Genetic Diversity Research Articles

Plasticity, not genetics, shapes individual responses to thermal stress in non-native populations of the European green crab (Carcinus maenas).

Temperature is a major driver of individual performance in ectotherms, with this impact depending on stressor intensity and duration. Differences in individual response across temperature, time, and populations are shaped by the interplay between evolutionary adaptation and phenotypic plasticity. Some populations are able to thrive in novel and changing environments despite limited genetic diversity, raising the question of how plasticity and adaptation interact after significant genetic diversity loss. The European green crab (Carcinus maenas) is a textbook example of this phenomenon: invasive populations boast a broad thermal tolerance and exceptional thermal flexibility even after repeated genetic bottlenecks. Despite this loss of diversity overall, prior work has found a strong population-level association between variation at a specific extended genomic region (supergene), cold tolerance, and sea surface temperature. We conducted a series of three experiments using righting response to characterize sublethal thermal tolerance and plasticity in introduced green crab populations, then determined if these factors were associated with supergene genotype for individual adult crabs. Crabs showed signs of stress after exposure to a 30°C heat shock in one experiment. Interestingly, a second experiment exposing C. maenas to repeated 24-hour heat shocks showed that prior heat shock conferred beneficial plasticity during a subsequent event. The third experiment examined cold acclimation over multiple timepoints up to 94 hours. At 5°C, certain crabs exhibited an acclimatory response where righting slowed dramatically at first, and then gradually sped up after a longer period of cold exposure. Several crabs failed to right at 1.5°C, which could be indicative of dormancy employed to reduce energy consumption in colder conditions. There were no significant relationships between individual plasticity and supergene genotype in any experiment. Linking population-level genetic associations with individual-level physiology is complex, and reflects the impact of environmental conditions such as temperature throughout life history in shaping adult phenotype. Our results highlight the robust thermal tolerance and plasticity that adult green crabs maintain despite a substantial reduction in genetic diversity, and underscore the importance of probing population-level genotype-phenotype associations at the individual level.

Isolation effects and soil properties drive genetic differentiation in Ormosia microphylla populations.

The genetic characteristics of six wild populations of Ormosia microphylla were investigated and their soil properties were analyzed by using Hyper-seq sequencing technology. Based on the findings, targeted protection strategies are proposed. Genetic diversity analysis revealed moderate overall genetic diversity of O. microphylla populations, with the ZD showing the highest and the JX the lowest genetic diversity. Compared to the populations outside the tiankeng, the LY, located in a Karst tiankeng, exhibited lower genetic diversity. This reduced genetic diversity of LY was possibly influenced by the combined influence of selective pressures unique to the tiankeng environment as well as the founder effect. Genetic structure analysis further indicated that the optimal number of clusters for the six populations was K = 7. The LY exhibited a relatively pure genetic constitution, whereas the other populations exhibited more complex genetic structures. Phylogenetic analysis and assessments of genetic differentiation coefficients further demonstrated significant genetic distance of the LY from the other populations, with a high degree of differentiation. Overall, there was a significant level of genetic differentiation among the six populations. Soil analysis revealed that total organic content and Fe were significantly higher compared to other elements across the six populations. In addition, compared to other populations, the LY exhibited notable variations in soil characteristics, such as higher levels of Fe, K, TK, and Ca. Additionally, the pH of the soil harboring LY was neutral, whereas that of other populations was acidic. IBD analysis, after removing the LY, revealed that the outcomes changed from non-significant to significant, highlighting the critical role of the isolation effect of Karst tiankeng and geographical barriers in promoting genetic differentiation among populations. IBE analysis further indicated a significant impact of K and TK content in the soil on genetic differentiation between populations.

