Differences in gut microbiome composition are linked with health, disease and ultimately host fitness; however, the molecular mechanisms underlying that relationship are not well characterized. Here, we modified the fish gut microbiota using antibiotic and probiotic feed treatments to address the effect of host microbiome on gene expression patterns. Chinook salmon (Oncorhynchus tshawytscha) gut gene expression was evaluated using whole transcriptome sequencing (RNA-Seq) on hindgut mucosa samples from individuals treated with antibiotic, probiotic and control diets to determine differentially expressed (DE) host genes. Fifty DE host genes were selected for further characterization using nanofluidic qPCR chips. We used 16S rRNA gene metabarcoding to characterize the rearing water and host gut microbiome bacterial communities. Daily administration of antibiotics and probiotics resulted in significant changes in fish gut and aquatic microbiota as well as more than 100 DE genes in the antibiotic and probiotic treatment fish, relative to healthy controls. Normal microbiota depletion by antibiotics mostly led to downregulation of different aspects of immunity and upregulation of apoptotic process. In the probiotic treatment, genes related to post-translation modification and inflammatory responses were up-regulated relative to controls. Our qPCR results revealed significant effects of treatment (antibiotic and probiotic) on rabep2, aifm3, manf, prmt3 gene transcription. Moreover, we found significant associations between members of Lactobacillaceae and Aeromonadaceae with host gene expression patterns. Overall, our analysis showed that the microbiota had significant impacts on many host signaling pathways, specifically targeting immune, developmental, and metabolic processes. Our characterization of some of the molecular mechanisms involved in microbiome-host interactions will help develop new strategies for preventing/ treating microbiome disruption-related diseases.

Foraging behaviours encompass strategies to locate resources and to exploit them. In many taxa these behaviours are controlled by a major gene called for, but mechanisms vary between species. In the parasitoid wasp Venturia canescens, sexual and asexual populations coexist in sympatry but differ in their foraging behaviours. Here we explored the molecular bases underpinning this divergence in foraging behaviours by testing two mutually non-exclusive hypotheses: firstly the divergence in the for gene results in difference in foraging strategies, and second this latter is due to a divergence in whole-genome expression. Using comparative genomics, we showed that the for gene was conserved across insects considering both sequence as well as gene model complexity. Polymorphism analysis did not support the occurrence of two allelic variants diverging across the two populations, yet asexual population exhibited less polymorphism compared to the sexual one. Sexual and asexual transcriptomes sharply split up, with 10.9% of differentially expressed genes, but these were not enriched in behavioural related genes. We showed that the for gene was more expressed in asexual female heads than in sexual ones, and that asexuals were the ones that explored more the environment and exploited more host patches. Overall, these results suggested that a fine tuning in the for gene expression between populations may have led to distinct foraging behaviours. We hypothesized that reproductive polymorphism and coexistence in sympatry of sexual and asexual populations specialized to different ecological niches via divergent optima on phenotypic traits, could imply adaptation through different expression patterns of the for gene and at many other loci throughout the genome.

The blacklegged tick, Ixodes scapularis, is a vector of Borrelia burgdorferi sensu stricto (s.s.), the causative agent of Lyme disease, part of a slow-moving epidemic of Lyme borreliosis spreading across the northern hemisphere. There are well-known geographic differences in the vectorial capacity of these ticks associated with genetic variation. Despite the need for detailed genetic information in this disease system, previous phylogeographic studies of these ticks have been restricted to relatively few populations or genetic loci. Here we present the most comprehensive phylogeographic study of I. scapularis conducted by using 3RAD and surveying 353 ticks from 33 counties throughout the range of I. scapularis. We found limited genetic variation among populations from the Northeast and Upper Midwest, where Lyme disease is most common, and higher genetic variation among populations from the South. We identify four genetic clusters of I. scapularis that are consistent with four major geographic regions, plus a distinct Central Florida group. In regions where Lyme disease is increasing in frequency, the I. scapularis populations genetically group with ticks from historically highly Lyme-endemic regions. Finally, we identify ten variable DNA sites that contribute the most to population differentiation. These variable sites cluster on one of the chromosome-scale scaffolds for I. scapularis and are within identified genes. Our findings illuminate the need for additional research to identify loci causing variation in the vectorial capacity of I. scapularis and where additional tick sampling would be most valuable to further understand disease trends caused by pathogens transmitted by I. scapularis.

