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PubMed1990

Selection response in traits with maternal inheritance.

Maternal inheritance is the non-Mendelian transmission of traits from mothers to their offspring. Despite its presence in virtually all organisms, acting through a variety of mechanisms, the evolutionary consequences of maternal inheritance are not well understood. Here we review and extend a model of the inheritance and evolution of multiple quantitative characters with complex pathways of maternal effects. Extensions of the earlier model include common family environmental effects not associated with maternal phenotype, sexual dimorphism, and paternal effects (non-Mendelian influence of the father on offspring traits). We find that, in contrast to simple Mendelian inheritance, maternal inheritance produces qualitatively different evolutionary dynamics for two reasons: (1) the response to selection on a set of characters depends not only on their additive genetic variances and covariances, but also on maternal characters that influence them, and (2) time lags in the response to selection create a form of evolutionary momentum. These results have important implications for evolution in natural populations and practical applications in the economic improvement of domesticated species. We derive selection indices that maximize either the economic improvement in a single generation of artificial selection or the asymptotic rate of improvement in long-term selection programmes, based on individual merit or a combination of individual and family merit. Numerical examples show that accounting for maternal inheritance can lead to considerable increases in the efficiency of artificial selection.

Animals↗

PubMed2025

Diversity and evolutionary history of endogenous retroviruses in the genome of Manis pentadactyla.

Endogenous retroviruses (ERVs), remnants of ancient viral infections integrated into host genomes, serve as invaluable molecular fossils for studying viral evolution. In this study, we performed a genomic analysis of the Chinese pangolin (Manis pentadactyla), identifying novel full-length endogenous retroviruses, designated as Manis pentadactyla ERVs (MPERVs). MPERVs span three retroviral genera: Alpha-, Beta-, and Gamma-retroviruses. Using genomic screening and phylogenetic analysis, we classified MPERVs and reconstructed their evolutionary history, uncovering evidence of complex recombination events and cross-species transmission. Estimated insertion times for MPERVs range from very recent to 18.38 million years ago. MPERVs exhibit diverse structural features, notably including conserved retroviral domains and functional motifs and highlighting their preservation across extensive evolutionary periods. These findings shed light on the evolutionary dynamics of ERVs in Chinese pangolin and suggest the potential for expanded host ranges among certain retrovirus genera.IMPORTANCEEndogenous retroviruses are unique viruses distinguished by the fact that they are retained as part of the host genome after an exogenous retrovirus infects the host. The Chinese pangolin, as a host with a long independent evolutionary history, likely holds valuable insights in its genome regarding retrovirus endogenization and transmission. In this study, we identified the footprints of exogenous retroviruses from three different genera in the pangolin genome: Alpharetrovirus, Betaretrovirus, and Gammaretrovirus. Additionally, by calculating the integration times of the pangolin's endogenous retroviruses and analyzing the domains of the three main functional proteins (GAG, POL, and ENV), we found that the insertions are relatively young. This suggests that these endogenous retroviruses infected the Chinese pangolin long before their endogenization. This study represents the exploration of endogenous retroviruses in the Chinese pangolin genome, expanding our understanding of endogenous retroviruses in mammals. Furthermore, our findings provide new evidence for the phenomenon of the cross-species transmission of retroviruses prior to endogenization.

Endogenous Retroviruses↗

PubMed2025

Macrolide-resistant Mycoplasma pneumoniae resurgence in Chinese children in 2023: a longitudinal, cross-sectional, genomic epidemiology study.

