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How natural diversity is maintained is an evolutionary puzzle. Genetic variation can be eroded by drift and directional selection but some polymorphisms persist for long time periods, implicating a role for balancing selection. Here, we investigate the maintenance of a chromosomal inversion polymorphism in the seaweed fly Coelopa frigida . Using experimental evolution and quantifying fitness, we show that the inversion underlies a life-history trade-off, whereby each haplotype has opposing effects on larval survival and adult reproduction. Numerical simulations confirm that such antagonistic pleiotropy can maintain polymorphism. Our results also highlight the importance of sex-specific effects, dominance and environmental heterogeneity, whose interaction enhances the maintenance of polymorphism through antagonistic pleiotropy. Overall, our findings directly demonstrate how overdominance and sexual antagonism can emerge from a life-history trade-off, inviting reconsideration of antagonistic pleiotropy as a key part of multi-headed balancing selection processes that enable the persistence of genetic variation. Few studies empirically pinpoint how balanced polymorphisms are maintained. “Mérot et al”. identify an inversion polymorphism that is maintained in seaweed fly populations because of antagonistic pleiotropy that mediates a classic life history tradeoff between larval survival and adult reproduction.

Because significant global changes are currently underway in the Arctic, creating a large‐scale standardized database for Arctic marine biodiversity is particularly pressing. This study evaluates the potential of aquatic environmental DNA (eDNA) metabarcoding to detect Arctic coastal biodiversity changes and characterizes the local spatio‐temporal distribution of eDNA in two locations. We extracted and amplified eDNA using two COI primer pairs from ~80 water samples that were collected across two Canadian Arctic ports, Churchill and Iqaluit, based on optimized sampling and preservation methods for remote regions surveys. Results demonstrate that aquatic eDNA surveys have the potential to document large‐scale Arctic biodiversity change by providing a rapid overview of coastal metazoan biodiversity, detecting nonindigenous species, and allowing sampling in both open water and under the ice cover by local northern‐based communities. We show that DNA sequences of ~50% of known Canadian Arctic species and potential invaders are currently present in public databases. A similar proportion of operational taxonomic units was identified at the species level with eDNA metabarcoding, for a total of 181 species identified at both sites. Despite the cold and well‐mixed coastal environment, species composition was vertically heterogeneous, in part due to river inflow in the estuarine ecosystem, and differed between the water column and tide pools. Thus, COI‐based eDNA metabarcoding may quickly improve large‐scale Arctic biomonitoring using eDNA, but we caution that aquatic eDNA sampling needs to be standardized over space and time to accurately evaluate community structure changes. Despite the cold and well‐mixed coastal environment, eDNA composition was vertically heterogeneous, in part due to eDNA river inflow in the estuarine ecosystem, and differed between water column and tide pools. eDNA metabarcoding may quickly improve large‐scale Arctic biomonitoring, but we caution that water eDNA biomonitoring needs to be standardized over space and time to accurately evaluate community structure changes.

Amazonian blackwaters are extremely biodiverse systems containing some of Earth’s most naturally acidic, dissolved organic carbon -rich and ion‐poor waters. Physiological adaptations of fish facing these ionoregulatory challenges are unresolved but could involve microbially-mediated processes. Here, we characterize the physiological response of 964 fish-microbe systems from four blackwater Teleost species along a natural hydrochemical gradient, using dual RNA-Seq and 16 S rRNA of gill samples. We find that host transcriptional responses to blackwaters are species-specific, but occasionally include the overexpression of Toll-receptors and integrins associated to interkingdom communication. Blackwater gill microbiomes are characterized by a transcriptionally-active betaproteobacterial cluster potentially interfering with epithelial permeability. We explore further blackwater fish-microbe interactions by analyzing transcriptomes of axenic zebrafish larvae exposed to sterile, non-sterile and inverted (non-native bacterioplankton) blackwater. We find that axenic zebrafish survive poorly when exposed to sterile/inverted blackwater. Overall, our results suggest a critical role for endogenous symbionts in blackwater fish physiology. Amazonian blackwaters are acidic and physiologically-challenging, but are one of Earth’s most diversified ecosystems. This study revealed that fish survival in these hostile habitats depends on the colonization of their gills by endogenous blackwater Betaproteobacteria, with the potential to regulate host ionoregulatory processes.

Retaining sufficient genetic variation for both short and long-term sustainability is a chief aim of ex situ programs for threatened species. Conservation breeding and reintroduction programs exist but oftentimes little is known about the genetic variation of in situ or ex situ populations. We collected genetic samples from both wild and zoo populations of Canada’s most endangered anuran, the Oregon Spotted Frog ( Rana pretiosa ) to compare genetic diversity (observed and expected heterozygosity), inbreeding coefficients (F IS ), effective population sizes (Ne) and population structure using single-nucleotide polymorphisms (SNPs). We found low diversity in situ and lower diversity ex situ, with positive inbreeding coefficients indicating assortative mating in both wild and zoo populations. Ex situ breeding programs that allowed free mate choice retained more genetic variation compared to those where breeding groups were pre-determined. Mixed source zoo populations were less differentiated from their wild source populations than the latter were among themselves, indicating sufficient representation of wild populations in zoo populations. The patterns we uncover support continued collaboration of ex situ and in situ endeavours as supplementation will likely be required for the long-term viability of the very wild populations the zoos rely on for genetic sustainability.

