Evolutionary Dynamics Research Articles

Evolutionary integration of forelimb and hindlimb proportions within the bat wing membrane inhibits ecological adaptation.

Bats and birds are defined by their convergent evolution of flight, hypothesized to require the modular decoupling of wing and leg evolution. Although a wealth of evidence supports this interpretation in birds, there has been no systematic attempt to identify modular organization in the bat limb skeleton. Here we present a phylogenetically representative and ecologically diverse collection of limb skeletal measurements from 111 extant bat species. We compare this dataset with a compendium of 149 bird species, known to exhibit modular evolution and anatomically regionalized skeletal adaptation. We demonstrate that, in contrast to birds, morphological diversification across crown bats is associated with strong trait integration both within and between the forelimb and hindlimb. Different regions of the bat limb skeleton adapt to accommodate variation in distinct ecological activities, with flight-style variety accommodated by adaptation of the distal wing, while the thumb and hindlimb play an important role facilitating adaptive responses to variation in roosting habits. We suggest that the wing membrane enforces evolutionary integration across the bat skeleton, highlighting that the evolution of the bat thumb is less correlated with the evolution of other limb bone proportions. We propose that strong limb integration inhibits bat adaptive responses, explaining their lower rates of phenotypic evolution and relatively homogeneous evolutionary dynamics in contrast to birds. Powered flight, enabled by the membranous wing, is therefore not only a key bat innovation but their defining inhibition.

Evolutionary Dynamics and Pathogenicity Analysis of Feline Panleukopenia Virus in Xinjiang, China

Feline panleukopenia virus (FPV), a globally pervasive and highly pathogenic pathogen, has garnered significant attention recently due to the cross-species transmission of its variants. Despite the vast body of research conducted on FPV, studies exploring its evolutionary history, dynamics, and the factors driving its evolution remain scarce. The pathogenicity of strains with the prevalent mutations (A91S and I101T) in the VP2 protein has also not been fully elucidated. This study conducted a comparative analysis of FPV VP2 sequences sourced from Xinjiang province in China, other provinces in China, and other countries. It was confirmed that the evolutionary rate of FPV approached that of RNA viruses, at approximately 1.13 × 10−4 substitutions/site/year. The study reconstructed molecular models of the VP2 protein with the A91S and I101T mutations and used viral strains carrying these mutations to perform the animal regression experiment. It was confirmed that isolates with the A91S and I101T mutations could cause typical leukopenia and acute enteritis symptoms, suggesting that the mutant strains still possess certain pathogenicity. This is the first study to report on the evolutionary dynamics of FPV in Xinjiang, China, and it emphasized the importance of continuously monitoring FPV evolutionary dynamics.

Evolutionary Game Analysis of Electric Vehicle Distribution Entities with Shared Charging Facilities

This study investigates the evolutionary game dynamics among electric vehicle distribution entities in the context of shared charging facilities, addressing the critical issue of inadequate charging resources. To understand the behavior of different stakeholders under government incentive policies, we develop an evolutionary game model involving a government department and two logistics enterprises (A and B). Through stability analysis, we explore equilibrium conditions of evolutionarily stable strategies (ESSs) for the tripartite evolutionary game. To ensure the robustness of our findings, we conduct a MATLAB simulation analysis to validate the analytical results. Our findings highlight that government subsidies, the costs incurred by logistics enterprises to share charging facilities, and the additional distribution income derived from this sharing are critical in determining whether the evolutionary game can achieve a stable equilibrium state. This research enables logistics companies to optimize the use of charging resources, lower operating costs, and enhance delivery efficiency. Additionally, government subsidy policies play a crucial role in encouraging logistics enterprises to engage in charging facility sharing, thereby fostering the sustainable development of the entire logistics industry. Based on these insights, the paper offers practical recommendations to further promote the sharing of charging facilities in electric vehicle distribution.