BACKGROUND: After a prolonged period of low detection rates, Mycoplasma pneumoniae resurged in China, during September to November, 2023, raising global concern. This study aims to gain a better understanding of the genetic mechanisms underlying the 2023 increase in cases and the evolutionary dynamics of the epidemic populations, which has been previously hampered due to limited genomic data of this pathogen. METHODS: We sequenced 685 M pneumoniae isolates, including 248 isolates from 11 Chinese provinces and municipalities in 2023 and 437 isolates from Beijing (2013-22). By analysing these isolates and 436 publicly global sequences, we reconstructed the pathogen's evolutionary history using time-calibrated phylogenies and effective population size inference. We investigated potential genomic variations contributing to the 2023 resurgence through genome-wide association study and conducted phylogeographic analysis of the 2023 isolates across China. FINDINGS: Two macrolide-resistant epidemic clusters (T1-2-EC1 and T2-2-EC2) were responsible for the 2023 resurgence in China. Both clusters, having acquired the 23S ribosomal RNA A2063G mutation conferring macrolide resistance, emerged in approximately 1997 and 2014, respectively, and subsequently outcompeted their predecessor populations. This coincided with China's large-scale adoption of azithromycin for paediatric community-acquired pneumonia around the early 2000s. Aside from macrolide resistance, T1-2-EC1 independently acquired 17 clade-specific mutations and T2-2-EC2 four clade-specific mutations, which could further explain their increased competitiveness. Whole-genome analysis revealed no resurgence-specific mutations in the 2023 isolates. Phylogeographic analysis showed rapid mixing of T1-2-EC1 isolates between different sampled regions within China. INTERPRETATION: Our study provides evidence that the 2023 resurgence in China is a continuation of the pre-COVID epidemic, rather than emergence of novel variants. The high prevalence of macrolide resistance and rapid intranational spread emphasise the urgent need for enhanced global surveillance of this pathogen. FUNDING: National Key Research and Development Program of China, National Natural Science Foundation of China for Key Programs of China Grants, and Beijing High-Level Public Health Technical Talent Project.

Humans↗

PubMed2025

SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution.

The reconstruction of human evolutionary history has undergone repeated advances, each made possible by methodological innovations. In recent decades, genetic and genomic data played a central role in the reconstruction of major evolutionary events such as the out-of-Africa migration, and genetic simulations of human evolutionary history have come to play a major role in testing more specific hypotheses including proposed patterns of migration and admixture with archaic hominins. Increasing computational power has allowed human evolutionary history to be modeled at ever-larger scales, but simulations that encompass the complete human genome, including sex chromosomes and mitochondrial DNA, have been difficult due to the lack of support for whole-genome models in commonly used evolutionary simulation frameworks. With the recent introduction of SLiM 5 such simulations are now straightforward to construct, allowing the easy simulation of humans at whole-genome scale under different demographic models and evolutionary dynamics. We here present three versions of a reusable, customizable, open-source SLiM 5 model for simulating the molecular evolution of the full human genome. We also show some simple analyses of results from the model, to illustrate its utility. We hope this model, which we have nicknamed "SimHumanity" in jest, will facilitate further progress in the field of human evolutionary simulations.

SLiM↗

PubMed2025

Two-Step Loss of GLUTs in the High-Metabolism Passerines.

Glucose transporters (GLUTs) play vital roles in cellular metabolism. Understanding their evolutionary dynamics in birds is essential for elucidating avian physiology and adaptation. However, the choice of gene detection method in gene family analysis may affect the conclusion. Here, we present a comprehensive investigation of methodologies and GLUT gene loss events in avian lineages, focusing on the loss of GLUT4 and GLUT8. To illustrate the effects of these methods, we first employed BUSCO-based homolog identification, calculated pairwise evolutionary distances between different species, and performed separate blastn and blastp searches to identify homologs in two groups of animals. Our analyses revealed a significant decline in blastn accuracy with increasing evolutionary distance, represented by relative divergence times. Through a more robust blastp-based gene detection pipeline, we provide evidence for the loss of GLUT genes in birds based on 58 vertebrate genomes, including 47 bird species. Our results support the reported early loss of GLUT4 in Aves. We also newly emphasize the absence of GLUT8 in passerines, potentially due to adaptation to high-sugar diets in their ancestors. These findings enhance our knowledge of avian metabolism and the evolution of GLUT genes.

Animals↗

PubMed2026

Transgenerational continuity: Persistence as a dimension of inheritance and evolution.

