaying cosine rhythmicity. Cosine rhythmicity became more pronounced with age, showing strong maturation: 7 zOTUs at 3 months, 2 zOTUs at 6 months, and 86 zOTUs at 12 months. Notably, 105 zOTUs (7.02%) were associated with CFI, demonstrating a significant relationship between gut microbiota rhythms and sleep development. Among these, 27 zOTUs with sine dynamics and 96 zOTUs with cosine dynamics were linked to CFI, with this association strengthening as infants aged. ConclusionsThese results highlight the increasing synchronization between gut microbiota rhythmicity and sleep-wake cycles during infancy, pointing to a critical window for potential health interventions. This novel observation, previously reported in rodents and adults, underscores the role of gut microbiota in early human development, offering new avenues for enhancing developmental outcomes through targeted interventions.

developmental biology↗

bioRxiv2024

Zooplankton bacterial communities are influenced by infection status, environmental conditions and diet quantity across natural epidemics

Zooplankton-associated microbiomes play an important role for host health and contribute to ecosystem processes such as nutrient cycling. Yet, few studies have assessed how environmental gradients and biotic interactions, including parasitism and diet, may shape the microbiome composition of wild zooplankton. Here, we analysed the microbiomes of water fleas from the Daphnia longispina species complex using 16S rRNA gene sequencing and a long-term field dataset spanning six sampling events over 13 years. Sampling coincided with outbreaks of the virulent eukaryotic gut parasite Caullerya mesnili. Additionally, we explored how microbiome structure varied in relation to water parameters, phytoplankton density (i.e. Daphnia diet), and zooplankton density and community structure. Daphnia microbiomes displayed strong temporal variation, and comparatively small differences based on host infection status. Microbiome beta diversity correlated with phytoplankton density but not with its community composition, including green algae, protists and cyanobacteria. Environmental conditions, including temperature, dissolved oxygen and cyanobacterial abundance - previously found to drive Caullerya epidemics - were also associated with distinct microbiome structures. Importantly, microbiome beta diversity co-varied with infection prevalence, suggesting a link between microbiome shifts, epidemic size, and environmental conditions driving large epidemics. Dominant bacterial taxa correlated with Daphnia density, whereas the phylogenetic composition of rare taxa was associated with total zooplankton density. These findings demonstrate the dynamic nature of Daphnia microbiomes and suggest potential mechanisms by which they may mediate disease dynamics, particularly through associations with diet quantity, temperature, and host population density.

ecology↗

bioRxiv2024

Single-cell trait diversity explains niche and fitness differences in aquatic microbial communities

Two fundamental questions in ecology are how biodiversity is maintained and how it affects ecosystem functioning. Until now, it has been difficult to study the above mechanisms in natural microbial communities, yet they are important drivers of biogeochemical ecosystem functions. Here, we use a new approach to define and measure biodiversity in complex lake microbial communities (Lake Cadagno, Switzerland) based on the cell-to-cell variation in multiple functionally relevant phenotypic traits. We use stable isotope probing coupled to correlative imaging using confocal laser scanning microscopy (CLSM) and nanometer-scale secondary ion mass spectrometry (NanoSIMS) to obtain morphological (size), physiological (pigments) and metabolic (carbon and nitrogen isotope uptake and sulfur content) traits for a large number of individual cells along the environmental gradient found across lake depth. We show that cell-to-cell trait variation is significantly correlated with cell densities as a proxy for ecosystem functioning, whereas genetic diversity measured at the level of 16S and 18S is not. Our single-cell analysis provides evidence for a simultaneous increase in niche partitioning (measured as increased evenness in pigment composition) and decrease in fitness differences (measured as decreased variability in sulfur content) due to light limitation and competition for nutrients in deep layers of the lake. This leads to a negative relationship between niche and fitness differences. Our results suggest that niche and fitness differences in natural microbial communities can be understood at the level of single-cell traits, providing a mechanistic understanding of the relationship between microbial diversity and ecosystem functioning.

