The evolution of genotypic parallelism under shared environmental conditions provides strong evidence for the role of natural selection. However, analyses typically examine genomic signatures of selection long after the putative selection event and only assess the repeatability of responses across spatial population replicates. This impedes our ability to attribute a particular response to a given selection pressure and to distinguish non-parallel responses caused by stochastic processes from those caused by local selection. As such, the consistency of natural selection over space and time is unknown, and the role of persistent local selection pressures is unclear. Here, we leveraged the natural bar-built estuary system of Santa Cruz, California, to examine the repeatability of seasonal genomic change in threespine stickleback (Gasterosteus aculeatus) over space and time. By comparing allele-frequency shifts that are shared across locations (spatial repeatability) with those that are shared across years within locations (temporal repeatability), we identified both spatially shared and local components of putative selection. We found that repeated seasonal outlier responses occurred more often than expected under a neutral null model. Although repeatability declined as the number of estuaries sharing an outlier increased, enrichment above neutral expectations increased with broader spatial sharing, particularly for outliers repeated across both years. While the precise outlier SNPs varied across years, estuary-specific patterns of responses were broadly consistent, suggesting an important role for local conditions. Together, our findings show that temporal sampling can reveal components of putative selection that would be missed from spatial comparisons alone. More broadly, they highlight the importance of examining repeatability over both space and time to understand the parallel and non-parallel components of adaptive genomic change.
Shifts in reproductive mode represent key evolutionary innovations that shape species' life histories and evolutionary trajectories. Species showing bimodal reproductive strategies with multiple independent origins offer a rare opportunity to gain insights into the adaptive processes and mechanisms underlying convergent traits. The fire salamander, Salamandra salamandra, is the only amphibian exhibiting intraspecific variation in reproductive mode across multiple independent reproductive shifts, enabling investigation of the transition between larviparity (females give birth to aquatic larvae) and pueriparity (females give birth to fully developed terrestrial juveniles) within a single species and across different timescales. Pueriparity is an adaptive innovation that skips the aquatic larval stage, allowing individuals to exploit habitats with no available water bodies. The fire salamander is larviparous across most of its range, but pueriparity has evolved independently at least three times: once in the early Pleistocene within S. s. bernardezi in the mountains of northern Spain, and more recently on two land-bridge islands (NW Spain) inhabited by S. s. gallaica. To identify candidate genes associated with these distinct reproductive modes, we compared gene expression profiles of the uterus and oviduct of pregnant females across two independent evolutionary transitions using RNA-sequencing. We detected shared changes in maternal gene expression among pueriparous S. s. bernardezi and S. s. gallaica relative to their larviparous counterparts, in addition to differences unique to each independent evolutionary transition. Functional enrichment analyses indicated that differentially expressed genes were associated with reproductive timing, angiogenesis, and maternal signalling, consistent with the phenotypic differences observed in the uterine environment and embryonic development between the two reproductive modes. This study represents an important first step towards understanding the genomic basis of the evolution of pueriparity in a remarkable bimodal reproductive system, and provides transcriptomic resources and candidate genes for future research into the genomic architecture underlying this poorly understood adaptive trait.
Understanding transmission routes of parasites and pathogens is critical for the development of control measures and mitigation of impacts on host populations. Trichomonas gallinae is a widespread parasite in columbids worldwide, and has emerged as a lethal disease in passerines, particularly finches. The postulated transmission route from columbids to passerines via spillover at shared resources has not yet been empirically tested. Here, we screen 363 birds (261 columbids and 102 non-columbids) in the UK and France for the presence and strain identity of T. gallinae. To quantify potential environmental transmission, we also screened 51 food and water resources common in farmland, at 12 sites over a 2-year period. We isolated T. gallinae parasites from 79% of columbids, 36% of non-columbids, and 39% of environmental resources. Prevalence of the Type A strain was more than double in birds sampled at fed sites compared to those at unfed sites. Strain composition was mirrored in columbids, passerines, and shared food and water resources, providing compelling evidence that T. gallinae, especially the Type A strain, is transmitted via these shared resources. T. gallinae was isolated from high density feeding resources (where supplementary food was provided) nearly three times as often as low density resources (natural areas of seed-providing vegetation), meaning that careful management of supplementary resources has the potential to reduce T. gallinae prevalence in wild bird populations. Further work needs to test practical means of achieving this, but ensuring any supplementary feeding is provided at low density is likely to be critical to reducing parasite transmission.