Transgenerational continuity (TC) describes the persistence of inherited molecular architectures across generations. Progress in identity-by-descent (IBD) detection, recombination dynamics, and epigenetic research highlights the growing need for a more comprehensive model of inheritance. This theoretical framework synthesizes evidence from genomics, population studies, and epigenetics to outline how inherited molecular architectures, which are transmitted through IBD, together with heritable epigenetic modifications, can preserve ancestral information across generations. IBD captures genomic continuity across three nested scales, where recent familial segments link close relatives, population-level haplotypes are shared across cohorts, and archaic fragments from Neanderthal and Denisovan admixture persist as molecular fossils of ancient lineages. Although recombination and selection reshape these regions, their persistence across time scales highlights the evolutionary durability of genomic continuity. Epigenetic memory reflects regulatory persistence, whereby molecular modifications can preserve functional states across cell divisions and sometimes across generations. Together with familial and population-level IBD persistence and the long-term retention of introgressed haplotypes, these findings demonstrate that inherited molecular architectures can persist across multiple timescales. Evolutionary processes shape this persistence. Purifying selection preferentially removes deleterious inherited variants, whereas positive selection can favor the persistence of functionally relevant genomic architectures. From this perspective, evolutionary dynamics arise not only from the generation of variation, but also from the differential persistence of inherited molecular architectures through selection. Transgenerational continuity therefore provides a conceptual framework in which persistence serves as an explanatory dimension of inheritance and evolution that complements variation and explains the persistence of biological identity across generations and evolutionary time.

Biological identity↗

PubMed2025

The Genetic Basis of Elongated Tails in Birds: Evidence for Sexual Selection as a Driver of Convergent Evolution.

Elongated tails are exaggerated ornaments observed in various bird species, and their functional and evolutionary dynamics have attracted considerable attention. Empirical studies consistently show that sexual selection is a major drive of tail elongation. However, the genetic basis of this trait remains poorly understood. To address this gap, we performed comparative genomic analyses of 23 bird species, including 7 with extremely long tails and 16 with relative short tails. Genes related to feather development exhibited amino acid convergence replacement (e.g., APC) or displayed faster evolutionary rates (e.g., LEF1, WISP3) in the long-tailed species. Importantly, we identified convergence replacements of amino acids and rapid evolution in genes related to reproductive functions (e.g., PAQR7) and immunity (e.g., ADA), suggesting that elongated tails may serve as honest signals of genetic quality. In conclusion, this study provides genomic evidence supporting the role of sexual selection in the evolution of elongated tails, revealing an intricate interplay between sexually selected traits, fitness, and immune competence.

Animals↗

PubMed2026

Tandem duplication-driven expansion and UV-B stress adaptation of the LHC gene family in Artemisia annua L.

BACKGROUND: Artemisia annua L., is the primary natural source of the antimalarial drug artemisinin. In nature, fluctuating light is a major environmental stress that affects plant growth and artemisinin biosynthesis. Although the light-harvesting chlorophyll a/b-binding (LHC) superfamily plays a key role in mediating plant responses to fluctuating light, systematic research of this gene family in A. annua has not yet been conducted, limiting our understanding of light adaptation in this medicinally important species. RESULTS: This study investigated the evolutionary dynamics and functional adaptation of the light-harvesting chlorophyll a/b-binding (LHC) superfamily in A. annua, with a focus on the early light‑induced protein (ELIP) subfamily. Comparative genomics of 24 plant species showed that the LHC superfamily recently expanded in the examined Asteraceae lineages through duplication events. In A. annua, 229 LHC genes identified from four haplotype genomes comprised 205 allelic and 24 haplotype-specific loci, with the ELIP subfamily expanding significantly via tandem duplication. Notably, compared to non-Asteraceae plants, ELIPs exhibited a uniform single-exon architecture, indicating it is a genomic feature unique to Asteraceae plants. Population genomics of 41 individuals showed dynamic copy number variations ranging from 1 to 4 copies per locus. Interestingly, a structurally disrupted ELIP allele remained transcriptionally active and produced long aberrant transcripts, showing that this subfamily is still actively evolving. Under UV-B stress, AaELIP loci showed synchronized induction trend but differed in expression levels, suggesting a division into major and auxiliary roles within the expanded tandem cluster. Overall, while the response of ELIPs to light stress is evolutionarily conserved, this dramatic expansion and structural streamlining of AaELIPs may represent a key evolutionary adaptation that enhances the plant's ability to cope with intense light and radiation stress. CONCLUSIONS: Collectively, this study demonstrates a significant expansion of the LHC superfamily in A. annua, especially within the ELIP subfamily, as well as its robust response to UV-B treatment, underscoring the essential role of ELIPs in mediating light stress responses. These findings provide a valuable foundation for future research to uncover the molecular mechanisms underlying A. annua's adaptation to complex light environments.

Artemisia annua↗

PubMed2025

Unraveling evolutionary pathways: allopolyploidization and introgression in polyploid Prunus (Rosaceae).