microbiology↗

bioRxiv2023

Legionella relative abundance in shower hose biofilms is associated with specific microbiome members

Legionella are natural inhabitants of building plumbing biofilms, where interactions with other microorganisms influence their survival, proliferation, and death. Here, we investigated the associations of Legionella with prokaryotic and eukaryotic microbiomes in biofilm samples extracted from 85 shower hoses of a multiunit residential building. Legionella spp. relative abundance in the biofilms ranged between 0 - 7.8%, of which only 0 - 0.46% was L. pneumophila. Our data suggest that some microbiome members were associated with high (e.g., Chthonomonas, Vrihiamoeba) or low (e.g., Aquabacterium, Vannella) Legionella relative abundance. The correlations of the different Legionella variants (30 Zero-Radius OTUs detected) showed distinct patterns, suggesting separate ecological niches occupied by different Legionella species. This study provides insights into the ecology of Legionella with respect to: 1) the colonization of a high number of real shower hoses biofilm samples; 2) the ecological meaning of associations between Legionella and co-occurring prokaryotic/eukaryotic organisms; 3) critical points and future directions of microbial-interaction-based-ecological-investigations.

microbiology↗

bioRxiv2022

Infection by a eukaryotic gut parasite in wild Daphnia sp. associates with a distinct bacterial community

Host-associated bacterial communities can play an important role in host fitness and resistance to diseases. Yet, few studies have investigated tripartite interaction between a host, parasite and host-associated bacterial communities in natural settings. Here, we use 16S amplicon sequencing to compare gut- and body-bacterial communities of wild water fleas belonging to the Daphnia longispina complex, between uninfected hosts and those infected with the common and virulent eukaryotic gut parasite Caullerya mesnili (Family: Ichthyosporea). We report community-level changes in host-associated bacteria with the presence of the parasite infection; namely decreased alpha diversity and increased beta diversity at the site of infection, i.e. host gut (but not host body). We also report decreased abundance of bacterial taxa proposed elsewhere to be beneficial for the host, and an appearance of taxa specifically associated with infected hosts. Our study highlights the host-microbiota-infection link in a natural system and raises questions about the role of host-associated microbiota in natural disease epidemics as well as the functional roles of bacteria specifically associated with infected hosts.

ecology↗

bioRxiv2021

Water column stability as an important factor controlling nitrite-dependent anaerobic methane oxidation in stratified lake basins

Anaerobic oxidation of methane (AOM) with nitrate/nitrite as the terminal electron acceptor may play an important role in mitigating methane emissions from lacustrine environments to the atmosphere. We investigated AOM in the water column of two connected but hydrodynamically contrasting basins of a south-alpine lake in Switzerland (Lake Lugano). The North Basin is permanently stratified with year-round anoxic conditions below 120 m water depth, while the South Basin undergoes seasonal stratification with the development of bottom water anoxia during summer. We show that below the redoxcline of the North Basin a substantial fraction of methane was oxidized coupled to nitrite reduction by Candidatus Methylomirabilis. Incubation experiments with 14CH4 and concentrated biomass from showed at least 43-52%-enhanced AOM rates with added nitrate/nitrite as electron acceptor. Multiannual time series data on the population dynamics of Candidatus Methylomirabilis in the North Basin following an exceptional mixing event in 2005/2006 revealed their requirement for lasting stable low redox-conditions to establish. In the South Basin, on the other hand, we did not find molecular evidence for nitrite-dependent methane oxidizing bacteria. Our data suggest that here the dynamic mixing regime with fluctuating redox conditions is not conducive to the development of a stable population of relatively slow-growing Candidatus Methylomirabilis, despite a hydrochemical framework that seems more favorable for nitrite-dependent AOM than in the North Basin. We predict that the importance of N-dependent AOM in freshwater lakes will likely increase in future because of longer thermal stratification periods and reduced mixing caused by global warming.