Soil physical structure is a critical determinant of agricultural landscape resilience, yet standard pedotransfer functions estimate soil hydraulic and structural properties using static abiotic variables, often overlooking the biological mechanisms that actively organize soil structure. This study evaluates the predictive power of multi-kingdom microbiome data (prokaryotes, fungi and microeukaryotes) for three key soil functions: soil organic carbon (SOC) stock, mean weight diameter (MWD) and macroporosity. Using a dataset of 2251 agricultural soil samples from Quebec, Canada, we benchmarked four machine learning algorithms (HGBR, RFR, XGBoost, SVR) and four data aggregation strategies. The integration of microbiome data with texture and climate variables achieved high peak predictive accuracy ( R 2 range: 0.70-0.82). Methodologically, high-resolution compositional approaches (ASV-level centered log-ratio) and kingdom-balanced absolute abundances consistently outperformed taxonomic or functional aggregations. The loss of predictive power at the family level indicates that traits governing soil physical modification are phylogenetically shallow and strain-specific. Interpretability analysis using Shapley Additive Explanations (SHAP) revealed a clear functional hierarchy in soil assembly. Specific prokaryotic and fungal features drove biochemical stabilization and physical scaffolding via the microbial carbon pump and structural enmeshment dynamics. In contrast, the architectural openness of macroporosity was fundamentally constrained by abiotic physical limits (e.g., texture). Within this physical framework, specific microbial taxa, including anaerobic bacteria and microeukaryotic amoebae, functioned not as active engineers, but as high-sensitivity bio-indicators of the resulting aeration and hydrological connectivity. These results define soil physical organization as a biologically mediated hierarchy rather than a passive geological byproduct. Consequently, we propose shifting from static pedotransfer functions to a dynamic biotransfer framework that leverages multi-kingdom omic signatures to monitor soil physical resilience and crop adaptation potential.
Genomic mechanisms of local adaptation must be highly responsive in geographic regions where climate is changing rapidly. The Levant region is a critical biodiversity hotspot and the distribution edge for many species, including the wild ancestor of domesticated barley. This region is under an accelerated desertification process, thus enforcing a rapid genomic response to the projected environmental changes. To elucidate the genomic basis of rapid local adaptation, we studied wild barley populations using an ecological-genetic sampling design that decouples environmental variation from demographic background. We collected and sequenced 300 wild barley individuals and evaluated the phenotypes of 3600 progeny plants over 3 years. Our genomic analyses revealed that local adaptation is associated with clusters of candidate genes forming haplotype blocks. These clusters are enriched with environment and stress responsive genes, including flowering time regulators, drought and heat responsive genes. We identified six candidate adaptive haplotype blocks which span 1-8 Mbp and are distributed across chromosomes 1H, 2H, 4H and 5H, each segregating as two major haplotypes. Additionally, we integrated over 2600 occurrence records into ecological and evolutionary modelling to assess the genomic vulnerability of populations to projected future climates. Our study identifies candidate genomic regions and environmental drivers of local adaptation in wild barley and highlights the advantage of haplotype blocks architecture in orchestrating an efficient response to rapid environmental change. We highlight the ecological factors most strongly associated with the observed evolutionary responses and provide insights and guidelines for biodiversity conservation and implementation of crop wild relatives in breeding.
