Evolution Research Articles

The crossroads of clonal evolution, differentiation hierarchy and ontogeny in leukemia development.

Transformative technologies to sequence tumor genomes at large scale and single-cell resolution have exposed the repertoire of genetic alterations that are present in leukemia genomes, the timing of their acquisition and patterns of their co-occurrence. In parallel, single-cell multi-omics technologies are allowing us to map the differentiation paths and hierarchical structures of malignant cells and giving us a glimpse into hematopoietic development in prenatal life. We propose that interrogating how the genetic evolution, differentiation hierarchy and ontogeny of malignant myeloid cells intersect with each other, using new experimental systems and multimodal technologies, will fuel the next generation of research breakthroughs.

A governability lesson for the Blue Economy: the collapse of mobile salmon aquaculture in the Norwegian coastal zone

Inspired by governability and evolutionary governance theory, this paper studies innovative aquaculture technologies that aim to contribute to the transition toward a sustainable blue economy. By tracing path, inter-, and goal dependencies, we explore a case related to developing new production systems in the Norwegian salmon aquaculture industry. As further development using conventional production systems is deemed unsustainable, the government has incentivised technological innovation to alleviate environmental and spatial pressures limiting industry expansion. We describe the work behind enrolling one innovative technology into the coastal governance system. As we find, there are conflicts between the conditions in governance that technological innovations depend on for realisation versus the conditions the governance system depends on for governability. Through our relational approach, we display how innovation challenges governability and that achieving Blue Economy objectives may require considerable political and administrative reorganisation of the existing governance setup.

Ultrahigh-Resolution Mass Spectrometry Advances for Biogeochemical Analysis: From Seafloor Sediments to Petroleum and Marine Oil Spills.

This Perspective explores the transformative impact of ultrahigh-resolution mass spectrometry (UHR-MS), particularly Fourier transform ion cyclotron resonance (FT-ICR-MS), in the characterization of complex environmental and petroleum samples. UHR-MS has significantly advanced our ability to identify molecular formulas in complex mixtures, revolutionizing the study of biogeochemical processes and organic matter evolution on wide time scales. We start by briefly reviewing the main technological advances of UHR-MS in the context of petroleum and environmental applications, highlighting some of the challenges of the technology such as quantitation and structural identification. We then showcase a selection of impactful applications published in the last 20+ years. In the field of environmental lipidomics, high-resolution analysis of lipids in sediments enables multiproxy studies and provides novel insights into past environmental conditions. UHR-MS has also facilitated the characterization of kerogen, a complex, poorly soluble mixture formed from sedimented organic matter over geological time scales, and the identification of polar compounds within its fractions. In petroleum (geo)chemistry, UHR-MS has enabled the identification of biomarkers such as petroporphyrins, asphaltenes, and high-molecular-weight naphthenic acids, shedding light on the molecular complexity of crude oil. The application of UHR-MS in oil spill science has revealed significant molecular transformations during weathering processes, such as photo-oxidation, which are crucial for assessing the environmental impact of past spills and improving the preparedness for future spills. These advancements underscore the role of this maturing analytical technology in deepening our understanding of geochemical processes and biogeochemical cycles, highlighting its potential for future research directions in organic geochemistry.

Research and Simulation Application of Automatic Generation of Judging Curves for IoT Mobile Devices in Train Driving Operations Incorporating Hybrid Genetic Algorithms