Genetic Diversity and Phylogenetic Relationships of Castor fiber birulai in Xinjiang, China, Revealed by Mitochondrial Cytb and D-loop Sequence Analyses

Castor fiber birulai is a subspecies of the Eurasian beaver that has a relatively small population size compared to other Castor subspecies. There is limited genetic research on this subspecies. In this study, mitochondrial cytochrome b (Cytb) and D-loop sequences were analysed in genetic samples obtained from 19 individuals residing in the Buergen River Basin, Xinjiang, China. The Cytb region presented a single haplotype, whereas three haplotypes were identified in the D-loop region. The genetic diversity within the Chinese population was low (D-loop Hd = 0.444; Pi = 0.0043), markedly lower than that observed in other geographical populations of C. fiber. Phylogenetic reconstructions and haplotype network analyses revealed substantial genetic differentiation between C. f. birulai and other Eurasian lineages (Fst > 0.95), supporting the status of C. f. birulai as a distinct evolutionary lineage. Although the genetic distance between the Chinese and Mongolian populations was relatively small (distance = 0.00269), significant genetic differentiation was detected (Fst = 0.67055), indicating that anthropogenic disturbances—such as hydraulic infrastructure and fencing along the cross-border Bulgan River—may have impeded gene flow and dispersal. Demographic analyses provided no evidence of recent population expansion (Fu’s Fs = 0.19152), suggesting a demographically stable population. In subsequent studies, we recommend increasing nuclear gene data to verify whether the C. f. birulai population meets the criteria for Evolutionarily Significant Unit classification, and strengthening cross-border protection and cooperation between China and Mongolia.

Circulated echovirus 18 strains in Guangdong Province and worldwide: A novel perspective on genetic diversity and recombination patterns

ABSTRACT Echovirus 18 (E18) has re-emerged as a global public health concern in recent years because of its association with severe neonatal systemic diseases that pose a risk of high mortality. The lack of effective intervention strategies for E18 infections is largely attributed to limited knowledge regarding molecular epidemiology and recombination patterns. In this study, we obtained seven full-length E18 sequences from infants in Guangdong Province and combined them with representative sequences from GenBank. Using this expanded dataset, we analysed the molecular epidemiological features, genetic characteristics, and recombination patterns of E18. Global statistics reveal a distinct double-peak pattern in the frequency of E18 infections throughout the year in the Northern Hemisphere. All strains isolated from clinical specimens were classified as genotype C2, which has emerged as the predominant circulating strain in Guangdong Province and globally. Several potential recombination events with E30 were identified among these seven strains, particularly in the P2 and P3 non-structural regions. This study offers new insights into the global dissemination, genetic diversity, and phylodynamics of E18, potentially providing valuable information for designing antiviral vaccines and the implementation of sustainable surveillance strategies to enhance virus prevention and control during public health crises.

Genetic Diversity Study in Tomato (Solanum lycopersicum L.) Discovered by Simple Sequence Repeats (SSR) Markers

Tomato (Solanum lycopersicum L.) is a globally important vegetable crop and enhancing its genetic diversity is critical for developing improved cultivars. This study evaluated the genetic diversity among eight tomato genotypes DVRT 2, IIHR 335, ATL 17-06, GAT 5, GAT 8, ATL 18-04, NTL 12-02 and GP 11 using 15 polymorphic Simple Sequence Repeat (SSR) markers out of 47 screened. A total of 87 alleles were detected, with an average of 6.00 alleles per locus, indicating substantial polymorphism. Major allele frequency ranged from 0.062 to 0.167, averaging 0.135, suggesting balanced allele distribution. The PIC values ranging from 0.501 to 0.845 demonstrated high genetic variability. Particularly, SSR287, SSR598 and TES856 were identified as highly informative markers with PIC values above 0.8. Cluster analysis grouped the genotypes into three main clusters, with genetic distances ranging from 0.67 to 1.00. DVRT 2 exhibited the highest divergence (1.00). The findings underscore a wide genetic base among the genotypes, offering valuable insights for future breeding programs aimed at improving yield potential, stress resilience and nutritional quality in tomato.