Allopolyploidization, resulting from hybridization and subsequent whole-genome duplication (WGD), is a fundamental mechanism driving evolutionary diversification across various lineages within the Tree of Life. The polyploid Prunus (Rosaceae), significant for its economic and agricultural value, provides an ideal model for investigating the evolutionary dynamics associated with allopolyploidy. In this study, we utilized deep genome skimming (DGS) data to demonstrate a comprehensive analytical framework for elucidating the underlying allopolyploidy that includes a newly adapted tool (DGS-Tree2GD) tailored explicitly for accurately detecting WGD events. Additionally, we introduced two methods to evaluate the contribution of incomplete lineage sorting (ILS) to lineage diversification. Phylogenomic discordance analyses revealed that allopolyploidization, rather than ILS, played a dominant role in the origin and dynamics of polyploid Prunus. Moreover, we inferred that the uplift of the Himalayas from the Middle to Late Miocene was a key driver in the rapid diversification of the Maddenia clade, an endemic group in East Asia. This geological event facilitated extensive hybridization and allopolyploidization, particularly the introgression between the Himalayas-Hengduan and Central-Eastern China clades. This case study demonstrates the robustness and efficacy of our analytical approach in precisely identifying WGD events and elucidating the evolutionary mechanisms underlying allopolyploidization in polyploid Prunus.

Polyploidy↗

PubMed1986

Nonequilibrium thermodynamics and different axioms of evolution.

Proponents of two axioms of biological evolutionary theory have attempted to find justification by reference to nonequilibrium thermodynamics. One states that biological systems and their evolutionary diversification are physically improbable states and transitions, resulting from a selective process; the other asserts that there is an historically constrained inherent directionality in evolutionary dynamics, independent of natural selection, which exerts a self-organizing influence. The first, the Axiom of Improbability, is shown to be nonhistorical and thus, for a theory of change through time, acausal. Its perception of the improbability of living states is at least partially an artifact of closed system thinking. The second, the Axiom of Historically Determined Inherent Directionality, is supported evidentially and has an explicit historical component. Historically constrained dynamic populations are inherently nonequilibrium systems. It is argued that living, evolving systems, when considered to be historically constrained nonequilibrium systems, do not appear improbable at all. Thus, the two axioms are not compatible. Instead, the Axiom of Improbability is considered to result from an unjustified attempt to extend the contingent proximal actions of natural selection into the area of historical, causal explanations. It is thus denied axiomatic status, and the effects of natural selection are subsumed as an additional level of constraint in an evolutionary theory derived from the Axiom of Historically Determined Inherent Directionality.

Biological Evolution↗

PubMed2025

Single-cell mutational burden distributions in birth-death processes.

Genetic mutations are footprints of cancer evolution and reveal critical dynamic parameters of tumour growth, which otherwise are hard to measure in vivo. The mutation accumulation in tumour cell populations has been described by various statistics, such as site frequency spectra (SFS), single-cell division distributions (DD) and mutational burden distributions (MBD). While DD and SFS have been intensively studied in phylogenetics especially after the development of whole genome sequencing technology of bulk samples, MBD has drawn attention more recently with the single-cell sequencing data. Although those statistics all arise from the same somatic evolutionary process, an integrated understanding of these distributions is missing and requires novel mathematical tools to better inform the ecological and evolutionary dynamics of tumours. Here we introduce dynamical matrices to analyse and unite the SFS, DD and MBD and derive recurrence relations for the expectations of these three distributions. While we successfully recover classic exact results in pure-birth cases for the SFS and the DD through our new framework, we derive a new expression for the MBD and approximate all three distributions when death is introduced. We demonstrate a natural link between the SFS and the single-cell MBD, and show that the MBD can be regenerated through the DD. Counter-intuitively, the single-cell MBD is mainly driven by the stochasticity arising in the DD, rather than the extra stochasticity in the number of mutations at each cell division.

Single-Cell Analysis↗

PubMed1989

Antagonistic co-evolution and the evolution of genotypic randomization.

