Molecular Ecology

Urbanization is reshaping freshwater ecosystems, with well-documented effects across gradients of land-use change, hydrologic alteration, and habitat degradation. However, how biodiversity is organized among neighboring urban aquatic habitats that differ in hydrologic connectivity, disturbance transmission, residence time, management history, and opportunities for species movement is often less clear. This creates a challenge for interpreting urban fish communities at local scales as species occurrence may reflect both contemporary habitat filtering and historical contingencies including native persistence, interbasin transfer, stocking, and nonindigenous introductions. Here we use eDNA detections, historical records, phylogenetic information, and species trait data to investigate the fish assemblages of the Charlotte metropolitan region. We detect a highly mixed fauna that also depicts a strong signature of structured biodiversity profiles across taxonomic, phylogenetic, functional, and life-history dimensions between habitat types. In particular, bounded habitats contained assemblages with larger-bodied species that are fecund and faster to reproduce relative to free-flowing habitats. Species-level occurrence models did not support a simple trait-by-habitat rule. Instead our results demonstrate that urban aquatic habitats can sort historically mixed regional species pools into predictable assemblage-level life-history profiles while simultaneously retaining signatures of evolutionary and historical biogeographic contingency.

Heritable bacterial symbionts are pervasive in terrestrial arthropods, often imposing reproductive manipulations to promote their own spread within host populations. Co-infections are common, potentially allowing symbiont co-infectors to hitchhike through a host population. However, adverse thermal conditions can disrupt these communities, particularly when co-infectors vary in their thermal sensitivity. We used a multi-generation experiment to test whether warm (29 {degrees}C) conditions disrupted spread of heritable symbionts through uninfected populations of the spider, Mermessus fradeorum. We tested two common infection combinations: a single infection with a cytoplasmic incompatibility (CI) inducing Rickettsiella or a feminizing co-infection that included a feminizing Wolbachia, the same Rickettsiella, and up to three apparent hitchhikers (two additional Wolbachia strains and Tisiphia). We initiated replicate populations with 1/3 of one infection type and 2/3 uninfected spiders, evaluating population infection rate over 5 spider generations under different temperature regimes. Under cool (21{degrees}C) conditions, Wolbachia feminization drove co-infection to 88% and Rickettsiella CI drove single infection to 83% of host populations. Vertical transmission for all symbionts was high (97-99%) and hitchhiking symbionts also spread effectively. Under warm conditions, feminization and CI efficacy were reduced, and symbionts suffered variably reduced vertical transmission. Warm conditions ultimately destroyed the co-infecting symbiont consortium and impeded symbiont spread. On its own, though, Rickettsiella was still able to increase, despite reduced strength of CI. We hypothesize that contrasting tensions between feminizing spread of the symbiont consortium versus environmentally driven loss of function and transmission may explain observed patterns of mixed infections in field populations of this spider.

Marine diatoms contribute to about 20% of global primary production. We present the first basin-scale, multiyear assessment of diatom communities in the North Pacific, combining taxonomically high-resolution RuBisCO large subunit gene (rbcL) metabarcoding with concurrent environmental measurements. Using a nine-year time series of daily samples resolved at the species level via ~500 bp rbcL fragments, we performed multivariate analyses across biogeographic provinces, identifying significant correlations between community structure and environmental drivers such as temperature and macronutrient availability. We report the prevalence of a previously overlooked centric diatom species in the North Pacific, Eunotogramma lunatum, which appears to be near-dominant even in subarctic high-nitrate, low-chlorophyll waters where pennate diatoms are typically favored. These results demonstrate the power of rbcL for large-scale ocean monitoring and provide a critical baseline for future studies of diatom population dynamics, climate change impacts, and ecosystem resilience in a key marine region.