Genetic structure and microsatellite-based genetic variation influenced by habitat fragmentation in pudu deer (Pudu puda) from southern Chile

Landscape alterations have strong impacts on the distribution of genetic variation within and between populations, and understanding these effects can provide insights for design conservation strategies. We analyzed 20 georeferenced individuals of pudu deer (Pudu puda) of three populations from southern Chile to obtain genetic diversity and distance parameters based on five polymorphic microsatellite loci. The genetic population structure was assessed by using STRUCTURE 2.3.4 and the effective population sizes (Ne) with NeEstimator 2.0 software. Habitat fragmentation metrics were also analyzed to correlate these data with the genetic variation focused to assess the effect of native forest fragmentation on the genetic structure of pudu deer. The mean number of alleles ranges from 2.8 to 4.2, while the mean number of private alleles ranged from 0.4 to 1.2. The mean observed heterozygosity ranged from 0.423 to 0.547. All populations displayed significant deficits of heterozygotes (FIS = 0.091-0.189, P < 0.0001). The FST on the whole populations and loci was low (mean FST = 0.0942) and without statistical significance (P > 0.05), indicating no genetic differentiation among populations. The STRUCTURE analysis did not reveal a population structure, and the NeEstimator found a markedly low Ne in a population compared to other analyzed populations. Multiple regression analysis indicates that two fragmentation metrics, namely, the proportion of the landscape covered by forest (PLAND) and the patch density (PD), negatively and significantly affected the number of alleles per locus as well as the observed heterozygosity (PLAND, β = -0.8740, P < 0.05; PD, β = -0.6594, P < 0.05). This result suggests that a greater degree of habitat fragmentation contributes to a decrease in genetic variation of pudu deer. Therefore, maintaining the native forest continuity across the distribution range of pudu deer could contribute to preserving the genetic diversity, enhancing the long-term survival of this mammal.

Estimation of Genetic Variability and Trait Association for Yield and Yield Related Traits of Chilli (Capsicum annuum L.)

The selection of superior traits in plants is a key component of natural selection. Genetic diversity in plant populations is one of the fundamental drivers of natural selection and serves as a valuable resource for crop improvement through trait selection. The present experiment was conducted on chilli (Capsicum annuum L.) during the autumn–winter season of 2024–2025, with the primary objective of assessing the genetic variability, heritability (in the broad sense), and genetic advance as a percentage of mean among chilli genotypes. The experimental material consisted of 35 genotypes, including a check variety (Kashi Anmol), laid out in a Randomized Complete Block Design (RCBD) with three replications. Observations were recorded for thirteen quantitative traits. Among all the traits, the highest phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) were observed for ascorbic acid content (39.13% and 37.48%, respectively), followed by average fruit weight (35.45% and 31.86%), fruit yield per plant (34.54% and 31.84%), fruit length (28.11% and 22.83%), and plant height (22.65% and 19.45%). Heritability (in the broad sense) estimates ranged from 24.56% (in days to mature red ripe stage) to 98.18% (in ascorbic acid content). High heritability was recorded for ascorbic acid (98.18%), followed by fruit yield per plant (94.37%), pedicel length (90.00%), average fruit weight (88.68%), fruit length (88.00%), number of fruits per plant (79.89%), and plant height (74.90%). Based on these findings, it can be concluded that there exists substantial genetic variability within the studied chilli genotypes. The high heritability coupled with high genetic advance for key traits such as ascorbic acid content, fruit yield, and fruit size indicates that selection would be effective and genetic improvement through breeding is feasible. Therefore, there is ample scope for successful crop enhancement aimed at improving yield and yield-attributing traits in the current chilli germplasm.

Uncovering genetic diversity and admixture of British Africans with HLA alleles inferred from whole genome sequencing.

The human leukocyte antigen (HLA) region is highly diverse and plays a crucial role in immune regulation and antigen presentation. Accurate HLA typing is essential for understanding disease susceptibility, transplantation compatibility, and pharmacogenetics. However, its application in African descent populations is challenging due to complex linkage disequilibrium patterns and the lack of ancestry-matched populations in HLA reference panels. Here, we leveraged the latest whole-genome sequencing (WGS) data from UK Biobank African individuals to perform better HLA genotyping, and further utilized allelic and haplotypic data to explore population genetics patterns of this region. With WGS-inferred HLA alleles, we identified specific admixture patterns (predominant West and East African and minor European ancestries) within British African population, revealing their complex evolutionary history. Not only did we reveal the genetic diversity within this population, but also highlighted its differences from African Americans, ancestral Africans, and other global populations. We further identified regional ancestry differences in the HLA genomic region, highlighting discordance between global and local admixture estimates. British Africans also presented unique HLA frequency distributions for both typical and disease-associated alleles or haplotypes. These findings emphasize the need for expanding African-specific HLA reference panel and prove better HLA typing can be achieved by coupling sequencing technologies with computational approaches. The HLA genetic characteristics observed in British Africans provide valuable insights into population-specific immune responses and susceptibility. Overall, this study advances our understanding of HLA diversity and genetic admixture in British African population, with important implications for both disease mechanism and clinical utility.