Antagonistic co-evolution, such as the pursuit and flight of host-parasite co-evolution, easily generates cyclical co-evolutionary dynamics. It is well known that a fluctuating, contrary environment may favour the evolution of recombination, but previous analyses have shown that the optimal rate of recombination declines as the period of the environmental fluctuations gets longer. It is here shown that the direction of selection for recombination (for higher or lower rates) may only be sensitive to fluctuation period if the fluctuations are generated by non-co-evolving features of the environment, such as changes in climate. In the simple model of this paper, co-evolutionary cycling provides an advantage for recombination that is independent of period length. This independence of period length necessitates a new framework for understanding the advantage of recombination in the context of co-evolution. In the model studied in this paper it is the phase difference of the host and parasite trajectories that is the relevant feature, and phase relationships are independent of the co-evolutionary cycle time. That is, the phase difference of the oscillations is independent of their frequency.

Biological Evolution↗

PubMed2025

Distinct evolutionary trajectories of subgenomic centromeres in polyploid wheat.

BACKGROUND: Centromeres are crucial for precise chromosome segregation and maintaining genome stability during cell division. However, their evolutionary dynamics, particularly in polyploid organisms with complex genomic architectures, remain largely enigmatic. Allopolyploid wheat, with its well-defined hierarchical ploidy series and recent polyploidization history, serves as an excellent model to explore centromere evolution. RESULTS: In this study, we perform a systematic comparative analysis of centromeres in common wheat and its corresponding ancestral species, utilizing the latest comprehensive reference genome assembly available. Our findings reveal that wheat centromeres predominantly consist of five types of centromeric-specific retrotransposon elements (CRWs), with CRW1 and CRW2 being the most prevalent. We identify distinct evolutionary trajectories in the functional centromeres of each subgenome, characterized by variations in copy number, insertion age, and CRW composition. By utilizing CENH3-ChIP data across various ploidy levels, we uncover a series of CRW invasion events that have shaped the evolution of AA subgenome centromeres. Conversely, the evolutionary process of the DD subgenome centromeres involves their expansion from diploid to hexaploid wheat, facilitating adaptation to a larger genomic context. Integration of complete einkorn centromere assemblies and Aegilops tauschii pan-genomes further revealed subgenome-specific centromere evolutionary trajectories. By inclusion of synthetic hexaploid from S2-S3 generations, alongside 2x/6 × natural accessions, we demonstrate that DD subgenome centromere expansion represents a gradual evolutionary process rather than an immediate response to polyploidization. CONCLUSIONS: Our study provides a comprehensive landscape of centromere adaptation, evolution, and maturation, along with insights into how retrotransposon invasions drive centromere evolution in polyploid wheat.

Centromere↗

PubMed2026

Population-level genomic surveillance of human norovirus using wastewater-based whole-genome sequencing.

Wastewater-based surveillance has garnered increasing attention as a valuable approach for capturing community-level infection dynamics that are often difficult to detect through clinical reporting systems alone. In this study, we analyzed human norovirus genotype distributions and whole-genome-level variations in wastewater samples collected in Gwangju, Korea. These results were interpreted in conjunction with a documented foodborne outbreak to evaluate the epidemiological relevance of wastewater-based monitoring. Human norovirus concentrations were quantified using TaqMan Array Card-based RT-qPCR, and whole-genome next-generation sequencing (NGS) was performed to obtain viral read counts and reads per kilobase per million filtered reads values. Overall, strong correlations were observed between RT-qPCR-based concentrations and NGS-derived metrics. Genotype dynamics varied among wastewater treatment plants, reflecting differences in catchment size and local population characteristics. In particular, the relative abundance of GII.17[P17] increased during epidemiological week 50, temporally coinciding with a documented local foodborne outbreak. Variant analysis revealed that wastewater samples exhibited mixed nucleotide patterns, with multiple alleles coexisting at varying relative frequencies rather than fixed substitutions. Notably, some nonsynonymous variants detected in clinical samples were also observed in wastewater samples collected surrounding the outbreak period. Together, these findings demonstrate that wastewater-based whole-genome surveillance can capture both genotype-level shifts and nucleotide-level dynamics at the population scale, highlighting its potential as a complementary tool for monitoring community-level norovirus circulation and outbreak-associated genotype dynamics.IMPORTANCEWastewater-based surveillance is increasingly recognized as a promising approach for capturing community-level infection dynamics that are often missed by clinical surveillance. In this study, we applied whole-genome sequencing to wastewater samples collected in Gwangju, South Korea, to comprehensively characterize human norovirus genotype distributions and genetic variation. Distinct genotype patterns were observed across wastewater treatment plants, reflecting differences in catchment population size and local characteristics. Notably, an increase in the GII.17[P17] genotype detected in wastewater coincided with a foodborne outbreak investigated in Gwangju, demonstrating the potential of wastewater surveillance to reflect ongoing community transmission and emerging outbreak-associated genotypes. In addition, wastewater samples contained diverse and coexisting genetic variants, capturing population-level viral diversity and evolutionary dynamics that are not readily detected through clinical surveillance alone. These findings highlight the value of wastewater-based whole-genome surveillance for monitoring community-level viral circulation and support its integration as a complementary strategy to existing clinical surveillance systems.