Most evidence of the consequences of climate change in natural systems has focussed on shifts in mean temperature (1,2), but the effects of extreme climatic events (ECEs) remain far less understood. This is particularly true for very severe ECEs that may occur only once every few decades. Understanding the consequences of these severe events for natural populations is nonetheless critical, since their frequency is predicted to rise under current climate change (3). Here we combine a unique long-term dataset spanning almost five decades of breeding (>20,000 events) and morphological data (>120,000 observations) in adult and nestling great tits (Parus major) and blue tits (Cyanistes caeruleus) with fine-scale temperature records to examine the effects of an unprecedented heatwave in May 2026 on breeding success and morphology. Average temperature during the heatwave (22-29 May 2026) was 7.85 C above the historical record, reaching +10.5 C (+4.32 SD) at its peak (25-26 May). These record-breaking temperatures significantly reduced adult breeding success and nestling bmass relative to expectation in the absence of a heat-wave. Given the heatwave was widespread (Fig. 1A), our findings from a single, exceptionally well-studied population are likely to generalise to other species exposed to the same event, providing key evidence that severe ECEs can substantially harm wild populations.

Circadian clocks enable mosquitoes to anticipate recurring environmental variations and coordinate behaviors critical for survival and disease transmission, such as locomotion, reproduction, host-seeking, and blood-feeding, with times of day when performance is maximal. In Aedes aegypti, locomotor activity follows a robust diurnal rhythm shaped by endogenous circadian clocks and environmental cues, among which light has been shown to be the primary source of temporal information. While early studies established the role of light in regulating locomotor activity, behavior, oviposition and pupation, it remains unclear which features of a light cycle drive changes in circadian rhythms. This question is increasingly relevant as Ae. aegypti is frequently exposed to artificial and dynamic lighting conditions in urban environments. Here, we investigated how transient changes in light schedules influence circadian rhythms in locomotor activity by systematically manipulating the timing, duration, and direction of light exposure. Using a high-throughput assay, we tested over 1900 individuals, including wild-type and timeless knockout mutants, and showed that a single day of al tered lighting is sufficient to induce robust phase shifts, with no evidence of masking effects. A 6-hour light pulse was sufficient to re-entrain mosquitoes regardless of the timing of the pulse, and phase shifts were primarily driven by the offset time of the light pulse, indicating that light-offset acts as a major zeitgeber. Together, these findings challenge conventional assumptions about the timescale of circadian synchronization and highlight the remarkable plasticity of mosquito behavior in response to anthropogenic light. Eventually, these effects could explain the rapid adaptation of the species to urban environments and have potential consequences for disease transmission dynamics.

Elucidating the biological and molecular mechanisms that govern male fertility and mating behavior in mosquitoes is critical for optimizing genetic and sterile insect technique-based vector control strategies. Here, we examined age-related changes in male reproductive capacity in Anopheles culicifacies, using female egg output as an indirect indicator of male fertility. Our results demonstrated that male reproductive age follows a non-linear pattern of fertility. Morphometric analysis from emergence to day 13 post-eclosion revealed a strong correlation between seminal vesicle capacity and female fecundity, suggesting that age-dependent gonadal development directly influences reproductive potential. At the molecular level, we identified AcLITAF6 as a key regulator of male reproductive homeostasis. RNAi-mediated knockdown of AcLITAF6 impaired apoptosis-associated and phagocytic clearance, reduced sperm viability, and decreased female productive outcomes. Conclusively, we reveal a previously unrecognized role of LITAF in sperm quality control and male reproductive fitness, highlighting AcLITAF6 as a potential target for mosquito population suppression strategies.