Measuring inbreeding via runs of homozygosity (ROH) captures realized autozygosity and can infer inbreeding timing through ROH length. A growing body of literature links the proportion of the genome in ROH (FROH) to fitness outcomes across taxa, yet systematic synthesis has been lacking. Here, we conduct a systematic review and meta-analysis to quantify FROH-fitness associations, identify drivers of variation and derive conservation-relevant recommendations. Narrative synthesis of 44 studies revealed that inbreeding depression operates through multiple interconnected pathways (survival, maternal effects, disease susceptibility, reproduction). Critically, purging cannot be relied upon to eliminate inbreeding depression as substantial fitness costs persist even in historically small populations. Meta-analysis of 62 effect sizes revealed a significant negative association between genomic inbreeding and fitness across taxa (Fisher's z = -0.103, r = -0.10, p < 0.0001). Study group, whether wildlife, livestock or humans, explained 22.5% of variance, with wildlife showing strongest effects (6-fold stronger than humans). Survival traits showed the greatest sensitivity to the effects of ROH (r = -0.22). Additionally, ROH detection methodology significantly influenced effect sizes: comprehensive approaches (all ROH lengths) detected stronger depression (r = -0.18) than long-ROH-only analyses (r = -0.08, p = 0.008), indicating cumulative genetic load matters. Overall, results indicate significant but variable fitness associations with ROH, with effect magnitude depending on biological context and methodological approach. Comprehensive ROH-based approaches show promise as conservation monitoring tools, but limited wildlife studies, particularly for non-mammalian taxa, highlight an urgent need for standardized protocols and expanded empirical research.
Isolated populations are susceptible to decline through the accumulation of deleterious mutations and inbreeding depression. As a consequence of habitat alteration, isolated populations are also expected to become increasingly prevalent. Still, some isolated populations have evaded decline through the purging of deleterious mutations. Expanding our knowledge of the scenarios under which purging occurs could therefore improve conservation efforts. Although theoretical and captive studies suggest that genetic purging hinges on a population's demographic history, the factors that shape the probability of purging in natural populations are less resolved. Here, we infer demographic parameters and quantify genetic variation in four Canadian populations of beluga whale to gain insight into purging. In particular, we explore the dynamics of the Saint Lawrence Estuary (SLE), a population that shows signatures of genetic erosion. We find that the SLE has been isolated for hundreds of generations and has accumulated a high mutation load in the absence of purging. We also find evidence of inbreeding from throughout the history of the SLE, excluding the most recent generations. Among deleterious alleles in the SLE, we identify eight clusters unique to neonate mortality-four of which are associated with cellular responses to inorganic substances. Given industrial pollution in the SLE, this finding indicates a relationship between environment, genetic variation and neonate mortality. Our results suggest that the likelihood of purging in natural populations may be reduced when mutation load accumulates via sustained isolation, highlighting the importance of demographic history in shaping conservation risk.
Lichens are unique among symbiotic organisms because their distinctive features develop only through interactions between the partners and differ from the appearance of each partner when grown separately in culture. Traditionally, lichen phenotype has been assumed to be determined by the mycobiont; however, exceptions exist that challenge the universal validity of this rule. One example is the phenomenon of 'phantom phenotypes', where lichens with genetically indistinguishable mycobionts exhibit distinct morphologies, sometimes better explained by differences among other symbiotic partners. In previous work, we documented such a case in the Cladonia bellidiflora complex, a group of red-fruited macrolichens with striking morphological and ecological variation, in which photobiont identity corresponded more closely to phenotype than the mycobiont when studied using five molecular markers. Here, we investigate this phenomenon using restriction-site associated DNA sequencing (RADseq) of both fungal and algal symbionts, combined with Sanger sequencing of ITS rDNA and the actin locus of the photobiont. Our results indicate that recent fungal divergence, together with correlated photobiont differentiation, is associated with the observed phenotypic differentiation, highlighting the importance of sensitive methods in similar cases. Specifically, RADseq analyses revealed a clear split between C. bellidiflora and all sorediate taxa, including C. polydactyla and C. umbricola, which showed no genomic differentiation, supporting their recognition as a single species. Additionally, substrate preference, symbiont associations and dispersal strategy appear to have acted in parallel to shape diversification in this complex. Photobiont data revealed unexpected patterns: esorediate C. bellidiflora associated with narrow photobiont sets, whereas sorediate lineages harboured a broader photobiont pool.