Comparative mitochondrial genomics of Thelebolaceae in Antarctica: insights into their extremophilic adaptations and evolutionary dynamics

Species of Antarctomyces and Thelebolus (Thelebolaceae), primarily found in Antarctic environments, exhibit psychrophilic adaptations, yet their mitochondrial genomes have not been extensively studied. Furthermore, few studies have compared the mitochondrial genomes of psychrophilic, psychrotrophic, and mesophilic fungi. After successful sequencing and assembly, this study annotated the mitochondrial genomes of Antarctomyces psychrotrophicus CPCC 401038 and Thelebolus microsporus CPCC 401041. We also performed a comparative analysis with the previously characterized mitochondrial genomes of psychrotrophic and mesophilic fungi. The analysis revealed that nad4L was the most conserved gene across the mitochondrial genomes, characterized by its synonymous and non-synonymous substitution rates (Ks and Ka), genetic distance, and GC content and skew within the protein-coding genes (PCGs). Additionally, the mitochondrial genomes of psychrophilic and psychrotrophic fungi showed a higher proportion of protein-coding regions and a lower GC content compared to those of mesophilic fungi, underscoring the genetic basis of cold adaptation. Phylogenetic analyses based on these mitochondrial genes also confirmed the phylogenetic relationships of Thelebolaceae in the class Leotiomycetes. These findings advance our understanding of the phylogenetic relationships and evolutionary dynamics within the family Thelebolaceae, highlighting how different environmental temperatures influence fungal mitochondrial genomic structure and adaptation.

Comparative case study of evolutionary insights and floral complexity in key early-diverging eudicot Ranunculales models

Famously referred to as “Darwin’s abominable mystery,” the rapid diversification of angiosperms over the last ~140 million years presents a fascinating enigma. This diversification is underpinned by complex genetic pathways that evolve and rewire to produce diverse and sometimes novel floral forms. Morphological innovations in flowers are shaped not only by genetics but also by evolutionary constraints and ecological dynamics. The importance of model organisms in addressing the long-standing scientific questions related to diverse floral forms cannot be overstated. In plant biology, Arabidopsis thaliana, a core eudicot, has emerged as a premier model system, with its genome being the first plant genome to be fully sequenced. Similarly, model systems derived from crop plants such as Oryza sativa (rice) and Zea mays (maize) have been invaluable, particularly for crop improvement. However, despite their substantial utility, these model systems have limitations, especially when it comes to exploring the evolution of diverse and novel floral forms. The order Ranunculales is the earliest-diverging lineage of eudicots, situated phylogenetically between core eudicots and monocots. This group is characterized by its exceptional floral diversity, showcasing a wide range of floral morphologies and adaptations that offer valuable insights into the evolutionary processes of flowering plants. Over the past two decades, the development of at least five model systems including, Aquilegia, Thalictrum, Nigella, Delphinium and Eschscholzia within the Ranunculales order has significantly advanced our understanding of floral evolution. This review highlights the conservation and divergence of floral organ identity programs observed among these models and discusses their importance in advancing research within the field. The review also delves into elaborate petal morphology observed in Aquilegia, Nigella, and Delphinium genera, and further discusses the contributions, limitations, and future research directions for Ranunculales model systems. Integrating these diverse models from the early-diverging eudicot order has enhanced our understanding of the complex evolutionary pathways that shape floral diversity in angiosperms, bridging the knowledge gaps essential for a comprehensive understanding of floral evolution.

Comparative satellite DNA mapping in species of the genus Prochilodus (Teleostei, Characiformes) and its evolutionary implications.

Satellite DNA (satDNA) sequences are dynamic components of the eukaryotic genome, that can play significant roles in species diversification. The Prochilodontidae family, which includes 21 Neotropical fish species, is characterized by a conserved karyotype of 2n = 54 biarmed chromosomes, with variation in some species and populations regarding the presence or absence of B chromosomes. This study aimed to investigate whether the chromosomal distribution of specific satDNA sequences is conserved among three Prochilodus species (P. lineatus, P. costatus, and P. argenteus) regarding organization and number of loci, and to compare their genomes using comparative genomic hybridization (CGH). Our results demonstrated that most satDNA sequences share a similar distribution pattern across the three species, and CGH analysis corroborated that their karyotypes are very similar in terms of repetitive DNA distribution. We also identified a potential CENP-B box sequence within PliSat01, a satDNA located in the pericentromeric region of all analyzed species. In contrast, PliSat04 and PliSat14 displayed differential locations and variations in the number of loci per genome, underscoring the dynamic nature of repetitive sequences even in species with otherwise highly conserved genomes. These findings represent the first evidence of karyotype diversification in Prochilodus, highlighting the evolutionary dynamism of satDNA sequences.