A control system for automatically generating a train operation evaluation curve based on a hybrid genetic algorithm has been proposed in order to improve the safety of automatic train operation. The system is based on Internet of Things (IoT) mobile devices and utilizes various sensors such as accelerometers, gyroscopes, barometers, and GPS to collect real-time data on the driver’s acceleration, angular velocity, air pressure, and position, among other parameters. 5G wireless communication technology is used to achieve high-speed data transmission and real-time communication with the cloud. Based on cloud data, a spatial grid area planning model is constructed to automatically generate the train operation evaluation curve. Using a spatial dynamic programming method, the entire network of Electric Multiple Unit (EMU) trains is treated as a whole, and a dynamic model of the EMU train is constructed. The spatial area parameters of the EMU train’s automatic driving operation evaluation curve are combined with the dynamic model analysis method. By identifying and analyzing environmental parameters such as train speed and distance, the EMU train’s automatic driving operation evaluation curve is optimized. A hybrid genetic evolution learning optimization algorithm is used to fit the motion spatial parameters of the EMU train’s automatically generated driving operation evaluation curve, and a spatial behavior analysis simulation is created for the EMU train’s automatically generated control driving operation curve. Through the use of hybrid genetic evolution learning optimization technology, adaptive control and automatic driving operation curve simulation planning for the automatically generated driving operation evaluation curve of the maglev train are achieved, as well as simulation and algorithm optimization design for the automatically generated driving operation evaluation curve of the maglev train. The simulation results show that the method has good adaptability and strong automatic control capability. The experimental results demonstrate the control effect of the proposed method on energy consumption and train stopping error, indicating that the proposed method can effectively improve the parameter adjustment and offset correction ability of the evaluation curve generated by the high-speed train driving operation.

How can statistical models improve the accuracy of phylogenetic tree reconstruction?

When building the phylogenetic tree, current methods for calculating phylogenetic trees often lack the desired level of accuracy. This research paper explores the role of statistical models in enhancing the precision of phylogenetic tree reconstruction. The phylogenetic tree plays an important role in phylogenetic analysis and evolutionary biology. An accurate phylogenetic tree underpins our understanding of the major transitions in evolution, such as the emergence of new body plans or metabolism. Recent advancements in statistical modeling have more elaborate improvements than traditional methods. For example, Bayesian inference and maximum likelihood estimation provide frameworks for evaluating phylogenetic relationships by incorporating probability distributions and likelihood functions. These models account for the inherent uncertainties and variations in genetic data, leading to more accurate tree constructions. Moreover, using statistical models allows for the incorporation of complex evolutionary processes such as variable rates of evolution across lineages, horizontal gene transfer, and hybridization events. Techniques like Markov Chain Monte Carlo (MCMC) and bootstrap methods enhance the reliability of the inferred phylogenies by providing measures of confidence for the estimated relationships. Using these advanced statistical approaches, researchers can gain more accurate and reliable phylogenetic trees. Through a comprehensive review of current methodologies and case studies, this study aims to highlight statistical models' significant impact on evolutionary biology and the broader field of phylogenetics analysis and evolutionary biology.

A microRNA is the effector gene of a classic evolutionary hotspot locus.

In Lepidoptera (butterflies and moths), the genomic region around the gene cortex is a "hotspot" locus, repeatedly implicated in generating intraspecific melanic wing color polymorphisms across 100 million years of evolution. However, the identity of the effector gene regulating melanic wing color within this locus remains unknown. We show that none of the four candidate protein-coding genes within this locus, including cortex, serve as major effectors. Instead, a microRNA (miRNA), mir-193, serves as the major effector across three deeply diverged lineages of butterflies, and its role is conserved in Drosophila. In Lepidoptera, mir-193 is derived from a gigantic primary long noncoding RNA, ivory, and it functions by directly repressing multiple pigmentation genes. We show that a miRNA can drive repeated instances of adaptive evolution in animals.

A reinterpretation of the past 2.5 billion years of Earth’s tectonic history: Two episodes each of plate and single-lid tectonics