Many endangered species have been rescued from the brink of extinction, yet their long-term viability remains uncertain due to the prolonged genetic consequences of severe bottlenecks. In particular, the combined effects of inbreeding and hybridization with closely related species remain poorly understood. Using a comparative conservation genomic framework, we investigated these issues in the Chinese crested tern (Thalasseus bernsteini), a critically endangered seabird once presumed extinct but which has increased to approximately 100 individuals over the past two decades and its close relative, the great crested tern (T. bergii). We demonstrate that the Chinese crested tern has experienced ongoing genetic erosion. Its prolonged population decline has intensified genetic drift and reduced the efficiency of purifying selection, resulting in genome-wide accumulation of highly deleterious mutations. Highly inbred individuals also carry significantly more homozygous deleterious mutations than less inbred individuals. In both species, runs of homozygosity (ROH) show a relative enrichment of moderately and weakly deleterious mutations. Even more concerning, we found an enrichment of moderately and weakly deleterious mutations in putatively introgressed regions in both species, suggesting that occasional hybridization may have facilitated the spread of deleterious variants and could potentially compromise long-term fitness. These findings highlight that severe bottlenecks have lasting genomic consequences and that both inbreeding and hybridization can increase the genetic vulnerability of small populations-underscoring the importance of management strategies that promote population growth and sustained genetic monitoring.
Understanding long-term phytoplankton community dynamics is essential for assessing ecological resilience and informing lake management under global change. However, centennial-scale patterns of phytoplankton dynamics remain poorly resolved due to the limited taxonomic resolution of traditional fossil-based paleoecological approaches. In this study, a combination of sedimentary DNA (sedDNA) and subfossil diatom analysis was used to investigate changes in the phytoplankton community over the past two centuries and associated sedimentary biogeochemical responses in Lake Xiliang, a subtropical lake in the Yangtze River Basin, China. The sedDNA data captured major shifts in both eukaryotic and cyanobacterial communities, revealing distinct ecological phases linked to human activities and regional climate warming. Under near-natural conditions with minimal human disturbance, phytoplankton communities typically exhibit low diversity and are characterized by oligotrophic taxa such as xanthophytes and Gyrosigma. After the 1930s, increases in epiphytic Staurosira and declines in tychoplanktonic Aulacoseira suggest reduced river-lake connectivity and weaker water-column turbulence following the construction of the Jinshui Sluice, likely facilitating macrophyte expansion. In recent decades, intensified anthropogenic pressures combined with regional warming have driven a shift toward more diverse phytoplankton assemblages enriched in cyanobacteria, reflecting elevated nutrient inputs and rising temperatures. The observed associations between phytoplankton community changes and sedimentary geochemical proxies suggest that phytoplankton dynamics may not only have responded to environmental change but also contributed to sedimentary biogeochemical cycling, particularly total organic carbon accumulation and calcium-related processes such as photosynthesis-induced carbonate precipitation. These findings illustrate long-term phytoplankton community dynamics and underscore the value of sedDNA for reconstructing ecological trajectories in lake ecosystems.
Adaptation to novel environments is often associated with behavioural changes, but how decision-making processes and their genetic underpinnings evolve during ecological divergence remains poorly understood. Human-modified environments provide an ideal context in which to investigate how species adjust their behaviours in response to altered ecological conditions. We used oviposition site selection in two incipient mosquito species segregating along gradients of anthropogenic disturbance to investigate how differences in sensory perception modulate behavioural shifts accompanying ecological divergence. Using two-choice assays, we tested oviposition preferences in 1046 gravid female mosquitoes from field and laboratory populations by offering a choice between water collected from natal and foreign natural breeding sites. We found that females of Anopheles gambiae, a species adapted to rural environments, preferentially oviposited in natal water and deposited 89% of their eggs in a single breeding site. In contrast, females of its sibling species, Anopheles coluzzii, which is adapted to urban environments, exhibited weaker natal-water preference and frequently distributed their egg clutches between multiple breeding sites. To assess the extent of chemosensory divergence between these cryptic species, we analyzed amino acid substitutions within odorant, ionotropic and gustatory receptor gene families using whole-genome sequencing data. Despite limited differentiation across the gene families overall, several loci implicated in the detection of carboxylic acids, amines and volatile compounds exhibited elevated genetic divergence between species. Our work suggests that shifts in decision making associated with ecological divergence between emerging species can arise prior to substantial differentiation throughout the genome or across chemosensory receptor gene families.