Inversions encounter relaxed genetic constraints and balance birth and death of TPS genes in Curcuma

Evolutionary dynamics of inversion and its impact on biochemical traits are a puzzling question. Here, we show abundance of inversions in three Curcuma species (turmeric, hidden ginger and Siam tulip). Genes within inversions display higher long terminal repeat content and lower expression level compared with genomic background, suggesting inversions in Curcuma experience relaxed genetic constraints. It is corroborated by depletion of selected SNPs and enrichment of deleterious mutations in inversions detected among 56 Siam tulip cultivars. Functional verification of tandem duplicated terpene synthase (TPS) genes reveals that genes within inversions become pseudogenes, while genes outside retain catalytic function. Our findings suggest that inversions act as a counteracting force against tandem duplication in balancing birth and death of TPS genes and modulating terpenoid contents in Curcuma. This study provides an empirical example that inversions are likely not adaptive but affect biochemical traits.

Evolution of dispersal in river networks.

Evolution of dispersal is a fascinating topic at the intersection of ecology and evolutionary dynamics that has generated many challenging problems in the analysis of reaction-diffusion equations. Early results indicated that lower random diffusion rates are generally beneficial. However, in riverine environments with downstream drift, high diffusion may be optimal, depending on downstream boundary conditions. Most of these results were obtained from modeling a single river reach, yet many rivers form intricate tree-shaped networks. We study the evolution of dispersal on a metric graph representing the simplest such possible network: two upstream segments joining to form one downstream segment. We first show that the shape of the positive steady state of a single population depends crucially on the geometry of the network, here considered as the relative length of the three segments. We then study the evolution of dispersal by considering the possibility of "invasion" of a second type (invader) at the steady state of the first type (resident). We show that the geometry of the network determines whether higher or intermediate dispersal is favored.

Pedagogical content knowledge in physical education preservice teachers in view of researching on lesson studies

PurposeResearching on lesson studies in initial training of physical education (PE) teachers in Portugal, our group is especially interested in the potential of this methodology for developing the pedagogical content knowledge (PCK) of future PE teachers. The purpose of the present text is to synthesize the knowledge relating to this subject.Design/methodology/approachExploratory searches in four multiple search databases were carried out, resulting in 51 records. Information about authors, year of publication, purposes, methodology and results was collected and analyzed.FindingsResults highlight the diversity of purposes. The interview is recurrent in the qualitative studies, while the questionnaire is used in all the large quantitative studies. Regarding the findings, it appears the centrality of PCK, its development potential and its measurability, the consistency of the concept and its evolutionary dynamics, as well as the constructive criticism of initial teacher training models and practices.Originality/valueTo emphasize the relationship between lesson studies and the development of PCK in initial teacher training of PE teachers.

Analysis of control measures inducing the evolution of infectious viral diseases

With the continuation of the infectious disease, pathogens mutate and interact with the resident pathogen. In this paper, we develop an SIR model that considers the evolution of viral virulence under the regulation of different defense strengths. By using infectious disease dynamics and evolutionary adaptive dynamics, we obtain the evolutionary criteria allowing for evolutionary branching and continuously stable strategy across varying intensities of prevention and control measures. Our study finds that robust prevention and control measures can contribute to a rapid evolutionary trend toward higher virulence. We perform a critical function analysis to reveal the evolutionary consequences of trade-offs of arbitrary shape and analyze a diverse range of evolutionary dynamics. Furthermore, we investigate the coexistence of two different strains and construct an evolutionary model to obtain their invasion fitness functions and the evolutionarily singular coalition of the dimorphism. We contemplate the presence of secondary branching on a significantly extended evolutionary time scale. Last, we conduct the numerical simulations to prove our theoretical findings. This reveals the law that the evolutionary state of pathogens is affected by the intensity of prevention and control strategies. The results and methods can be used as references for studying the effects of other factors on virus evolution.