Context Pumping stations pose a threat to fish globally through land use change, habitat fragmentation and entrainment risk, with the catadromous and critically endangered European eel particularly impacted. Objectives/methods Establish, model, assess and understand the present-day distribution of European eel and resident fishes in 152 pumping station catchments in a once extensive wetland (The Fens) using eDNA metabarcoding (855 samples over two and half years), with specific focus on anthropogenic influences on hydrological connectivity and habitat quality. A removal survey design maximised confidence in negative results while minimising time and consumable costs. Results Eel occurrence upstream of pumping stations was low (occupancy = 28.3%) and positively associated with catchment area, fish species richness and natural hydrological connectivity (gravity drainage or flooding) and negatively associated with distance from the tidal limit. Fish species richness replaced catchment area and improved model performance, potentially acting as a biotic indicator of habitat quality and connectivity. Pumped catchments with manually operated upstream water transfers had reduced eel presence, potentially linked to the direction of water flow or the timing of operation. By contrast, fish species richness increased in these catchments during summer, suggesting displacement into unsuitable long-term habitats. Physical habitat maintenance had no detectable effect on eel occurrence or fish species richness. Conclusions This study provides the first landscape-scale assessment of European eel distribution and drivers of occurrence in pumped river catchments. The highly novel and comprehensive insights have implications for European eel conservation as well as infrastructure and catchment management, including compliance with legislation (EC Regulation No. 1100/2007).

Extrafloral nectaries (EFNs) are a widespread plant defense mutualism trait and are highly convergent, appearing in hundreds of plant lineages worldwide. Here we investigate a report of possible EFNs in Erythranthe angulosa, a recently-described California wildflower. We integrate field observations, insect bioassays, an induction experiment, and microscopy to test for signatures of EFN function, finding no evidence that the distinctive axillary swellings produced by E. angulosa function as EFNs. We also uncovered two distinct morphs at the type locality of E. angulosa that diverge in the number of axillary swellings produced, as well as other shoot architecture traits such as stem thickness, leaf size, and branch number. Although the axillary swellings appear to not function as EFNs, they remain a compelling morphological variant within the yellow monkeyflowers that may perform storage or another unknown function.

Brettanomyces bruxellensis is a yeast species associated with diverse fermentation environments and characterized by extensive genetic diversity, including diploid, autotriploid, and allotriploid lineages resulting from independent hybridization events. These lineages are associated with distinct ecological niches and provide a framework for studying metabolic trait evolution in complex genomes. Nitrate assimilation is a relatively uncommon trait among yeasts and has been reported in B. bruxellensis, but its distribution and evolutionary history within the species remain poorly understood. Here, we combined phenotypic characterization of 151 strains with genomic analyses of 946 whole-genome sequences to investigate nitrate assimilation. Growth assays revealed that nitrate assimilation is widespread but unevenly distributed across genetic lineages, with some populations largely retaining the trait whereas others have frequently lost it. Genomic analyses identified extensive variation affecting the nitrate assimilation gene cluster composed of YNR1, YNI1, and YNT1. Nitrate assimilation was strongly associated with both gene copy number and predicted gene functionality, with nitrate-assimilating strains generally carrying more functional copies of the cluster. Leveraging the complex genomic architecture of the species, we independently analyzed primary and acquired genomes in allotriploid lineages and uncovered contrasting evolutionary trajectories following hybridization. While nitrate assimilation genes were generally maintained in primary genomes, acquired genomes showed a higher prevalence of gene loss and predicted loss-of-function variants, revealing asymmetric dynamics between subgenomes. Altogether, our results suggest that nitrate assimilation represents an ancestral trait that has been differentially maintained across B. bruxellensis lineages through a combination of copy number variation, gene degeneration, and genome-specific evolutionary dynamics. These findings provide new insights into how genome architecture and polyploid evolution shape the maintenance and loss of metabolic traits in an industrially relevant yeast species.

Plant cold acclimation emerges from coordinated adjustments in photosynthesis, primary metabolism, and intracellular carbon allocation. Yet, the regulatory role of subcellular metabolite compartmentation in natural variation of cold acclimation remains insufficiently understood. Here, we investigated four Arabidopsis thaliana accessions grown either individually or in bulk to determine how growth configuration and genotype shape the metabolism of sugars and organic acids during cold exposure. Using non-aqueous fractionation, we quantified plastidial, cytosolic, and vacuolar sugar pools alongside whole-cell carbohydrates, organic acids, enzyme activities, photosynthetic parameters, and stress markers. A neural-network classifier revealed that subcellular sugar distribution together with sugar amounts and organic acids provided the strongest discriminatory power among accessions, surpassing photosynthetic traits and enzyme activities. Our findings demonstrate that natural variation in cold acclimation is strongly determined by genotype-specific subcellular metabolite architectures, and that the cultivation strategy modulates these intracellular signatures. We conclude that subcellular compartmentation of metabolites represents a cellular control layer for natural variation of cold acclimation and resilience in Arabidopsis thaliana.