Accumulating evidence for trade-offs involving metabolic traits has demonstrated their importance in evolution of organisms. Metabolic models with different level of complexity have already been considered when investigating mechanisms that explain various metabolic trade-offs. Here we provide a systematic review of modelling approaches that have been used to study and explain trade-offs between: (i) kinetic properties of individual enzymes, (ii) rates of metabolic reactions, (iii) rate and yield of metabolic pathways and networks, (iv) different metabolic objectives in single organisms and in metabolic communities, and (v) metabolic concentrations. In providing insights into mechanisms underlying these five types of metabolic trade-offs obtained from constraint-based metabolic modelling, we emphasize the relation of metabolic trade-offs to the classical black box Y-model that provides conceptual explanation for resource acquisition-allocation trade-offs. In addition, we identify several pressing concerns and offer a perspective for future research in the identification and manipulation of metabolic trade-offs by relying on the toolbox provided by constraint-based metabolic modelling for single organisms and microbial communities.

Trade-offs between traits arise and reflect constraints imposed by the environment and physicochemical laws. Trade-off situations are expected to be highly relevant for sessile plants, which have to respond to changes in the environment to ensure survival. Despite increasing interest in determining the genetic and molecular basis of plant trade-offs, there are still gaps and differences with respect to how trade-offs are defined, how they are measured, and how their genetic architecture is dissected. The first step to fill these gaps is to establish what is meant by trade-offs. In this review we provide a classification of the existing definitions of trade-offs according to: (1) the measures used for their quantification, (2) the dependence of trade-offs on environment, and (3) whether data based on which they are inferred are from a single individual across different environments or a population of individuals in single or multiple environments. We then compare the approaches for quantification of trade-offs based on phenotypic, between-individual, and genetic correlations, and stress the need for developing further quantification indices particularly for trade-offs between multiple traits. Lastly, we highlight the genetic mechanisms underpinning trade-offs and experimental designs that facilitate their discovery in plants, with focus on usage of natural variability. This review also offers a perspective for future research aimed at identification of plant trade-offs, dissection of their genetic architecture, and development of strategies to overcome trade-offs, with applications in crop breeding.

Environmental pollution can result in poor sperm quality either directly or indirectly. However, adaptive and compensatory sperm morphology change and motility improvement rapidly evolved in tree sparrow (Passer montanus) inhabited the polluted area within the past 65 years. To identify the genetic underpinnings of the rapidly evolved sperm phenotype, both the population genomic and transcriptomic methods were used in our study. We identified a gene encoding serine/threonine protein kinase PIM1 which may drive the rapid phenotypic evolution of sperm. An unprecedent and remarkably expansion of PIM gene family caused by tandem and segmental duplication of PIM1 was subsequently noticed in tree sparrow genome. Most of the PIM1 duplicates showed a testis-specific expression pattern, suggesting their functions related to male reproduction. Furthermore, the elevated expression level of PIM1 was consistent with our earlier findings of longer and faster swimming sperm in polluted site, indicating an important role of duplicated PIM1 in facilitating rapid evolution of sperm. Our results suggested that the duplicated PIM1 provide sources of genetic variation that enable rapid evolution of sperm under environmental heavy metal pollution. The findings in this study verified the duplicated genes can be targets of selection and predominant sources for rapid adaptation to environmental change and shed lights on the sperm evolution under environmental stress.

Invasive species can successfully and rapidly colonize new niches and expand ranges via founder effects and enhanced tolerance towards environmental stresses. However, the underpinning molecular mechanisms (i.e., gene expression changes) facilitating rapid adaptation to harsh environments are still poorly understood. The red seaweed Gracilaria vermiculophylla, which is native to the northwest Pacific but invaded North American and European coastal habitats over the last 100 years, provides an excellent model to examine whether enhanced tolerance at the level of gene expression contributed to its invasion success. We collected G. vermiculophylla from its native range in Japan and from two non-native regions along the Delmarva Peninsula (Eastern United States) and in Germany. Thalli were reared in a common garden for four months at which time we performed comparative transcriptome (mRNA) and microRNA (miRNA) sequencing. MRNA-expression profiling identified 59 genes that were differently expressed between native and non-native thalli. Of these genes, most were involved in metabolic pathways, including photosynthesis, abiotic stress, and biosynthesis of products and hormones in all four non-native sites. MiRNA-based target-gene correlation analysis in native/non-native pairs revealed that some target genes are positively or negatively regulated via epigenetic mechanisms. Importantly, these genes are mostly associated with metabolism and defense capability. Thus, our gene expression results indicate that resource reallocation to metabolic processes is most likely a predominant mechanism contributing to the range-wide persistence and adaptation of G. vermiculophylla in the invaded range. This study therefore provides a novel molecular insight into the speed and nature of invasion-mediated rapid adaption.