This paper reinterprets the past 2.5 billion years of Earth’s tectonic history as four alternating episodes when plate tectonics dominated and when it did not. Solar System exploration over the past 50 years reveals that 75% of the four actively convecting silicate bodies (Venus, Earth, Mars, and Io) do not have plate tectonics. Instead, their deformed and magmatically active lithospheres are better characterized as coherent, if deformed, single lids. I identified geologic indicators of plate tectonic regimes and single-lid tectonic regimes, used published compilations of these, and worked backward in time to 2.5 Ga. This analysis reveals four distinct tectonic episodes, two each of plate tectonics and single-lid tectonics. The youngest is the current episode of plate tectonics (PT2), which began at ca. 800 Ma. PT2 was preceded by an ∼600-m.y.-long episode of single-lid tectonics during the Mesoproterozoic (SL2). SL2 was preceded by an ∼300-m.y.-long episode of plate tectonics in mid-Paleoproterozoic time (PT1). The oldest post-2.5 Ga tectonic episode was an enigmatic ∼200-m.y.-long interval of single-lid tectonics in early Paleoproterozoic time (SL1). Each episode is separated from earlier and later episodes by transitional periods lasting 100−200 m.y. This reinterpretation of Earth’s post-2.5 Ga tectonic history helps to explain why Earth’s mantle is warmer than it would be if it had cooled as rapidly as it is cooling today—that is, if plate tectonics operated continuously during this time. It also moots the question of “When did plate tectonics start?” and suggests that a better question is, “How far back in time can we confidently reconstruct Earth’s tectonic history?” The reframed question provides new research opportunities and insights into mineralization, climate, and biologic evolution, and opens the door to a better understanding of Archean, especially Late Archean, tectonics.

Gene acquisition by giant transposons primes eukaryotes for rapid evolution via horizontal gene transfer.

Horizontal gene transfer (HGT) disseminates genetic information between species and is a powerful mechanism of adaptation. Yet, we know little about its underlying drivers in eukaryotes. Giant Starship transposons have been implicated as agents of fungal HGT, providing an unprecedented opportunity to reveal the evolutionary parameters behind this process. Here, we characterize the ssf gene cluster, which contributes to formaldehyde resistance, and use it to demonstrate how mobile element evolution shapes fungal adaptation. We found that ssf clusters have been acquired by various distantly related Starships, which each exhibit multiple instances of horizontal transfer across fungal species (at least nine events, including between different taxonomic orders). Many ssf clusters have subsequently integrated into their host's genome, illustrating how Starships shape the evolutionary trajectory of fungal hosts beyond any single transfer. Our results demonstrate the key role Starships play in mediating rapid and repeated adaptation via HGT, elevating the importance of mobile element evolution in eukaryotic biology.

Scatter Search for Optimal Sizing of a Hybrid Renewable Energy System for Scheduling Green Hydrogen Production

At present, energy demands are mainly covered by the use of fossil fuels. The process of fossil fuel production increases pollution from oil extraction, transport to processing centers, treatment to obtain lighter fractions, and delivery and use by the final consumers. Such polluting circumstances are aggravated in the case of accidents involving fossil fuels. They are also linked to speculative markets. As a result, the trend is towards the decarbonization of lifestyles in advanced societies. The present paper addresses the problem of the optimal sizing of a hybrid renewable energy system for scheduling green hydrogen production. A local system fully powered by renewable energies is designed to obtain hydrogen from seawater. In order to monetize excess energy, the grid connection of the system is considered under realistic energy market constraints, designing an hourly purchasing strategy. This crucial problem, which has not been taken into account in the literature, is solved by the specific dispatch strategy designed. Several optimization methods have been used to solve this problem; however, the scatter search method has not previously been employed. In this paper, the problem is faced with a novel implementation of this method. The implementation is competitive in terms of performance when compared to, on the one hand, the genetic algorithm and differential evolution methods, which are well-known state-of-the-art evolutionary algorithms, and, on the other hand, the optimal foraging algorithm (OFA), a more recent algorithm. Furthermore, scatter search outperformed all other methods in terms of computational cost. This is promising for real-world applications that require quick responses.

Rare events analysis and computation for stochastic evolution of bacterial populations

In this article, we develop a computational approach for estimating the most likely trajectories describing rare events that correspond to the emergence of non-dominant genotypes. This work is based on the large deviations approach for discrete Markov chains describing the genetic evolution of large bacterial populations. We demonstrate that a gradient descent algorithm developed in this article results in the fast and accurate computation of most likely trajectories for a large number of bacterial genotypes. We supplement our analysis with extensive numerical simulations demonstrating the computational advantage of the designed gradient descent algorithm over other, more simplified, approaches.

Pristionchus - Beetle associations: Towards a new natural history.