Genetic Diversity and Phylogenetic Analysis Among Multidrug-Resistant Pseudomonas spp. Isolated from Solid Waste Dump Sites and Dairy Farms

The excessive use of antimicrobials drives the emergence of multidrug resistance (MDR) in bacterial strains, which harbor resistance genes to survive under diverse drug pressures. Such resistance can result in life-threatening infections. The predominance of MDR Pseudomonas spp. poses significant challenges to public health and environmental sustainability, particularly in ecosystems affected by human activities. Characterizing MDR Pseudomonas spp. is crucial for developing effective diagnostic tools and biosecurity protocols, with broader implications for managing other pathogenic bacteria. Strains were diagnosed through 16S rRNA PCR and sequencing, complemented by phylogenetic analysis to evaluate local and global evolutionary connections. Antibiotic susceptibility tests revealed extensive resistance across multiple classes, with MIC values surpassing clinical breakpoints. This study examined the genetic diversity, resistance potential, and phylogenetic relationships among Pseudomonas aeruginosa strain DG2 and Pseudomonas fluorescens strain FM3, which were isolated from solid waste dump sites (n = 30) and dairy farms (n = 22) in West Bengal, India. Phylogenetic analysis reveals distinct clusters that highlight significant geographic linkages and genetic variability among the strains. Significant biofilm production under antibiotic exposure markedly increased resistance levels. RAPD-PCR profiling revealed substantial genetic diversity among the isolates, indicating variations in their genetic makeup. In contrast, SDS-PAGE analysis provided insights into the protein expression patterns that are activated by stress, which are closely linked to MDR. This dual approach offers a clearer perspective on their adaptive responses to environmental stressors. This study underscores the need for vigilant monitoring of MDR Pseudomonas spp. in anthropogenically impacted environments to mitigate risks to human and animal health. Surveillance strategies combining phenotypic and molecular approaches are essential to assess the risks posed by resilient pathogens. Solid waste and dairy farm ecosystems emerge as critical reservoirs for the evolution and dissemination of MDR Pseudomonas spp.

An expert-curated dataset on cave-dwelling spider communities in the Western Italian Alps –an open tool for eco-evolutionary research

Biodiversity data is essential for eco-evolutionary research. However, data is often scarce for difficult-to-study ecosystems, such as caves and other subterranean environments. Here, we present a taxonomically and geographically consistent database of subterranean spiders from the Italian Western Alps, a coherent biogeographical region with a long history of subterranean fauna diversification. The database (https://doi.org/10.6084/m9.figshare.28524383.v1) comprises 370 geo-referenced subterranean sites (caves, mines, and other artificial subterranean systems). For each site, we provide information on the composition of the spider community (with species richness ranging from 1 to 8 species per site), along with local geomorphological and site features. Collectively, these communities account for 31 unique species and 945 unique geo-referenced occurrence records, which are made available via the Global Biodiversity Information Facility (GBIF: https://www.gbif.org/dataset/72eef995-01bd-44f2-937a-23dbfe66283d). In addition to the database, we provide a phylogeny for all species based on the cytochrome c oxidase subunit I (COI) gene fragment. This, combined with the interoperability of the European subterranean spider trait database (doi: 10.6084/m9.figshare.16574255.v2), enables the estimation of taxonomic, functional, and genetic diversity within these subterranean communities. We illustrate the utility of this database by estimating and mapping taxonomic, functional, and genetic richness across the Western Italian Alps, providing a comprehensive multi-dimensional view of subterranean spider biodiversity. Although restricted in geographical scope, we envision this database as a promising open resource for eco-evolutionary research and hope the broader scientific community will widely use it. Indeed, the joint availability of distribution data, traits, and phylogenetic information allows quantifying ecologically relevant differences among species, identifying functionally unique taxa, and assessing patterns of adaptation and specialization in subterranean environments, among many other questions.