Animal mitochondrial rRNAs are commonly viewed as structurally reduced, yet sponge mt SSU rRNAs range from compact to highly expanded structures. Using nine conserved structural anchors, we compared 216 taxonomically resolved records from four classes and 22 orders, including 16 freshwater Spongillida and 200 marine sponges. Twelve homologous hypervariable substructures were coded as structural types, and their ordered combinations as composite types. We identified 38 structural types and 62 composite types across molecules ranging from 853 to 2,019 nt. Hexactinellida and freshwater Spongillida were each uniform for a distinct composite type but differed markedly in overall structure: hexactinellid mt SSU rRNAs were compact, whereas those of Spongillida were long and contained four to five candidate insertion regions. These results show that a conserved scaffold can accommodate extensive lineage-associated structural variation and provide a practical framework for comparing highly divergent mitochondrial rRNAs.

Protists play important roles in food chains and symbioses in soil and aquatic environments, displaying an enormous morphological and functional diversity. While most commonly found protist species are well known to science, our global-scale environmental DNA survey across soil, water, and sediments reveals dozens of novel, phylum-level phylogenetic lineages that remain to be characterized for basic morphology and function. A vast majority of these undescribed taxa occur in marine water and sediments, but some are common in soil. Most of these novel taxa have distinct substrate and habitat preferences and biogeographic patterns. To accord these lineages scientific agency and enable unambiguous scientific communication, we propose formal names for 150 species to phylum-level taxa from 25 deep lineages based on eDNA and rRNA gene long-read sequence information.

Across different modalities, signals play a core role in attracting mates and influencing mating success. In several non-human primate species, females produce calls during mating that are thought to promote male competition over receptive females. The extent to which social system characteristics modulate the function of copulation calls remains less clear. We studied copulation calls in wild Guinea baboons (Papio papio), who live in a multilevel society structured around units in which females associate and mate almost exclusively with a single male. We hypothesised that females use copulation calls as an indirect form of mate competition, with competition increasing in larger units. In addition, we hypothesised that females are more likely to mate again after calling. We analysed 6116 copulations between 2014 and 2025, involving 99 reproductively active females and 78 subadult and adult males. Females produced copulation calls in 72.7% of copulations, with large inter-individual variation. Neither unit size nor its interaction with the female's swelling size or the presence of simultaneously receptive females affected the probability of calling. A survival analysis with a subset of the data (2353 copulations) revealed no effect of calling on the latency to the next mating. Our results render the hypothesis that female Guinea baboons use calls in indirect mate competition unlikely. Yet, the probability of calling varied with sexual swelling size, suggesting that calls signal female fertility. Possibly, Guinea baboon copulation calls represent an evolutionary remnant, no longer under selective pressure, and can be considered index signals of female fertility.

Bacterial genome-wide association studies (GWAS) offer a powerful approach to identify the genetic basis of a trait measured in a set of sequenced isolates. As the number of sequenced isolates has grown, the limiting factor for GWAS has become phenotyping enough isolates to achieve statistical power. To overcome the need for large-scale phenotyping, we developed Bayesian Adaptive Sequential Sampling GWAS (BASS-GWAS), which couples Bayesian adaptive experimental design with a sparse regression model to select maximally informative isolates for phenotypic testing. BASS-GWAS efficiently recovered causal loci for three antimicrobial resistance traits in Neisseria gonorrhoeae, requiring many fewer phenotyped isolates than random sampling. We applied BASS-GWAS to discover variants enabling gyrBD429N-dependent cross-resistance to the novel topoisomerase inhibitors zoliflodacin and gepotidacin. After phenotyping fewer than 30 isolates, we identified and then validated both parCD86N and a gyrA-parE-based pathway as enabling cross-resistance. BASS-GWAS provides a practical and statistically principled solution for efficient bacterial GWAS.