Photosymbiodemes are a special case of lichen symbiosis where one lichenized fungus engages in symbiosis with two different photosynthetic partners, a cyanobacterium and a green alga, to develop two distinctly looking photomorphs. We investigated differential gene expression in photosymbiodemes of the lichen Peltigera britannica at different temperatures representing mild and putatively stressful conditions and compared gene expression of thallus sectors containing cyanobacterial photobionts with thallus sectors with both green algal and cyanobacterial photobionts. Firstly, because of known ecological differences between photomorphs, we investigated symbiont-specific responses in gene expression to temperature increases. Secondly, we quantified photobiont-mediated differences in fungal gene expression. High temperatures expectedly led to an upregulation of genes involved in heat shock responses in all organisms in whole transcriptome data. As expected, the expression of genes involved in photosynthesis was increased in both photobiont types at 15 and 25 °C. The green algae exhibited thermal stress responses mainly at 25 °C, the fungus and the cyanobacteria already at 15 °C, demonstrating symbiont-specific responses to environmental cues and symbiont-specific ecological optima. Furthermore, photobiont-mediated differences in fungal gene expression could be identified, with upregulation of distinct biological processes in the different morphs, showing that interaction with specific symbiosis partners profoundly impacts fungal gene expression.

Symbiosis often occurs between partners with distinct life history characteristics and dispersal mechanisms. Many bacterial symbionts have genomes comprised of multiple replicons with distinct rates of evolution and horizontal transmission. Such differences might drive differences in population structure between hosts and symbionts and among the elements of the divided genomes of bacterial symbionts. These differences might, in turn, shape the evolution of symbiotic interactions and bacterial evolution. Here we use whole genome resequencing of a hierarchically-structured sample of 191 strains of Sinorhizobium meliloti collected from 21 locations in southern Europe to characterize population structures of this bacterial symbiont and its host plant Medicago truncatula. Sinorhizobium meliloti genomes showed high local (within-site) variation and little isolation by distance. This was particularly true for the two symbiosis elements pSymA and pSymB, which have population structures that are similar to each other, but distinct from both the bacterial chromosome and the host plant. The differences in population structure may result from among-replicon differences in the extent of horizontal gene transfer, although given limited recombination of the chromosome, different levels of purifying or positive selection may also contribute to among-replicon differences. Discordant population structure between hosts and symbionts indicates that geographically and genetically distinct host populations in different parts of the range might interact with genetically similar symbionts, potentially minimizing local specialization.

Any random genetic change is more likely to impair than improve fitness, a situation that owes to the fact that contemporary genotypes bear a history of having been shaped by natural selection for a very long time. Most mutations are thus deleterious and generate a genetic load that can be difficult to handle in small populations and increase the risk of extinction. We used functional annotation and evolutionary conservation scores to study deleterious variation in 200+ genomes from the highly inbred Scandinavian wolf population, founded by only three wolves and suffering from inbreeding depression, and neighboring populations in northern Europe. The masked load was high in Russia and Finland with deleterious alleles segregating at lower frequency than neutral variation. Genetic drift in the Scandinavian population led to the loss of ancestral alleles and fixation of deleterious variants. The per-individual realized load increased with the extent of inbreeding and reached several hundred homozygous deleterious genotypes in protein-coding genes, and a total of more than 50,000 homozygous deleterious genotypes in the genome. Arrival of immigrants gave a temporary genetic rescue effect with ancestral alleles re-entering the population and moving deleterious alleles into heterozygote genotypes. However, in the absence of permanent connectivity inbreeding has then again led to the exposure of deleterious mutations. These observations provide genome-wide insight into the character of genetic load and genetic rescue at the molecular level, and in relation to population history. They emphasize the importance of securing gene flow in the management of endangered populations.

The koala, one of the most iconic Australian wildlife species, is facing several concomitant threats that are driving population declines. Some threats are well known and have clear methods of prevention (e.g. habitat loss can be reduced with stronger land-clearing control), whereas others are less easily addressed. One of the major current threats to koalas is chlamydial disease, which can have major impacts on individual survival and reproduction rates, and can translate into population declines. Effective management strategies for the disease in the wild are currently lacking, and to date we know little about the determinants of individual susceptibility to disease. Here we used a rare opportunity to investigate the genetic basis of variation in susceptibility to chlamydia using one of the most intensively studied wild koala populations. We combine data from veterinary examinations, chlamydia testing, genetic sampling and movement monitoring. Out of our sample of 342 wild koalas, 60 were found to have chlamydia. Using genotype information on 8649 SNPs to investigate the role of genetic characteristics in determining disease status, we found no evidence of inbreeding depression, but a heritability of 0.14 (95%CI: 0.06 – 0.23) for the probability that koalas had chlamydia. Heritability of susceptibility to chlamydia could be relevant for future disease management in koalas, as it suggests the potential to select for disease resilience through assisted breeding.