Chromosome-level genome assembly of Elaeocarpus petiolatus (Elaeocarpaceae).

Elaeocarpus petiolatus is an ecologically and economically important species in tropical and subtropical forests. Despite its significance, the lack of genomic resources has hindered research on the genetic diversity and adaptive traits of E. petiolatus. To address this gap, we present a comprehensive chromosome-level genome assembly of E. petiolatus generated using advanced PacBio high-fidelity (HiFi) long-read sequencing and Hi-C technology. The assembly spans 322.45 Mb, with a scaffold N50 of 20.58 Mb, indicating that 37.11% of the genome is composed of repetitive elements. We identified 25,295 protein-coding genes, of which 96.74% were functionally annotated. This high-quality genome provides a critical resource for understanding the genetic mechanisms underlying environmental adaptability and biosynthesis of bioactive compounds in E. petiolatus, thereby supporting conservation efforts and sustainable forest management. The assembled genome and associated sequencing data are publicly available, facilitating further evolutionary and functional studies on the Elaeocarpaceae family.

A Solution Method for Non-Linear Underdetermined Equation Systems in Grounding Grid Corrosion Diagnosis Based on an Enhanced Hippopotamus Optimization Algorithm

As power grids scale and aging assets edge toward obsolescence, grounding grid corrosion has become a critical vulnerability. Conventional diagnosis must fit high-dimensional electrical data to a physical model, typically yielding a nonlinear under-determined system fraught with computational burden and uncertainty. We propose the Enhanced Biomimetic Hippopotamus Optimization (EBOHO) algorithm, which distills the river-dwelling hippo’s ecological wisdom into three synergistic strategies: a beta-function herd seeding that replicates the genetic diversity of juvenile hippos diffusing through wetlands, an elite–mean cooperative foraging rule that echoes the way dominant bulls steer the herd toward nutrient-rich pastures, and a lens imaging opposition maneuver inspired by moonlit water reflections that spawn mirror candidates to avert premature convergence. Benchmarks on the CEC 2017 suite and four classical design problems show EBOHO’s superior global search, robustness, and convergence speed over numerous state-of-the-art meta-heuristics, including prior hippo variants. An industrial case study on grounding grid corrosion further confirms that EBOHO swiftly resolves the under-determined equations and pinpoints corrosion sites with high precision, underscoring its promise as a nature-inspired diagnostic engine for aging power system infrastructure.

First interspecific multi-parent advanced generation inter-cross (MAGIC) population in Capsicum peppers: development, phenotypic evaluation, genomic analysis, and prospects

Abstract This work presents the first eight-way multi-parental advanced generation inter-cross (MAGIC) population in pepper. This interspecific MAGIC population was built with six Capsicum annuum accessions and two C. chinense accessions, selected for encompassing a representative and wide genetic diversity, and being complementary for morphological, agronomic, and fruit quality traits. The population in its third selfing generation has been phenotyped with reliable descriptors and genotyped using genotyping-by-sequencing (GBS) to assess its overall diversity, homozygosity, parental contributions, and genetic structure. A great variability was found in the phenotyping study, showing many forms of recombination of all the founder lines. Even more, new phenotypic combinations were found, as well as transgressive inheritance in quantitative traits. The S3-generation contained a balanced distribution of the parental genomes and each S3-individual seemed to contain a unique genomic combination of the founder lines reaching a high homozygosity. In this regard, a preliminary genome-wide association study (GWAS) was performed for highly heritable traits to evaluate the potential of this population for future breeding prospects. Strong associations were found for most traits analysed, like stem pubescence and fruit colour at maturity stage, with associated genes related to response to stress and defence functions; or fruit wall consistency, with associated genes related to lipid metabolism. Our results show that this first Capsicum MAGIC population is a valuable genetic resource for research and breeding purposes in peppers, by identifying genomic regions associated to traits of interest and its potential for future GWAS in more complex agronomical and fruit quality traits.