microbiology↗

bioRxiv2021

Spatio-temporal patterns of multi-trophic biodiversity and food-web characteristics across a river catchment

Accurate characterisation of ecological communities with respect to their biodiversity and food-web structure is essential for conservation. However, combined empirical study of biodiversity and multi-trophic food-webs at a large spatial and temporal resolution has been prohibited by the lack of appropriate access to such data from natural systems. Here, we assessed biodiversity and food-web characteristics across a 700 km2 riverine network over seasons using environmental DNA. We found contrasting biodiversity patterns between major taxonomic groups; local richness showed seasonally dependent and statistically significant increases and decreases towards downstream positions within the catchment for fish and bacteria respectively, while invertebrate richness remained unchanged with increased downstream position. The local food-webs, formed by these taxonomic groups, also showed a variation in their structure, such as link density and nestedness, to both space and time, yet these patterns did not necessarily mirror those of biodiversity and functional feeding characteristics. In order to conserve species diversity as well as their functional trophic integrity of communities, patterns of biodiversity and food-web characteristics must thus be jointly studied, as our results suggest that they are not directly scalable to each other even at the same spatial and temporal scales.

ecology↗

bioRxiv2021

Epithelial GPR35 protects from Citrobacter rodentium infection by preserving goblet cells and mucosal barrier integrity

Goblet cells secrete mucin to create a protective mucus layer against invasive bacterial infection and are therefore essential for maintaining intestinal health. However, the molecular pathways that regulate goblet cell function remain largely unknown. Although GPR35 is highly expressed in colonic epithelial cells, its importance in promoting the epithelial barrier is unclear. In this study, we show that epithelial Gpr35 plays a critical role in goblet cell function. In mice, cell type-specific deletion of Gpr35 in epithelial cells but not in macrophages results in goblet cell depletion and dysbiosis, rendering these animals more susceptible to Citrobacter rodentium infection. Mechanistically, scRNA-seq analysis indicates that signaling of epithelial Gpr35 is essential to maintain normal pyroptosis levels in goblet cells. Our work shows that the epithelial presence of Gpr35 is a critical element for the function of goblet cell-mediated symbiosis between host and microbiota.

immunology↗

bioRxiv2020

Transcriptome profiling of a multiuse model species Lymnaea stagnalis (Gastropoda) for ecoimmunological research

Host immune function can contribute to numerous ecological/evolutionary processes. Ecoimmunological studies, however, typically use one/few phenotypic immune assays and thus do not consider the complexity of the immune system. Therefore, "omics" resources that allow quantifying immune activity across multiple pathways are needed for ecoimmunological models. We applied short-read based RNAseq (Illumina NextSeq 500, PE-81) to characterise transcriptome profiles of a multipurpose model species Lymnaea stagnalis (Gastropoda). We used a genetically diverse snail stock and exposed individuals to immune elicitors (injury, bacterial/trematode pathogens) and changes in environmental conditions that can alter immune activity (temperature, food availability). Immune defence factors identified in the de novo assembly indicated uniform aspects of molluscan immunity: pathogen-recognition receptors (PRR) and lectins activate Toll-like receptor (TLR) pathway and cytokines that regulate cellular and humoral defences. However, also apparent differences to other taxa were detected (i.e., modest numbers of antimicrobial peptides and fibrinogen related proteins). Identified factors also indicate that several of them might contribute to the phenotypic immune assays used on this species. Experimental treatments revealed factors from non-self recognition (lectins) and signalling (TLR pathway, cytokines) to effectors [e.g., antibacterial proteins, phenoloxidase (PO) enzymes] whose gene expression depended on immune activations and environmental conditions, as well as components of snail physiology/metabolism that may drive these effects. Interestingly, gene expression of many factors (e.g., PRR, lectins, cytokines, PO enzymes, antibacterial proteins) showed high among-individual variation. Such factors are important to include in ecoimmunological research because they may explain among-individual differences in parasite resistance and fitness in natural populations.

genomics↗

bioRxiv2020

Impact of transposable elements on methylation and gene expression across natural accessions of Brachypodium distachyon.