The reconstruction of evolutionary dynamics of processed pseudogenes indicates deep silencing of “retrobiome” in naked mole rat

Approximately half of mammalian genomes are occupied by retrotransposons, highly repetitive interspersed genetic elements expanded through the mechanism of reverse transcription. The evolution of this "retrobiome" involved a series of explosive amplifications, presumably associated with high mutation rates, interspersed with periods of silencing. A by-product of retrotransposon activity is the formation of processed pseudogenes (PPGs)-intron-less, promoter-less DNA copies of messenger RNA (mRNA). We examined the proportion of PPGs with varying degrees of deviation from their ancestor mRNAs as an indicator of the intensity of retrotranspositions at different times in the past. Our analysis revealed a high proportion of "young'' (recently acquired) PPGs in the DNA of mice and rats, indicating significant retrobiome activity during the recent evolution of these species. The ongoing process of new PPG entries in mouse germ line DNA was confirmed by identifying diversity in PPG content within the single strain of mice, C57BL/6. In contrast, the highly abundant PPGs of the naked mole rat (NMR) exhibited substantial deviation from their mRNAs, with a near-complete lack of PPGs without mutations, indicative of the silencing of the retrobiome in the most recent evolutionary past, preceded by a period of high activity. This distinctive feature of the NMR genome was confirmed through the analysis of a broad range of mammalian species. The peculiar evolutionary dynamics of PPGs in the NMR, an organism with exceptional longevity and resistance to cancer, may reflect the role played by the retrobiome in aging and cancer.

Dynamics of Sandy Shorelines and Their Response to Wave Climate Change in the East of Hainan Island, China

Beach erosion and shoreline dynamics are strongly affected by alterations in nearshore wave intensity and energy, especially in the context of global climate change. However, existing works do not thoroughly study the evolution of the sandy coasts of eastern Hainan Island, China, nor their responses to wave climate change driven by climate variability. This study focuses on the open sandy coast and assesses shoreline evolutionary dynamics in response to wave climate variability over a 30-year period from 1994 to 2023, using an open-source software toolkit that semi-automatically identify the shorelines (CoastSat v2.4) and reanalysis wave datasets (ERA5). The shorelines of the study area were extracted from CoastSat, and then tidal correction and outlier correction were performed for clearer shorelines. Combining the shoreline changes and wave conditions derived from ERA5, the dynamics of the shorelines and their response to wave climate change were further studied. The findings reveal that the average long-term shoreline change rate along the eastern coast of Hainan Island is 0.03 m/year, with 44.8% of transects experiencing erosion and 55.2% showing long-term accretion. And distinct evolutionary patterns emerge across different sections. Interannual variability is marked by alternating erosion and siltation cycles, while most sections of the coast experiences clear seasonal fluctuations, with accretion typically occurring during summer and erosion occurring in winter. El Niño–Southern Oscillation (ENSO) cycles drive changes in parameters including significant wave height, mean wave period, wave energy flux, and mean wave direction, leading to long-term changes in wave climate. The multi-scale behavior of the sandy shoreline responds distinctly to the ongoing changes in wave climate triggered by ENSO viability, with El Niño events typically resulting in accretion and La Niña periods causing erosion. Notably, mean wave direction is the metric most closely linked to changes in the shoreline among all the others. In conclusion, the interplay of escalating anthropogenic activities, natural processes, and climate change contributes to the long-term evolution of sandy shorelines. We believe this study can offer a scientific reference for erosion prevention and management strategies of sandy beaches, based on the analysis presented above.

Comparative analysis of complete chloroplast genomes of 14 Asteraceae species.