Divergence in migratory behaviour represents a striking and common axis of life-history variation in animals. Plastic changes in adult animals in preparation for migration are well known, but the differences in early development between migratory and non-migratory forms are not well documented. These differences might contribute to reproductive isolation because of the potentially substantial divergence in metabolism and physiology. Here we document substantial differences between migratory ecotypes in sarcomeric development and energetic pathways from immediately after hatching. On North Uist (Scottish Western Isles), migratory and non-migratory ('resident') three-spined stickleback (Gasterosteus aculeatus) ecotypes breed in sympatry in brackish lagoons, providing an ideal system for investigating early developmental and energetic strategies associated with migration. Using relative-quantitative proteomics, we compared protein abundance in migratory, resident and reciprocal hybrid crosses of the three-spined stickleback 2 days after hatching. Migratory stickleback exhibited higher abundance of muscle, metabolic and collagen-associated proteins, indicating early investment in growth and preparation for the energetic demands of migration and sustained swimming. In contrast, resident stickleback showed increased abundance of maternal provisioning proteins, delayed hatching and higher hatching success, consistent with a strategy of producing fewer but high-quality offspring. Hybrids generally exhibited intermediate protein abundances, but there was some evidence of negative transgression in proteins related to mitochondrial function which might contribute to reduced fitness through mitonuclear incompatibility. Together, these results reveal early biochemical differences consistent with divergent energy allocation and reproductive strategies between migratory and resident stickleback.
Urbanization has become one of the leading causes of habitat transformation affecting ecosystem functioning. However, the transcriptomic response to urbanization remains poorly understood. Here, we conducted a transcriptomic analysis along an urbanization gradient under different warming temperatures. We further explored the genes underlying phenotypic variation along an urbanization gradient using weighted gene co-expression network analysis (WGCNA). We collected adult females in eight ponds spanning an urbanization gradient (percentage of impervious surface) in Southern Poland and raised their larvae in growth chambers under three temperature treatments: current 22°C, + 3°C, and + 6°C above current temperature. When larvae reached the prefinal instar, they were phenotyped for traits related to development and size, and collected for a gene expression analysis. We found that 24 genes varied in expression along a continuous urbanization gradient and were related to proteolysis, extracellular organization and perception. In addition, some genes showed a significant interaction urbanization × temperature and were associated with detection of chemical stimulus and perception. The WGCNA revealed two gene modules associated with urbanization and some phenotype traits, especially with development time. Genes associated with phenotypic differentiation along the urbanization gradient were part of many different pathways including signal transmission, cell cycle and DNA repair. In conclusion, we demonstrated that the transcriptomic response along an urbanization gradient was context-dependent, here on temperature, suggesting that some genes responding to urbanization also exhibited thermal plasticity. Our work highlights the importance of urbanization in inducing phenotypic and gene expression changes in organisms.
Commensal mammals offer unique opportunities to study how human-mediated dispersal, admixture, and secondary contact shape genomic variation during range expansion, yet for one of the most successful invasive commensals globally, the western house mouse Mus musculus domesticus, invasion dynamics across Africa remain largely unexplored. Here, we present a large-scale population genomic analysis of 380 whole-genome sequences, including 303 newly sequenced low-coverage genomes, of which 216 are from 13 distinct African populations, enabling us to investigate how human-mediated dispersal and secondary contact with native species shape the genomic legacy of a commensal mammal invasion. Ancestry analyses reveal contributions from at least three major Eurasian source lineages contributing to African populations: an Iberian-West Asian lineage present in Morocco, Algeria, and Niger; a Mediterranean lineage represented in Tunisia; and a Northern European lineage dominant in West and Central Africa. Demographic inferences indicate both recent and ancient episodes of divergence and population contraction. In West and Central Africa, divergence times broadly overlap with European maritime expansion and colonial trade. In contrast, North African populations exhibit older coalescent signals, consistent with early participation in the western Mediterranean radiation. We also detect substantial introgression from the native Mus spretus into North African populations in regions of sympatry. Collectively, our results reveal that the African invasion of the house mouse was not a single demographic process but a mosaic of population-specific histories shaped by multiple introductions, shifting connectivity through time, admixture, and interspecific gene flow. These findings reinforce the importance of population-level perspectives in invasion genomics, especially for commensal mammals whose dispersal is closely tied to human movement, and establish the most extensive open genomic resource for wild African house mice.