Transposable elements (TEs) constitute a large fraction of plant genomes and are mostly present in a transcriptionally silent state through repressive epigenetic modifications such as DNA methylation. TE silencing is believed to influence the regulation of adjacent genes, possibly as DNA methylation spreads away from the TE. Whether this is a general principle or a context-dependent phenomenon is still under debate, pressing for studying the relationship between TEs, DNA methylation and nearby gene expression in additional plant species. Here we used the grass Brachypodium distachyon as a model and produced DNA methylation and transcriptome profiles for eleven natural accessions. In contrast to what is observed in Arabidopsis thaliana, we found that TEs have a limited impact on methylation spreading and that only few TE families are associated to a low expression of their adjacent genes. Interestingly, we found that a subset of TE insertion polymorphisms is associated with differential gene expression across accessions. Thus, although not having a global impact on gene expression, distinct TE insertions may contribute to specific gene expression patterns in B. distachyon. Significance statementTransposable elements (TEs) are a major component of plant genomes and a source of genetic and epigenetic innovations underlying adaptation to changing environmental conditions. Yet molecular evidence linking TE silencing and nearby gene expression are lacking for many plant species. We show that in the model grass Brachypodium DNA methylation spreads over very short distances around TEs, with an influence on gene expression for a small subset of TE families.

genomics↗

bioRxiv2020

Specific and conserved patterns of microbiota-structuring by maize benzoxazinoids in the field

BackgroundPlants influence their root and rhizosphere microbial communities through the secretion of root exudates. However, how specific classes of root exudate compounds impact the assembly of these root-associated microbiotas is not well understood. Maize roots secrete benzoxazinoids (BXs), a class of indole-derived defense compounds, and thereby impact the assembly of their microbiota. Here, we investigated the broader impacts of BX exudation on root and rhizosphere microbiotas of adult maize plants grown under natural conditions at different field locations in Europe and the US. We examined the microbiotas of BX-producing and multiple BX-defective lines in two genetic backgrounds across three soil types. ResultsOur analysis showed that the secretion of BXs affected community composition of rhizosphere and root microbiota, with the most pronounced effects observed for root fungi. The impact of the two genetic backgrounds was weaker than that of the presence or absence of BXs, suggesting that BX exudation is a key trait by which maize structures its associated microbiota. BX-producing plants were not consistently enriching microbial lineages across the three soil types. Instead, BX exudation consistently depleted Flavobacteriaceae and Comamonadaceae, and enriched various plant pathogenic fungi in the roots. ConclusionsThese findings reveal that BXs have a selective impact on root and rhizosphere microbiota composition across different field locations. Taken together, this study identifies the BX pathway as an interesting breeding target to manipulate plant-microbiome interactions.

plant biology↗

bioRxiv2020

Decision making and best practices for taxonomy-free eDNA metabarcoding in biomonitoring using Hill numbers

Environmental DNA (eDNA) metabarcoding raises expectations for biomonitoring to cover organisms that have hitherto been neglected or excluded. To bypass current limitations in taxonomic assignments due to incomplete or erroneous reference data bases, taxonomic-free approaches are proposed for biomonitoring at the level of operational taxonomic unites (OTUs). However, this is challenging, because OTUs cannot be annotated and directly compared to classically derived data. The application of good stringency treatments to infer validity of OTUs and the clear understanding of the consequences to such treatments is thus especially relevant for biodiversity assessments. We investigated how common practices of stringency filtering affect diversity estimates based on Hill numbers derived from eDNA samples. We collected eDNA at 61 sites across a 740 km2 river catchment, reflecting a spatially realistic scenario in biomonitoring. After bioinformatic processing of the data, we studied how different stringency treatments affect conclusions with respect to biodiversity at the catchment and site levels. The applied stringency treatments were based on the consistent appearance of OTUs across filter replicates, a relative abundance cut-off and rarefaction. We detected large differences in diversity estimates when accounting for presence/absence only, such that the detected diversity at the catchment scale differed by an order of magnitude between the treatments. These differences disappeared between the stringency treatments with increasing weighting of the OTUs abundances. Our study demonstrated the usefulness of Hill numbers for comparisons between data sets with large differences in diversity, and suggests best practice for data stringency filtering for biomonitoring.