The Asteraceae family, the largest and one of the most diverse families of angiosperms, presents significant challenges in taxonomic classification and systematic research due to its vast species diversity and morphological complexity. A comprehensive understanding of the chloroplast genomes within this family is essential for refining taxonomic classifications and advancing phylogenetic studies. In this study, we sequenced the complete chloroplast genomes of 14 Asteraceae species and conducted a thorough bioinformatic analysis of their characteristics. The chloroplast genomes, ranging from 150,907bp to 152,858bp, exhibit a typical quadripartite structure: a large single-copy (LSC) region (83,044bp to 84,625bp), a small single-copy (SSC) region (18,223bp to 18,673bp), and a pair of inverted repeats (IRs) (24,806bp to 25,201bp). These genomes encode 87 to 89 protein-coding genes (PCGs), 36 to 37 tRNA genes, and 8 rRNA genes, with high conservation in size, structure, gene content, and order. Comparative analysis with other Asteraceae species' chloroplast genomes revealed notable similarities and structural variations, particularly in the IR regions. Nucleotide polymorphism analysis identified four genes-trnY-GUA, trnE-UUC, ycf1, and rrn23-with higher Pi values, suggesting potential hotspots for evolutionary studies. Phylogenetic analysis using maximum likelihood (ML) and Bayesian inference (BI) approaches provided new insights, proposing the reclassification of Himalaiella auriculata and Jacobaea raphanifolia as independent genera, distinct from Saussurea and Senecio. This study presents a comprehensive analysis of the chloroplast genome structures and phylogenetic relationships of 14 Asteraceae species, offering critical data for future molecular identification, evolutionary biology, and population genetics research. The findings hold significant implications for the ongoing refinement of Asteraceae taxonomic classifications and enhance our understanding of the evolutionary dynamics within this complex family.

Rich dynamics of a hepatitis C virus infection model with logistic proliferation and time delays

AbstractIn this paper, we study a dynamic model of hepatitis C virus (HCV) infection with density‐dependent proliferation of uninfected and infected hepatocytes and two time delays, which is derived from a three‐dimensional model by the quasi‐steady‐state approximation. The model can exhibit forward bifurcation or backward bifurcation, and an explicit control threshold parameter is obtained for the case of backward bifurcation. It is shown that if the proliferation rate of infected hepatocytes is greater than the proliferation rate of uninfected hepatocytes by a certain amount, it becomes more difficult for the virus to be removed. The model has rich dynamical properties: (i) In some parameter regions, bistability can occur; (ii) both time delays (virus‐to‐cell delay) and (cell‐to‐cell delay) can lead to Hopf bifurcations; (iii) same length of time delays and can lead to at most one stability switch, but different time delays can lead to multiple stability switches. Several sufficient conditions for the global stability of the disease‐free equilibrium and the endemic equilibrium are obtained for both forward and backward bifurcation scenarios. In particular, several sharp results on global stability are obtained. Theoretical and numerical results portray the complexity of viral evolutionary dynamics in chronic HCV‐infected patients.

The burst of satellite DNA in Leptidea wood white butterflies and their putative role in karyotype evolution.

Satellite DNAs (satDNAs) are abundant components of eukaryotic genomes, playing pivotal roles in chromosomal organization, genome stability and evolution. Here, we combined cytogenetic and genomic methods to characterize the satDNAs in the genomes of Leptidea butterflies. Leptidea is characterized by the presence of a high heterochromatin content, large genomes and extensive chromosomal reshuffling as well as the occurrence of cryptic species. We show that, in contrast to other Lepidoptera, satDNAs constitute a considerable proportion of Leptidea genomes, ranging between 4.11%-11.05%. This amplification of satDNAs, together with the hyperactivity of transposable elements, contributes to the substantial genome expansion in Leptidea. Using chromosomal mapping, we show that, particularly LepSat01-100 and LepSat03-167 satDNAs, are preferentially localized in heterochromatin exhibiting variable distribution that could influence in the highly diverse karyotypes within the genus. The satDNAs also exhibit W-chromosome accumulation, suggesting their involvement in sex chromosome evolution. Our results provide insights into the dynamics of satDNAs in Lepidoptera genomes and highlight their role in genome expansion and chromosomal organization, which could influence the speciation process. The high proportion of repetitive DNAs in the genomes of Leptidea underscores the complex evolutionary dynamics revealing the interplay between repetitive DNAs and genomic architecture in the genus.