Exploring Meiotic Recombination and Its Potential Benefits in South African Beef Cattle: A Review

Meiotic recombination is a key evolutionary process that generates novel allele combinations during prophase I of meiosis, promoting genetic diversity and enabling the selection of desirable traits in livestock breeding. Although its molecular mechanisms are well-characterised in model organisms such as humans and mice, studies in African indigenous cattle, particularly South African breeds, remain scarce. Key regulators of recombination, including PRDM9, SPO11, and DMC1, play essential roles in crossover formation and genome stability, with mutations in these genes often linked to fertility defects. Despite the Bonsmara and Nguni breeds’ exceptional adaptability to arid and resource-limited environments, little is known about how recombination contributes to their unique genetic architecture and adaptive traits. This review synthesises the current knowledge on the molecular basis of meiotic recombination, with a focus on prophase I events and associated structural proteins and enzymes. It also highlights the utility of genome-wide tools, particularly high-density single nucleotide polymorphism (SNP) markers for recombination mapping. By focusing on the underexplored recombination landscape in South African beef cattle, this review identifies key knowledge gaps. It outlines how recombination studies can inform breeding strategies aimed at enhancing genetic improvement, conservation, and the long-term sustainability of local beef production systems.

Hepatitis E Virus (HEV) Infection in the Context of the One Health Approach: A Systematic Review

Hepatitis E virus (HEV) is a pathogen that has caused various epidemics and sporadic localized cases. It is considered to be a public health problem worldwide. HEV is a small RNA virus with a significant genetic diversity, a broad host range, and a heterogeneous geographical distribution. HEV is mainly transmitted via the faecal–oral route. However, some animals are considered to be natural or potential reservoirs of HEV, thus elucidating the zoonotic route of transmission via the environment through contact with these animals or consumption of their by-products. Other routes of human-to-human transmission are not negligible. The various human–animal–environment entities, taken under one health approach, show the circulation and involvement of the different species (mainly Paslahepevirus balayani and Rocahepevirus ratti) and genotypes in the spreading of HEV infection. Regarding P. balayani, eight genotypes have been described, of which five genotypes (HEV-1 to 4 and HEV-7) are known to infect humans, while six have been reported to infect animals (HEV-3 to HEV-8). Furthermore, the C1 genotype of the rat HEV strain (HEV-C1) is known to be more frequently involved in human infections than the HEV-C2 genotype, which is known to infect mainly ferrets and minks. Contamination can occur during run-off, flooding, and poor sanitation, resulting in all of these genotypes being disseminated in the environment, contaminating both humans and animals. This systematic review followed the PRISMA guidelines and was registered in PROSPERO 2025 CRD420251071192. This research highlights the importance of investigating the transmission routes and major circulating HEV genotypes in order to adopt a holistic approach for controlling its emergence and preventing future outbreaks. In addition, this article outlines the knowledge of HEV in Africa, underlining the absence of large-scale studies at the environmental, human, and animal levels, which could improve HEV surveillance on the continent.

Beyond sweetness: Rethinking the use and conservation of Stevia rebaudiana’s plant genetic resources for breeding

Abstract This work analyses the genetic potential of Stevia rebaudiana beyond its sweetening properties, aiming to reassess its conservation and utilization in breeding programmes. This focus is justified by the growing global demand for natural sweeteners and the challenges posed by extreme weather events and diseases affecting crop yield and quality. The relationship between the species’ genetic diversity and its response to biotic and abiotic stresses is explored, as well as the limitations of current conservation and breeding strategies. Findings reveal underutilized genetic resources, limited integration of genomic tools in breeding efforts and a lack of robust in situ conservation initiatives. Genotypic variability has been observed in response to diseases such as Septoria leaf spot, while abiotic factors, including salinity and drought, can significantly influence steviol glycoside content. It is concluded that an integrated approach, combining dynamic conservation, photoperiod‐informed breeding strategies, improvements in seed viability, omics‐based tools and coherent public policies, is essential to ensure crop resilience and genetic sovereignty, especially in regions of origin such as Paraguay. The sustainable use of Stevia’s genetic diversity could foster more sustainable, healthier and fairer production systems.

Genetic diversity and yield-biochemical trait correlations in oats from the Northwestern Himalayas

Genetic diversity and yield-biochemical trait correlations in oats from the Northwestern Himalayas

The Evolutionary Dynamics of Genetic Mutational Load Throughout Tomato Domestication History.