Identifying the molecular basis of reproductive isolation among diverging lineages represents an essential step toward understanding speciation in natural populations. Postzygotic barriers can lead to hybrid breakdown, a syndrome that has been documented in several systems, potentially involving the reactivation of transposable elements. In northeastern North America, two lake whitefish lineages have repeatedly colonized postglacial lakes ∼12,000 years ago, and a dwarf limnetic species has evolved multiple times from the normal benthic species. Reproductive isolation is incomplete between them; viable hybrids can be generated in the laboratory but significant mortality occurs and is associated with a malformed phenotype in backcross embryos, thus revealing a hybrid breakdown syndrome. By means of RNA-seq analyses, the objective of this study was to determine which genes were misregulated in hybrids and rigorously test the hypothesis of transposable element reactivation. We compared the transcriptomic landscape in pure embryos, F1-hybrids, and healthy and malformed backcrosses at the late embryonic stage. Extensive expression differences consistent with previously documented adaptive divergence between pure normal and dwarf embryos were identified for the first time. Pronounced transcriptome-wide deregulation in malformed backcrosses was observed, with over 15% of transcripts differentially expressed in all comparisons, compared with 1.5% between pure parental forms. Convincing evidence of transposable elements and noncoding transcripts reactivation in malformed backcrosses is presented. We propose that hybrid breakdown likely results from extensive genomic incompatibilities, plausibly encompassing transposable elements. Combined with previous studies, these results reveal synergy among many reproductive barriers, thus maintaining divergence between these two young whitefish species.

Human activities induce direct or indirect selection pressure on natural population and may ultimately affect population's integrity. While numerous conservation programs aimed to minimize human‐induced genomic variation, human‐induced environmental variation may generate epigenomic variation potentially affecting fitness through phenotypic modifications. Major questions remain pertaining to how much epigenomic variation arises from environmental heterogeneity, whether this variation can persist throughout life, and whether it can be transmitted across generations. We performed whole genome bisulfite sequencing (WGBS) on the sperm of genetically indistinguishable hatchery and wild‐born migrating adults of Coho salmon (Oncorhynchus kisutch) from two geographically distant rivers at different epigenome scales. Our results showed that coupling WGBS with fine‐scale analyses (local and chromosomal) allows the detection of parallel early‐life hatchery‐induced epimarks that differentiate wild from hatchery‐reared salmon. Four chromosomes and 183 differentially methylated regions (DMRs) displayed a significant signal of methylation differentiation between hatchery and wild‐born Coho salmon. Moreover, those early‐life epimarks persisted in germ line cells despite about 1.5 year spent in the ocean following release from hatchery, opening the possibility for transgenerational inheritance. Our results strengthen the hypothesis that epigenomic modifications environmentally induced during early‐life development persist in germ cells of adults until reproduction, which could potentially impact their fitness.

The primary focus of medicinal cannabis research is to ensure the stability of cannabis lines for consistent administration of chemically uniform products to patients. In recent years, tissue culture has emerged as a valuable technique for genetic preservation and rapid multiplication of cannabis clones. However, there is concern that the physical and chemical conditions of the growing media can induce somaclonal variation, potentially impacting the viability and uniformity of clones. To address this concern, we developed Comparative Restriction Enzyme Analysis of Methylation (CREAM), a novel method to assess DNA methylation patterns and used it to study a population of 78 cannabis clones maintained in tissue culture. Through bioinformatics analysis of the methylome, we successfully detected 2,272 polymorphic methylated regions among the clones. Remarkably, our results demonstrated that DNA methylation patterns were preserved across subcultures within the clonal population, allowing us to distinguish between two subsets of clonal lines used in this study. These findings significantly contribute to our understanding of the epigenetic variability within clonal lines in medicinal cannabis produced through tissue culture techniques. This knowledge is crucial for understanding the effects of tissue culture on DNA methylation and ensuring the consistency and reliability of medicinal cannabis products with therapeutic properties. Additionally, the CREAM method is a fast and affordable technology to get a first glimpse at methylation in a biological system. It offers a valuable tool for studying epigenetic variation in other plant species, thereby facilitating broader applications in plant biotechnology and crop improvement.