With continued global change, recovery of species listed under the Endangered Species Act is increasingly challenging. One rare success was the recovery and delisting of the Channel Island fox (Urocyon littoralis) after 90-99% population declines in the 1990s. While their demographic recovery was dramatic, less is known about their genetic recovery. To address genetic changes we conducted the first multi-individual and population-level direct genetic comparison of samples collected before and after the recent bottlenecks. Using whole exome sequencing, we found that already genetically depauperate populations were further degraded by the 1990s declines and remain low, particularly on San Miguel Island which underwent one of the most severe bottlenecks. The three other islands that experienced recent bottlenecks (Santa Rosa, Santa Cruz, and Santa Catalina islands) showed mixed results based on multiple metrics of genetic diversity. Previous island fox genomics studies showed low genetic diversity before the declines and no change after the demographic recovery, thus this is the first study to show a decrease in genetic diversity over time in U. littoralis. Additionally, we found that divergence between populations consistently increased over time, complicating prospects for using inter-island translocation as a conservation tool. The Santa Catalina subspecies is now federally listed as threatened, yet other de-listed subspecies are still recovering genetic variation which may limit their ability to adapt to changing environmental conditions. This study further demonstrates that species conservation is more complex than population size and that some island fox populations are not yet “out of the woods”.

Adaptive genetic divergence occurs when selection imposed by the environment causes the genomic component of the phenotype to differentiate. However, genomic signatures of natural selection are usually identified without information on which trait is responding to selection by which selective agent(s). Here, we integrate whole-genome-sequencing with phenomics and measures of putative selective agents to assess the extent of adaptive divergence in threespine stickleback occupying the highly heterogeneous lake Mývatn, NE Iceland. We find negligible genome wide divergence, yet multiple traits (body size, gill raker structure and defense traits) were divergent along known ecological gradients (temperature, predatory bird densities and water depth). SNP based heritability of all measured traits was high (h2 = 0.42 – 0.65), indicating adaptive potential for all traits. Whilst environment-association analyses identified thousands of loci putatively involved in selection, related to genes linked to neuron development and protein phosphorylation, only allelic variation linked to pelvic spine length was concurrently linked to environmental variation (water depth) - supporting the conclusion that divergence in pelvic spine length occurred in face of gene flow. Our results suggest that whilst there is substantial genetic variation in the traits measured, phenotypic divergence of Mývatn stickleback is mostly weakly associated with environmental gradients, potentially as a result of substantial gene flow. Our study illustrates the value of integrative studies that combine genomic assays of multivariate trait variation with landscape genomics.

Pollination is a key step of plant reproduction, allowing individual plants to produce offspring as father, mother or both. However, few studies exist that consider together male and female pollination success. This implies studying both mating system, through paternity analyses, and seed set, by measuring the percentage of flowers giving a seed. Studying these two processes together is needed as they are not independent: gaining fitness advantage through one sex can incur fitness costs through the other due to various tradeoffs including direct sexual interference. Hence, we developed the first spatially explicit mixed-mating model integrating these two interactive processes, by coupling a mating model with a fruit set model, therefore jointly exploring pollen export and import. We used as model an insect-pollinated tree species, chestnut. We carried out a paternity analysis based on nearly exhaustive sampling of potential pollen donors in an intensively studied plot of 273 trees belonging to three interfertile chestnut species and including both male-fertile and male-sterile individuals. We collected a large dataset of 1924 mating events. We further performed fruit set measurements for 216 trees. Our process-based model predicts fruit set with great accuracy, but only if we account for self-pollen interference and associated ovule discounting, a form of sexual interference. This model represents an important step forward for fundamental pollination studies aiming at comprehensively exploring pollen emission, transport and reception in a single study, thus clarifying the consequences of pollination on male and female fitness.