genotype dynamics↗

PubMed2026

Genome-wide identification and functional analysis of the BES1-like (VfBES1) gene family in Vernicia fordii reveals its role in floral development.

BACKGROUND: Vernicia fordii Hemsl (also known as Tung tree), an significant commercial oil-producing tree species, is a monoecious and diclinous species with male and female flowers on the same inflorescence; however, the molecular mechanisms governing its floral sex determination remain elusive, particularly the genetic basis underlying the skewed female-to-male flower ratio and the evolutionary dynamics of sex-related gene families, which severely restrict targeted breeding for yield enhancement. In the model plant Arabidopsis, the BRI1 EMS SUPPRESSOR 1 (BES1) transcription factor family plays a crucial role in Brassinosteroid (BR) signaling and reproductive development. However, its function remains largely unexplored in woody perennials. RESULTS: In this study, we introduce the genome-wide identification and functional characterization of the BES1-like (VfBES1) gene family in the Tung tree for the first time. Integrative multi-omics approaches reveal seven VfBES1 genes that are clustered into three phylogenetically distinct clades, each characterized by clade-specific motifs and structural simplicity. Segmental duplication events (VfBES1-1/VfBES1-5 and VfBES1-4/VfBES1-7) and promoter cis-element enrichment (hormone-responsive and abiotic stress-related motifs) highlight evolutionary innovation and functional diversification. Spatiotemporal expression profiling reveals VfBES1 genes' tissue- and stage-specific roles. VfBES1-1 predominantly expresses in female flowers and fruits, suggesting its possible roles in late-stage sex maintenance or ovule and fruit development. VfBES1-2 and VfBES1-6 exhibit male flower-specific and early floral developmental activation, respectively. Nuclear-localized VfBES1-6 displays co-expression with VfMYB35-1 gene, which is a regulator of male structure degeneration. CONCLUSIONS: Findings in this study shed light on the regulatory roles of VfBES1 genes in the floral development of the Tung tree, providing a reference for its precision breeding to enhance flowering synchrony and seed productivity. This study also provides a comparative framework for understanding the functional diversity of BES1-like genes in non-model woody plants.

Flowers↗

PubMed2026

Plasmids as persistent genetic reservoirs of bacterial defense systems in wastewater treatment.

BACKGROUND: Bacterial antiphage defense systems play essential roles in microbial ecology, yet their dynamics within urban wastewater systems (UWS) remain poorly characterized. RESULTS: In this study, we performed comprehensive metagenomic and plasmidome analyses on 78 wastewater samples collected during two seasons and four sampling points across UWS from three European countries. We observed a significant reduction in the abundance, diversity, and mobility potential of defense systems during biological treatment. However, these reductions were not directly correlated with changes in microbial abundance. Defense systems were significantly enriched on plasmids, particularly conjugative plasmids, where their gene density was approximately twice as high as on chromosomes and remained relatively stable across compartments. In contrast to chromosomal defense systems, plasmid-borne systems exhibited more frequent co-localization with a wide range of mobile genetic elements (MGEs)-associated genes, thereby facilitating multilayered dissemination networks. Furthermore, we detected a strong correlation between phage abundance and host defense system profiles, indicating ongoing phage-host co-evolutionary dynamics in these environments. CONCLUSIONS: In summary, our results demonstrate that UWS reduce the abundance and diversity of bacterial defense system genes. However, plasmid-associated defense systems can persist through shared mobile genetic reservoirs. These findings underscore the critical role of plasmids in bacterial immunity and provide new insights into defense system dynamics within urban wastewater environments.

Plasmids↗

PubMed2025

SARS-CoV-2 genomic diversity and within-host evolution in individuals with persistent infection in the UK: an observational, longitudinal, population-based surveillance study.