Prions, once mainly studied for their pathogenic roles, are now gaining recognition as adaptive elements in microbial physiology. Over one-third of wild yeast isolates harbor prion proteins, yet their impact on host-microbe interactions remains poorly characterized. Given the ecological dominance of yeasts in the Drosophila mycobiome, we leveraged the Drosophila melanogaster-Saccharomyces cerevisiae system to investigate how the mycobiome-derived prion, [MRPL10+], modulates host physiology. We show that flies exposed to [MRPL10+] yeast exhibit significantly enhanced cold tolerance and increased locomotor activity. This effect persists with heat-killed yeast and diluted culture, suggesting a stable, potent bioactive factor. Using the genetically diverse Drosophila Global Diversity Lines (GDL), we identified natural variation in responsiveness to [MRPL10+] yeast. Genome-wide association and functional RNAi screening revealed a gut-brain signaling axis involving genes critical for digestion, intercellular communication, transcription regulation, and neural transmission. Notably, serotonin and octopamine pathways were essential for [MRPL10+]-induced changes in cold tolerance and locomotion, implicating neuromodulatory circuits in prion-mediated microbial signaling. Our findings establish a mechanistic link between a fungal prion and host metabolic and neural adaptation. This work provides the first genetic dissection of a prion-mediated host-microbe interaction, laying the groundwork for investigating beneficial prions in complex microbial communities and highlighting a new dimension of the mycobiomes influence on animal physiology.

Blumeria graminis f. sp. avenae (Bga), the causal agent of oat powdery mildew, is one of the most host-specialized members of the B. graminis species complex. Despite its agricultural importance, the lack of a high-quality reference genome has limited studies of host specialization, virulence evolution and comparative genomics in this pathogen. Here, we generated the first chromosome-scale genome assembly of Bga using an integrative approach combining long- and short-read sequencing, Hi-C scaffolding and transcriptome data. The Bga genome exhibits hallmark features of powdery mildew fungi, including extensive repeat content and low gene density. Comparative analyses revealed that genome expansion is primarily associated with historical transposable element proliferation rather than recent transpositional activity. Genome organization is consistent with a functionally stratified "one-speed" model, in which genes associated with pathogenicity, including predicted effectors and infection-responsive genes, are preferentially located in transposable element-rich regions characterized by reduced synteny conservation and extended intergenic spaces. In contrast, conserved genes are concentrated in compact genomic regions and maintain strong syntenic conservation across cereal-infecting formae speciales. Hi-C analyses demonstrated a highly structured chromatin architecture and revealed genome organization patterns associated with infection-related gene expression. Comparative genomic analyses indicated that host specialization in Bga is driven by localized diversification of a relatively small subset of genes rather than large-scale genome restructuring. These results provide the first high-quality genomic resource for Bga and offer new insights into the evolutionary mechanisms underlying host specialization in powdery mildew fungi.

Antibiotic-induced disruption of plant-associated microbiomes has the potential to alter host health beyond the directly exposed generation, yet whether the effects of dysbiosis are transmitted through the seed microbiome remains unknown. Here, we investigated the intergenerational impacts of streptomycin-induced dysbiosis in tomato (Solanum lycopersicum), demonstrated that seed microbiome transfer (SMT) restores progeny microbiome function and disease resistance, and characterized the underlying physiological and genetic mechanisms. Parental streptomycin exposure altered the composition of progeny rhizosphere bacterial communities, reduced expression of defense-associated genes, and increased susceptibility to Xanthomonas perforans. Suppression of immune gene expression was strongly associated with increased disease severity, indicating that parental dysbiosis impaired progeny plants ability to mount effective immune responses. Transfer of the seed microbiome from healthy plant donors partially restored rhizosphere community composition, reduced disease severity and recovered defense gene expression of three genes. Together, our findings demonstrated that antibiotic exposure microbiome disturbance generates intergenerational legacy effects that influence plant immunity and disease susceptibility and seed microbiome transfer can counteract this dysbiosis across generations.