ecology↗

bioRxiv2019

Evolved for success in novel environments: the round goby genome

Since the beginning of global trade, hundreds of species have colonized territories outside of their native range. Some of these species proliferate at the expense of native ecosystems, i.e., have become invasive. Invasive species constitute powerful in situ experimental systems to study fast adaptation and directional selection on short ecological timescales. They also present promising case studies for ecological and evolutionary success in novel environments.\n\nWe seize this unique opportunity to study genomic substrates for ecological success and adaptability to novel environments in a vertebrate. We report a highly contiguous long-read based genome assembly for the most successful temperate invasive fish, the benthic round goby (Neogobius melanostomus), and analyse gene families that may promote its impressive ecological success.\n\nOur approach provides novel insights from the large evolutionary scale to the small species-specific scale. We describe expansions in specific cytochrome P450 enzymes, a remarkably diverse innate immune system, an ancient duplication in red light vision accompanied by red skin fluorescence, evolutionary patterns in epigenetic regulators, and the presence of genes that may have contributed to the round gobys capacity to invade cold and salty waters.\n\nA recurring theme across all analyzed gene families are gene expansions. This suggests that gene duplications may promote ecological flexibility, superior performance in novel environments, and underlie the impressive colonization success of the round goby. Gobiidae generally feature fascinating adaptations and are excellent colonizers. Further long-read genome approaches across the goby family may reveal whether the ability to conquer new habitats relates more generally to gene copy number expansions.

ecology↗

bioRxiv2019

Assessing different components of biodiversity across a river network using eDNA

O_LIAssessing individual components of biodiversity, such as local or regional taxon richness, and differences in community composition is a long-standing challenge in ecology. It is especially relevant in spatially structured and diverse ecosystems. Environmental DNA (eDNA) has been suggested as a novel technique to accurately measure biodiversity. However, we do not yet fully understand the comparability of eDNA-based assessments to previously used approaches. C_LIO_LIWe sampled may-, stone-, and caddisfly genera with contemporary eDNA and kicknet methods at 61 sites distributed over a large river network, allowing a comparison of various diversity measures from the catchment to site levels and providing insights into how these measures relate to network properties. We extended our survey data with historical records of total diversity at the catchment level. C_LIO_LIAt the catchment scale, eDNA and kicknet detected similar proportions of the overall and cumulative historically documented species richness (gamma diversity), namely 42% and 46%, respectively. We further found a good overlap (62%) between the two contemporary methods at the regional scale. C_LIO_LIAt the local scale, we found highly congruent values of local taxon richness (alpha diversity) between eDNA and kicknet. Richness of eDNA was positively related with discharge, a descriptor of network position, while kicknet was not. C_LIO_LIBeta diversity between sites was similar for the two contemporary methods. Contrary to our expectation, however, beta diversity was driven by species replacement and not by nestedness. C_LIO_LIAlthough optimization of eDNA approaches is still needed, our results indicate that this novel technique can capture extensive aspects of gamma diversity, proving its potential utility as a new tool for large sampling campaigns across hitherto understudied complete river catchments, requiring less time and becoming more cost-efficient than classical approaches. Overall, the richness estimated with the two contemporary methods is similar at both local and regional scale but community composition is differently assessed with the two methods at individual sites and becomes more similar with higher discharge. C_LI