BACKGROUND: Persistent SARS-CoV-2 infections in hospitalised immunocompromised individuals are known to facilitate accelerated within-host viral evolution, potentially contributing to the emergence of highly divergent variants. However, little is known about the evolutionary dynamics and transmission risks of persistent infections in the general population. We aimed to characterise the within-host evolution of SARS-CoV-2 during persistent infections identified through a large community surveillance study. METHODS: We used data from the Office for National Statistics COVID-19 Infection Survey (ONS-CIS), a large-scale, longitudinal, population-based surveillance study conducted in the UK from April, 2020, to March, 2023. For this analysis, we focused on infections with high viral load (cycle threshold ≤30) and available genome sequences, from seven major SARS-CoV-2 lineages (alpha, delta, BA.1, BA.2, BA.4, BA.5, and XBB). ONS-CIS participants were randomly selected from the general population and tested regularly by RT-PCR, regardless of symptoms. We defined persistent infections as those with sustained or rebounding high viral RNA titres for 26 days or longer. We examined associated host characteristics and used raw sequence data to identify de novo mutations and estimate within-host synonymous and non-synonymous evolutionary rates across the SARS-CoV-2 genome. FINDINGS: Between Nov 2, 2020, and March 21, 2023, we identified 576 persistent infections with at least two sequences, including 11 alpha, 106 delta, 102 BA.1, 204 BA.2, 16 BA.4, 133 BA.5, and 4 XBB. Persistent infections were more common in males than females (p<0·0001) and individuals older than 60 years (p=0·0027). The median within-host genome-wide evolutionary rate was 7·9 × 10-4 substitutions per site per year (IQR 7·0-9·0 × 10-4), with high inter-individual variability driven largely by non-synonymous mutations, particularly in the N-terminal and receptor-binding domains of the spike protein. Longer infection duration was associated with higher evolutionary rates, while no associations were found with age, sex, vaccination status, previous infection, or virus lineage. We found no clear evidence of transmission beyond the first month of infection in any of the 84 persistent infections lasting 56 days or longer. In total, we identified 379 recurrent mutations, including many with known or predicted negative fitness effects and low prevalence at the population level, as well as de novo reversions to the Wuhan-Hu-1 reference sequence, which were likely under positive selection within those individuals. INTERPRETATION: This study highlights the heterogeneous nature of within-host SARS-CoV-2 evolution in individuals with persistent infection in the community. Notably, a small subset of persistent infections with high viral loads underwent accelerated viral evolution or recurrently acquired hallmark mutations found in novel variants. In addition, onward transmission from a persistent infection during the later stages of infection is likely to be rare. These insights have important implications for prioritising genomic surveillance and managing patients with persistent infections. FUNDING: Department of Health and Social Care.

Humans↗

PubMed2026

Genomic distribution characteristics and interspecific differences of microsatellite landscapes in Felidae.

BACKGROUND: Microsatellites within genomes play crucial roles in regulating gene expression, DNA replication, and chromosomal structure and function. Analyzing the composition and distribution patterns of microsatellites in closely related species not only reveals their evolutionary dynamics and adaptive mechanisms but also provides essential technical support for applications in genetic breeding, species conservation, and disease research. As one of the world's most captivating animal groups, the landscape patterns of microsatellites across feline genomes remain to be systematically characterized. RESULTS: This study utilized high-quality genomic data to conduct a systematic comparative analysis of microsatellite landscape distribution patterns across the genomes of 13 felid species. The findings revealed that microsatellite abundance and distribution exhibit species-specific characteristics, with a non-random genomic distribution and a negative correlation between microsatellite abundance and repeat length. The predominant distribution pattern followed the sequence: single > double > quadruple > triple > quintuple > sextuple nucleotide repeats. Microsatellite abundance peaked in intergenic regions, whereas trinucleotide repeats were more prevalent within exons. Coding regions showed a marked preference for trinucleotide and hexanucleotide repeats. Enrichment analysis of GO and KEGG pathways indicated that coding sequences containing microsatellites were primarily involved in transcription and translation processes. CONCLUSIONS: Our study elucidates the distribution patterns and characteristics of microsatellites across diverse feline species, providing significant insights into their evolutionary mechanisms and functional roles. Furthermore, these findings establish a valuable reference and foundational dataset for the future development of high-quality, species-specific microsatellite markers in felids.

Animals↗