Predicting and anticipating rapid evolution.

Human impacts alter species interactions and evolutionary dynamics in wild populations.

The Accelerating Universe in a NoncommutativeAnalytically Continued Foliated Quantum Gravity

Abstract Based on an analytically continued Riemannian foliated quantum gravity
super-Hamiltonian, known as Branch Cut Quantum Gravity (BCQG) we propose
a novel approach to investigating the effects of noncommutative geometry on a
minisuperspace of variables, influencing the acceleration behavior of the universe’s
wave function and the cosmic scale factor. Noncommutativity is introduced through
a deformation of the conventional Poisson algebra, enhanced with a symplectic
metric. The resulting symplectic manifold provides a natural setting that enables
an isomorphism between canonically conjugate dual vector spaces, spanning the
BCQG cosmic scale factor and its complementary quantum counterpart. Using this
formulation, we describe the dynamic evolution of the universe’s wave function, the
cosmic scale factor, and its complementary quantum image. Our results strongly
suggest that the noncommutative algebra induces late-time accelerated growth of the
wave function, the universe’s scale factor, and its complementary quantum counterpart,
offering a new perspective on explaining the accelerating cosmic expansion rate and
the inflationary period. In contrast to the inflationary model, where inflation requires
a remarkably fine-tuned set of initial conditions in a patch of the universe, analytically
continued non-commutative foliated quantum gravity captures short and long scales,
driving the evolutionary dynamics of the universe through a reconfiguration of the
primordial cosmic content of matter and energy. This reconfiguration is encapsulated
into a quantum field potential, which leads to the generation of relic gravitational
waves, a topic for future investigation. Graphical representations and contour plots
indicate a characteristic torsion (or twist) deformation of spacetime geometry. This
result introduces new speculative elements regarding the reconfiguration of matter and
energy as a driver of spacetime torsion deformation, generating relic gravitational waves
and serving as an alternative topological mechanism for the universe’s acceleration.
However, these assumptions require further investigation.

Fundamental constraints to the logic of living systems.

It has been argued that the historical nature of evolution makes it a highly path-dependent process. Under this view, the outcome of evolutionary dynamics could have resulted in organisms with different forms and functions. At the same time, there is ample evidence that convergence and constraints strongly limit the domain of the potential design principles that evolution can achieve. Are these limitations relevant in shaping the fabric of the possible? Here, we argue that fundamental constraints are associated with the logic of living matter. We illustrate this idea by considering the thermodynamic properties of living systems, the linear nature of molecular information, the cellular nature of the building blocks of life, multicellularity and development, the threshold nature of computations in cognitive systems and the discrete nature of the architecture of ecosystems. In all these examples, we present available evidence and suggest potential avenues towards a well-defined theoretical formulation.

Extrachromosomal DNA driven oncogene spatial heterogeneity and evolution in glioblastoma.

ecDNA is the most common mechanism of focal oncogene amplification in IDH wt glioblastoma. EGFR and its variants on ecDNA are particularly potent, likely arising early in tumor development, providing a strong oncogenic stimulus to drive tumorigenesis. Wild-type and variant EGFR ecDNA heteroplasmy (co-occurrence) is common with EGFR vIII or c-terminal deletions being derived from EGFR wild-type ecDNA prior to the most recent clonal expansion. Tumors with ecDNA amplified EGFR versus PDGFRA exhibit different evolutionary trajectories. SPECIES model can infer spatial evolutionary dynamics of ecDNA in cancer.A delay between ecDNA accumulation and subsequent oncogenic mutation may give a therapeutic window for early intervention.

Genomic insights into high-altitude adaptation and evolutionary dynamics of Indian yaks in the Trans-Himalayan region

Genomic insights into high-altitude adaptation and evolutionary dynamics of Indian yaks in the Trans-Himalayan region