ecology↗

bioRxiv2018

SPECIES-SPECIFIC ROOT MICROBIOTA DYNAMICS IN RESPONSE TO PLANT-AVAILABLE PHOSPHORUS

O_LIPhosphorus (P) is a limiting element for plant growth. Several root microbes, including arbuscular mycorrhizal fungi (AMF), have the capacity to improve plant nutrition and their abundance is known to depend on P fertility. However, how complex root-associated bacterial and fungal communities respond to changes in P availability remains ill-defined.\nC_LIO_LIWe manipulated the availability of soil P in pots and compared the root microbiota of non-mycorrhizal Arabidopsis with mycorrhizal Petunia plants. Root bacteria and fungi were profiled using ribosomal operon gene fragment sequencing, we searched for P sensitive microbes and tested whether a P sensitive core microbiome could be identified.\nC_LIO_LIRoot microbiota composition varied substantially by P availability. A P sensitive core microbiome was not identified as different bacterial and fungal groups responded to low-P conditions in Arabidopsis and Petunia. P sensitive microbes included Mortierellomycotina in Arabidopsis, while these were AMF and their symbiotic endobacteria in Petunia. Of note, their P-dependent root colonization was reliably quantified by sequencing.\nC_LIO_LIThe species-specific root microbiota dynamics suggest that Arabidopsis and Petunia evolved different microbial associations under the selection pressure of low P availability. This implies that the development of microbial products that improve P availability requires the consideration of host-species specificity.\nC_LI

plant biology↗

bioRxiv2018

Environmental sources of bacteria and genetic variation in behavior influence host-associated microbiota

In many organisms, host-associated microbial communities are acquired horizontally after birth. This process is believed to be shaped by a combination of environmental and host genetic factors. We examined whether genetic variation in animal behavior could affect the composition of the animals microbiota in different environments. The freshwater crustacean Daphnia magna is primarily planktonic, but exhibits variation in the degree to which it browses in benthic sediments. We performed an experiment with clonal lines of D. magna showing different levels of sediment-browsing intensity exposed to either bacteria-rich or bacteria-poor sediment or whose access to sediments was prevented. We find that the bacterial composition of the environment and genotype-specific browsing intensity together influence the diversity and composition of the Daphnia-associated bacterial community. Exposure to more diverse bacteria did not lead to a more diverse microbiome, but greater abundances of environment-specific bacteria were found associated with host genotypes that exhibited greater browsing behavior. Our results indicate that individual behavior can mediate genotype-by-environment interaction effects on microbiome composition.\n\nSummary statementGenetic differences in Daphnia behavior contribute to the amount of environmental bacteria present in their microbiome

evolutionary biology↗

bioRxiv2018

Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon.

Grasses are essential plants for ecosystem functioning. Quantifying the selective pressures that act on natural variation in grass species is therefore essential regarding biodiversity maintenance. In this study, we investigate the selection pressures that act on two distinct populations of the grass model Brachypodium distachyon without prior knowledge about the traits under selection. We took advantage of whole-genome sequencing data produced for 44 natural accessions of B. distachyon and used complementary genome-wide scans of selection (GWSS) methods to detect genomic regions under balancing and positive selection. We show that selection is shaping genetic diversity at multiple temporal and spatial scales in this species and affects different genomic regions across the two populations. Gene Ontology annotation of candidate genes reveals that pathogens may constitute important factors of positive and balancing selection in Brachypodium distachyon. We eventually cross-validated our results with QTL data available for leaf-rust resistance in this species and demonstrate that, when paired with classical trait mapping, GWSS can help pinpointing candidate genes for further molecular validation. Thanks to a near-base perfect reference genome and the large collection of freely available natural accessions collected across its natural range, B. distachyon appears as a prime system for studies in ecology, population genomics and evolutionary biology.

evolutionary biology↗