Insects often harbor heritable symbionts that provide defense against specialized natural enemies, yet little is known about symbiont protection when hosts face simultaneous threats. In pea aphids (Acyrthosiphon pisum), the facultative endosymbiont Hamiltonella defensa confers protection against the parasitoid, Aphidius ervi, and Regiella insecticola protects against aphid-specific fungal pathogens, including Pandora neoaphidis. Here we investigated whether these two common aphid symbionts protect against a specialized virus A. pisum virus (APV), and whether their anti-fungal and anti-parasitoid services are impacted by APV infection. We found that APV imposed large fitness costs on symbiont-free aphids and these costs were elevated in aphids housing H. defensa. In contrast, APV titers were significantly reduced and costs to APV infection were largely eliminated in aphids with R. insecticola. To our knowledge, R. insecticola is the first aphid symbiont shown to protect against a viral pathogen, and only the second arthropod symbiont reported to do so. In contrast, APV infection did not impact the protective services either R. insecticola or H. defensa. To better understand APV biology, we produced five genomes and examined transmission routes. We found that moderate rates of vertical transmission, combined with horizontal transfer through food plants, were the major route of APV spread, although lateral transfer by parasitoids also occurred. Transmission was unaffected by facultative symbionts. In summary, the presence and species identity of facultative symbionts resulted in highly divergent outcomes for aphids infected with APV, while not impacting defensive services that target other enemies. These findings add to the diverse phenotypes conferred by aphid symbionts, and to the growing body of work highlighting extensive variation in symbiont-mediated interactions.

The blue shark Prionace glauca is a top predator with one of the widest geographic distributions of any shark species, yet classified as critically endangered in the Mediterranean Sea, and Near Threatened globally. Previous genetic studies did not reject the null hypothesis of a single global population across the worldwide species range. Blue shark situation was proposed as a possible archetype of the ‘grey zone of population differentiation’, coined to designate cases where population structure may be too recent or too faint to be detected using a limited set of markers. Here, blue shark samples collected throughout its global range were sequenced using a specific ddRAD method (DArTseq; Georges et al. 2018), which recovered 37,655 genome-wide single nucleotide polymorphisms (SNPs). Two main groups emerged, with Mediterranean Sea and Northern Atlantic samples significantly differentiated from the Indo-west Pacific samples. Significant pairwise FST values indicated further genetic differentiation within the Atlantic Ocean, and between the Atlantic Ocean and the Mediterranean Sea. Reconstruction of recent demographic history suggested the divergence between northern and southern oceanic populations emerged about 500 generations ago and revealed a drastic reduction in effective population size from a large ancestral population. Our results illustrate the power of high-density genome scans to detect population structure and reconstruct demographic history in highly migratory marine species. As the management of the blue shark fishery, either as target or as bycatch, does not account for this delineation, we strongly recommend that the results presented here be considered in future stock assessment and management plans.

Selection on quantitative traits by divergent climatic conditions can lead to substantial trait variation across a species range. In the context of rapidly changing environments, however, it is equally important to understand selection on trait plasticity. To evaluate the role of selection in driving divergences in traits and their associated plasticity within a widespread species, we compared molecular and quantitative trait variation in Populus fremontii (Fremont cottonwood) populations throughout Arizona. Using SNP data and genotypes from 16 populations reciprocally planted in three common gardens, we first performed QST-FST analyses to detect selection on traits and trait plasticity. We then explored the mechanistic basis of selection using trait-climate and plasticity-climate regressions. Three major findings emerged: 1) There was significant genetic variation in traits expressed in each of the common gardens and in the phenotypic plasticity of traits across gardens. 2) Based on QST-FST comparisons, there was evidence of selection in all traits measured; however, this result varied from no effect in one garden to highly significant in another, indicating that detection of past selection is environmentally dependent. We also found strong evidence of divergent selection on plasticity across environments for two traits. 3) Traits and/or their plasticity were often correlated with population source climate (R2 up to 0.77 and 0.66, respectively). This suggests that steep climate gradients across the Southwest have played a major role in shaping the evolution of divergent phenotypic responses in populations and genotypes now experiencing climate change.

Growing genetically resistant plants allows pathogen populations to be controlled and reduces the use of chemicals. However, pathogens can quickly overcome such resistance. In this context, how can we achieve sustainable crop protection? This crucial question has remained largely unanswered despite decades of intense debate and research effort. In this study, we used a bibliographic analysis to show that the research field of resistance durability has evolved into three subfields: (i) ‘plant breeding’ (generating new genetic material), (ii) ‘molecular interactions’ (exploring the molecular dialogue governing plant–pathogen interactions) and (iii) ‘epidemiology and evolution’ (explaining and forecasting of pathogen population dynamics resulting from selection pressure(s) exerted by resistant plants). We argue that this triple split of the field impedes integrated research progress and ultimately compromises the sustainable management of genetic resistance. After identifying a gap among the three subfields, we argue that the theoretical framework of population genetics could bridge this gap. Indeed, population genetics formally explains the evolution of all heritable traits, and allows genetic changes to be tracked along with variation in population dynamics. This provides an integrated view of pathogen adaptation, notably via evolutionary–epidemiological feedbacks. In this Opinion Note, we detail examples illustrating how such a framework can better inform best practice for developing and managing genetically resistant cultivars.