Drug resistance emerges repeatedly in outbreaks of Candida fungal pathogens, but little is known about its origins or persistence. Here, we investigated the evolutionary processes shaping echinocandin resistance in Candida auris, a globally emerging and predominantly clonal fungal pathogen. Genome-wide association across over 600 isolates identified mutations in the {beta}-1,3-glucan synthase gene FKS1 as the most significant driver of resistance to an echinocandin drug. Ancestral reconstruction of this population traced shared resistance mutations among small groups typically consisting of 2-3 closely related isolates, but clusters could include up to 16 isolates. Nearly all resistant clusters consisted of isolates collected in the same year and region, consistent with local transmission. To further examine population-level selection, we measured adaptive signatures in FKS1 and the highly diverged paralog FKS2 across 22,000 genomes. This revealed excess nonsynonymous polymorphisms in FKS1, primarily due to independent, recurrent mutations at resistance hotspots, consistent with parallel evolution and incomplete fixation of adaptive alleles. In FKS2, there is no evidence of hotspots and little support for diversifying selection. Together, these results indicate that resistance mutations emerge under strong genetic constraint, with adaptation restricted to only one FKS homolog and predominantly at mutational hotspots.

Intertidal mudflats are low hydrodynamic energy environments hosting microphytobenthic communities that experience strong spatiotemporal variability in light regimes, including changes in spectral quality and light intensity that can lead to cellular photooxidative stress. To cope with these fluctuations, autotrophs exhibit diverse and highly plastic adaptations that are often species-dependent and shaped by their ecological niches. This study investigates photophysiological responses and metabolic remodeling in a diatom assemblage originating from a natural winter microphytobenthic biofilm under contrasting red and blue light intensities. To this end, photosynthetic parameters were monitored alongside changes in lipophilic metabolites, including untargeted lipids and lipophilic pigments. While few metabolites showed temporal remodeling, rapid and contrasting changes were observed within 30 minutes in response to both spectral quality and light intensity. Red light treatments induced broader remodeling of lipophilic metabolites than blue light, whereas blue light appeared to have a greater impact on photosynthetic parameters. Moreover, red light induced xanthophyll-cycle responses comparable to those observed under blue light at equivalent incident intensity. We discuss these metabolic responses in relation to diatom photoadaptive strategies, placing these findings within the intertidal environmental framework. This work further underlines the importance of understanding rapid metabolic plasticity in coping with light fluctuations, providing new insights into the photoregulatory strategies of natural microphytobenthic communities.

Diatoms are major contributors to marine primary production, yet current approaches for monitoring their abundance and function rely on coarse satellite chlorophyll estimates or sparse cell count and carbon fixation measurements. Molecular markers are a promising approach for high-resolution measurement of both abundance and metabolic activity through analysis of environmental DNA (eDNA) and RNA (eRNA). We present an isothermal quantitative recombinase polymerase amplification (qRPA) assay targeting rbcL gene copies and transcripts of marine diatoms, operating at low temperature and producing results in less than 15 min. We demonstrate specificity and calibration across diverse diatom taxa, then apply the assay to eDNA and eRNA samples from the Mare Chiara Long-Term Ecological Research site in the Bay of Naples, Italy, alongside microscopy, chlorophyll, physicochemical, and carbon-fixation data. Diatom rbcL DNA tracked abundance across five orders of magnitude despite seasonal shifts in community composition. Combining molecular and optical data revealed increased cellular rbcL copies and chlorophyll in low-light winter populations, suggesting enhanced photosynthetic capacity despite lower abundance. Furthermore, rbcL RNA reflected total carbon fixation rates and identified populations with differing carbon fixation activity. These results support rapid, RPA-based rbcL quantification as a robust approach for biomolecular ocean observing.