Understanding the impact of domestication on deleterious mutations has fascinated evolutionary biologists and breeders alike. A 'cost of domestication' has been reported for some organisms through accumulation of gene disruptions or radical amino acid changes. However, recent evidence paints a more complex picture of this phenomenon in different domesticated species. In this study, we used genomic sequences of 253 tomato accessions to investigate the evolution of deleterious mutations and genomic structural variants (SVs) through tomato domestication history. We apply phylogeny-based methods to identify deleterious mutations in the domesticated tomato as well as its semi-wild and wild relatives. Our results implicate a downward trend throughout domestication in the number of genetic variants, regardless of their functional impact. This suggests that demographic factors have reduced overall genetic diversity, leading to lower deleterious load and SVs as well as loss of some beneficial alleles during tomato domestication. However, we detected an increase in proportions of nonsynonymous and deleterious alleles (relative to synonymous and neutral nonsynonymous alleles, respectively) during the initial stage of tomato domestication in Ecuador. Additionally, deleterious alleles in the commonly cultivated tomato seem to be more frequent than expected under a neutral hypothesis of molecular evolution. Our analyses also revealed frequent deleterious alleles in several well-studied tomato genes, probably involved in response to biotic and abiotic stress as well as fruit development and flavour regulation. To provide a practical guide for breeding experiments, we created TomDel, a public searchable database of 21,162 potentially deleterious alleles identified in this study (hosted on the Solanaceae Genomic Network; https://solgenomics.net/).

Biochemical Insights into Diverse Psilocybe Mushrooms and Their Metabolites as Sources of Neuroactive Agents: A Review.

Psilocybe species, commonly known as "magic mushrooms", are a group of hallucinogenic fungi known for their psychoactive compounds such as psilocybin, psilocin, baeocystin, and norbaeocystin. These species have been the focus of scientific study due to their potential therapeutic applications, despite their classification as controlled substances in many jurisdictions. This review aims to provide a comprehensive overview of various Psilocybe mushrooms, highlighting their chemical compositions, genetic diversity, and therapeutic potential, particularly in the treatment of mental health conditions such as depression, anxiety, PTSD, addiction, and cluster headaches. By reviewing existing scientific literature, this review examines the pharmacological effects and therapeutic applications of Psilocybe mushrooms. The review includes novel contributions such as the identification of alternative pathways for psilocybin synthesis and taxonomic consolidations among Psilocybe species. It also explores the cultural context and traditional uses of these mushrooms. The findings indicate that Psilocybe mushrooms exhibit significant potential for therapeutic use in mental health treatment. The review also underscores the importance of ongoing research into the pharmacological properties of these mushrooms to better understand their effects and potential benefits. Despite their current legal status, Psilocybe mushrooms hold considerable promise for future therapeutic applications. There is a need for further investigation to fully explore their potential in medical and cultural contexts. This review sets a foundation for future research and drug development endeavors, advocating for a more nuanced understanding of these complex biological entities.

Complementary genetic and epigenetic changes facilitate rapid adaptation to multiple global change stressors

To persist under unprecedented rates of global change, populations can adapt or acclimate. However, how these resilience mechanisms interact, particularly the role of epigenetic variation in long-term adaptation, is unknown. To address this gap, we experimentally evolved the foundational marine copepod Acartia tonsa for 25 generations under ocean acidification, warming, and their combination and then measured epigenomic, genomic, and transcriptomic responses. We observed clear and consistent epigenomic and genomic divergence between treatments, with epigenomic divergence concentrated in genes related to stress response and the regulation of transposable elements. However, epigenetic and genetic changes were inversely related and occurred in different regions of the genome; levels of genetic differentiation (F ST ) were up to 2.5× higher in regions where methylation did not differ between treatments compared to regions with significant methylation changes. This negative relationship between epigenetic and genetic divergence could be driven by local inhibition of one another or distinct functional targets of selection. Finally, epigenetic divergence was positively, though weakly, associated with gene expression divergence, suggesting that epigenetic changes may facilitate phenotypic change. Taken together, these results suggest that unique, complementary genetic and epigenetic mechanisms promote resilience to global change.