Climate change is predicted to impact existing ecological systems, leading to a requirement to improve our understanding of environmental adaptation in plants, particularly for conservation and the development of environmentally tolerant crop varieties. Environmental association analyses (EAAs) are a group of landscape genomic methods for detecting genetic markers or genes associated with environmental factors and therefore provide a top-down approach of studying the genetics of environmental adaptation. Here we review 138 EAA studies in plants, revealing the large diversity of methods at each stage of the analysis, including marker filtering, EAA model selection, the significance criteria used, candidate gene selection and any downstream analyses conducted. Following this, we compared four frequently used EAA models using genetic data from a panel of traditional rice (Oryza sativa) varieties from Vietnam, revealing a greater proportion of significant markers for recent GWAS models (FarmCPU and BLINK) compared to single locus mixed linear models (MLM) and latent factor mixed models (LFMM). Between zero and 22 environmentally associated markers overlapped between models and several genes in proximity to these loci have putative links to abiotic factors. Overall, this highlights the challenges in comparing the results of EAA studies, particularly regarding applying the results to crop breeding for future climates.
The gut microbiome is a dynamic ecosystem wherein microbes can exert beneficial, neutral or harmful effects on their host organism. Previous research has supported a large role for the environment in shaping avian gut microbiome diversity, but host-specific factors that regulate gut microbiome variation remain elusive. In hybrid zones, genetic recombination shuffles divergent alleles among backcrossed individuals allowing associations between genomic regions and specific traits to be identified. In this study, we use an association mapping approach to investigate the contribution of host alleles in shaping gut microbiome composition. We collected samples from across the Yellow-rumped Warbler hybrid zone (Setophaga coronata coronata × S. c. auduboni), including from distantly allopatric sites. The narrow width of this hybrid zone suggests that selection acts against hybrids, although the source of that selection is unclear. We quantified gut microbiome variation using 16S amplicon sequencing and produced genome-wide sequence data for hosts to link warbler genotypes to microbiome traits. This study is one of the first to identify candidate genes underlying gut microbiome variation in wild passerines. Notably, candidate loci include genes with immune function, redox status and gene regulation functions; two genes overlap with candidate genes identified in another avian system. Genetic differentiation was weak among candidate loci, indicating that alleles associated with gut microbiome variation are shared between subspecies. Our analysis of microbiome variation across nearly the full breeding range of an avian species complex yields important insights on the genetic factors that shape symbiotic interactions in vertebrate systems.
Early-life environmental and genetic factors play key roles in shaping the fitness of individuals by influencing life-history traits. The impact of early life conditions is hypothesized to be reflected at the cellular level on telomere length. In many animal species, telomeres shorten with age and their length early in life is often related to individual life expectancy. It is therefore essential to understand the relative importance of environmental and genetic factors influencing telomere length during this early developmental period. In this study we determine the relative influence of environmental and genetic components on telomere length in Tree swallows (Tachycineta bicolor) across various environments. To do so, we used data from 518 nestlings across 176 broods, collected over 2 years in a population breeding in southern Québec (Canada). We found no effect of environmental conditions on telomere length but found that nestlings from larger broods tended to have slightly longer telomeres. Parent-offspring regressions revealed a significant and positive association between nestling rTL and that of their mothers. While the association was also positive for fathers-offspring, it was slightly weaker and not statistically significant. Heritability of telomere length estimated using an animal model ranged between 0.34 and 0.55. Our results suggest that telomere length of Tree swallow nestlings is influenced by the proximal environment (i.e., within a brood) and by a genetic component. These findings suggest that broader-scale environmental conditions might not directly affect nestlings at this stage.