Understanding the genetic architecture of economically important traits is essential for the design and implementation of efficient breeding programs. Here, we analysed 3,653 Eastern oysters ( Crassostrea virginica ) from 62 crossing groups and 307 full-sib families, all genotyped with a 200 K SNP array, to (i) estimate heritability and genetic correlations for six growth-related traits, (ii) detect quantitative trait loci (QTL) and candidate genes, and (iii) compare the accuracy of pedigree- (PBLUP) versus genomic-based (GBLUP) predictions across marker densities, selection strategies (physical distance (PD) versus linkage disequilibrium (LD) and phenotype-based genotyping strategies. SNP-based Heritabilities ranged from 0.33 to 0.56, and genetic correlations among traits exceeded 0.61, indicating strong pleiotropy. GWAS revealed a polygenic architecture with a shared QTL on chromosome 2; the top SNP explained ≤ 1.1% of phenotypic variance. Except for the 0.5 K LD panel—where PBLUP was more accurate—and the 1 K LD panel—where both methods performed similarly—GBLUP outperformed PBLUP in all scenarios, with the greatest advantage observed for physically spaced (PD) panels. The highest accuracy (0.80) was achieved with the full 100 K SNP set. GBLUP models required panels containing ≥ 0.5 K PD (accuracy ≥ 0.55) or ≥ 2 K LD (accuracy ≥ 0.56) to significatively surpass PBLUP predictions. Training sets built from extreme phenotypes boosted accuracy in small to intermediate sample sizes (e.g., 0.74 at n  = 1,500 with 5 K PD SNPs versus 0.53 under random sampling). These results provide novel insights into not only the genomic regions controlling growth in this species but also about the utility of PD-based SNP panels and balanced sampling designs for enhancing GS accuracy in C. virginica .

Accurate data characterizing species distribution and abundance are critical for conservation and management of aquatic resources. Inventory methods, such as gillnet surveys, are widely used to estimate distribution and abundance of fish. However, gillnet surveys can be costly in terms of material and human resources, may cause unwanted mortality in the fish communities being studied, and is subject to size and species selection bias. Detecting allochthonous DNA released by species in their environment (i.e., environmental DNA, hereafter eDNA) could be used as a noninvasive and less costly alternative. In this study, we directly compare eDNA metabarcoding and gillnets for monitoring freshwater fish communities in terms of species richness and relative species abundance. Metabarcoding was performed with the 12S Mifish primers. We also used species‐specific quantitative PCR (qPCR) for the most abundant species, the walleye (Sander vitreus), to compare estimated relative abundance with metabarcoding and gillnet captures. Water sample collection, prior to gillnet assessment, was performed on 17 sites in the hydroelectric impoundment of the Rupert River (James Bay, Canada), comparing two water filtration methods. After controlling for amplification biases and repeatability, we show that fish communities’ complexity is better represented using eDNA metabarcoding than previously recorded gillnet data and that metabarcoding read count correlates with qPCR (r = 0.78, p < .001) in reflecting walleye abundance. Finally, based on partial redundancy analysis, we identified alpha chlorophyll, pH, and dissolved oxygen as environmental variable candidates that may influence differences in fish relative abundance between metabarcoding and gillnets. Altogether, our study demonstrates that the proposed eDNA metabarcoding method can be used as an efficient alternative or complementary technique adapted to the biomonitoring of the fish communities in boreal aquatic ecosystems. We showed that eDNA metacording outperform gillnets survey to detect freshwater fish communities. Our results also suggest that eDNA metabarcoding can be used to infer fish abundance and biomass. Together, it suggest that eDNA is a usable tool for fish conservation and management.

During the early stages of speciation, interspecific gene flow may be impeded by deleterious epistatic interactions in hybrids, which maintain parental allelic combinations at the speciation genes. The resulting semipermeable nature of the barrier to interspecific gene flow provides a valuable framework to identify the genes involved in hybrid mortality or sterility, as well as the evolutionary mechanisms that initially caused their divergence. The two Atlantic eels Anguilla anguilla and A. rostrata are partially isolated sister species that naturally hybridize, but whose genetic basis of postzygotic isolation remains unknown. We collected high-throughput sequencing data from the transcriptomes of 58 individuals and discovered 94 genes showing differentially fixed mutations between species. Evidence for positive selection at nuclear diagnostic genes was obtained using multilocus extensions of the McDonald–Kreitman test with polymorphism data from each species. In contrast, mitochondrial protein-coding genes experienced strong purifying selection and mostly diverged at synonymous sites, except for the mt-atp6 gene, which showed an atypically high nonsynonymous to synonymous rate ratio. Nuclear-encoded protein interactors of the mt-atp6 gene in the ATP synthase complex were significantly overrepresented in the list of nuclear diagnostic genes. Further analysis of resequencing data showed that positive selection has operated at both the mt-atp6 gene and its nuclear interactor atp5c1. These findings suggest that a cytonuclear incompatibility caused by a disruption of normal ATP synthase function in hybrids contributes to partial reproductive isolation between European and American eels.