Communication via aggregation pheromones is responsible for the behavioural and ecological characteristics of many species of weevils (Coleoptera). In insects, pheromones are detected by specialized odorant receptors (ORs), called pheromone receptors (PRs), which are usually highly expressed in olfactory sensory neurons localized in the antennae. Yet, PRs in Coleoptera remain understudied, which limits our understanding of their response characteristics and potential multiple evolutionary origins. In this study, we search for PRs in the American palm weevil, Rhynchophorus palmarum, a pest species that poses a major threat to oil palm and coconut production in the Americas, for which no PR responding to its aggregation pheromone (2E)-6-methyl-2-hepten-4-ol (rhynchophorol) has been characterized. Combining published RNA-seq data with new data generated in this study, we identified two ORs highly expressed in the weevil antennae that represent strong candidate aggregation PRs. Sequence-based binding pocket prediction revealed overall structural similarity between these two ORs, but amino acid differences were identified, suggesting functional divergence. Using the Xenopus oocyte heterologous expression system, we demonstrated that RpalOR32 displayed specificity and strong sensitivity to the aggregation pheromone rhynchophorol, with minor responses to several structurally related compounds, while RpalOR25 showed no responses to pheromones or host plant volatiles. The newly identified PR in R. palmarum appeared phylogenetically distant from the aggregation PR previously identified in the related species R. ferrugineus, confirming the independent origin of weevil PRs, even at the genus level.
The global movement of pests and pathogens can often be traced to human migratory activities that include the movement of agricultural crops. The causal agent of wheat powdery mildew, the ascomycete fungus Blumeria graminis f. sp. tritici (B. graminis f. sp. tritici), is internationally distributed and one of the most rapidly adapting phytopathogens. To investigate population genetic structure, diversity and migratory potential, reduced-representation sequencing was performed on a collection of 653 B. graminis f. sp. tritici isolates from 16 countries and 6 continents. Phylogenetic inference, clustering, and population differentiation analyses were conducted, along with gene-flow estimates based on an isolation-with-migration model. The analyses revealed that the global B. graminis f. sp. tritici population is genetically differentiated into (1) older populations from Eurasia that show high internal genetic diversity and admixture with one another, and (2) genetically less diverse populations that were founded in former European colonies. Notably, Brazilian strains were phylogenetically separated from those originating in countries with a shared history of British colonization. Low gene flow suggests that natural migration of virulent isolates from abroad is limited in the former colonies. In contrast, higher estimates of gene flow among Europe, China, and Russia suggest that migration may contribute to B. graminis f. sp. tritici adaptation to novel resistance sources within Eurasia.
The skin microbiome of humpback whales harbours diverse microbial communities that play a crucial role in host skin protection and environmental interaction. However, studies on cetacean skin microbiomes in the Southern Hemisphere focus on feeding grounds, with limited information on microbiome dynamics at breeding grounds and during migration across contrasting habitats. We characterised the skin microbiome of 46 humpback whales from two seasonal habitats: the Magellan Strait feeding ground and the Ecuadorian coast breeding ground, comparing age, sex, environmental conditions, and seawater. Amplicon sequencing of the 16S rRNA gene revealed no differences in alpha diversity, but habitat-specific compositional shifts were found. Psychrobacter was detected in both regions, with higher abundance in the feeding ground, while Tenacibaculum remained abundant across sites. Additional taxa exhibited habitat-specific patterns, including bacteria associated with thermal sensitivity and ultraviolet radiation-tolerance in the Magellan Strait, and lactic acid bacteria in Ecuador. Skin microbiomes were similar between age classes and sexes, but distinct from seawater. Our findings show that geographic and environmental factors, such as superficial seawater temperature and maximum ultraviolet B radiation, shape the skin microbiome of humpback whales, with certain taxa reflecting migratory behaviour across seasonal habitats.