The free-living nematode Pristionchus pacificus has been established as a model system in integrative evolutionary biology by combining laboratory studies with field work and evolutionary biology. Multiple genetic, molecular and experimental tools and a collection of more than 2,500P. pacificus strains and more than 50 Pristionchus species, which are available as living cultures or frozen stock collections, support research on various life history traits. Species of Pristionchus exhibit a number of complex traits unknown from Caenorhabditis elegans and most other free-living nematodes. First, P. pacificus can form two alternative mouth forms, an example of developmental plasticity that is increasingly studied to investigate the role of plasticity as a facilitator of evolutionary novelty. More than a decade of work has identified associated genetic and epigenetic mechanisms and revealed the evolutionary and ecological significance of feeding structure plasticity. Second, one of the two mouth morphs results in predatory behavior against other nematodes and is currently used to investigate the neurobiology of predation. Third, potential predation results in the risk of cannibalism among conspecifics. Strikingly, Pristionchus nematodes have developed a self-recognition system that allows the distinction of self (kin) and non-self. Given all these organismal features, this nematode has recently been considered a key example for research towards a new natural history (West-Eberhard, 2024). Here, I summarize recent work on Pristionchus with a focus on a 'new natural history'. In addition, I review some recent studies that indicate an interaction of Pristionchus with EPNs that was suggested based on various surveys in different ecological habitats.

Prevalence and virulence of Vibrio parahaemolyticus isolated from clinical and environmental samples in Huzhou, China

BackgroundVibrio parahaemolyticus has emerged as the leading cause of seafood-associated infections worldwide. Previous studies have shown that V. parahaemolyticus can be detected in both environmental and clinical samples. However, the molecular characteristics of V. parahaemolyticus isolated from these sources remain unknown.ResultsThis study examined 128 strains of V. parahaemolyticus isolated from clinical and environmental samples collected between 2020 and 2023 in Huzhou, China. We identified 73 serotypes; O10:K4, O3:K6, and O4:KUT were the dominant serotypes among clinical isolates. We examined the proliferation and motility of major epidemic strains from environmental and clinical samples. Genetic diversity and evolution were assessed by average nucleotide identity (ANI), phylogenetic tree construction, and multilocus sequence typing (MLST). Furthermore, we identified 13 novel sequence types (STs) among the environmental isolates, indicating that V. parahaemolyticus strains are widely distributed and evolve rapidly in the environment in Huzhou, China. We found 206 virulence genes among these isolates, indicating that environmental isolates possess numerous virulence genes. Additionally, we detected 4 strains carrying the tdh or trh gene, which may increase their pathogenicity. The prediction results of antibiotic resistance genes shown that environmental isolates may carry up to 104 resistance genes, compared to 30 in clinical isolates.ConclusionsWe observed that the environmental serotypes of V. parahaemolyticus exhibit greater diversity compared to clinical isolates, which are predominantly concentrated in three major serotypes. Furthermore, a considerable genetic distance was found between most clinical and environmental isolates. Notably, some clinical isolates show a closer genetic proximity to environmental isolates. Additionally, the distribution of virulence genes, specifically T3SS and tdh, significantly differs among isolates from these two distinct sources. The prediction results for antibiotic resistance genes suggest that environmental isolates may harbor a broader spectrum of resistance genes. The findings of this study provide new insights into the phylogenetic relationships between V. parahaemolyticus strains from clinical and environmental sources, and they enhance the MLST database.

An Evolutionary Psychology Perspective on Athletic Development and Performance: Differences Between Proximate and Ultimate Explanations.

Many areas of mainstream psychology have embraced the notions that understanding human behaviour can be improved by integrating developments from evolutionary science; however, evolutionary principles have not been as widely applied among sport researchers or practitioners, especially those examining athlete development and the psychology of competition and performance. In this paper, we discuss the distinction between ultimate and proximate explanations of psychological outcomes, and the relevance of this distinction for exploring issues related to skill acquisition and athlete development. We use three examples-deliberate practice, early sport play and sustained engagement-to highlight the benefits and challenges of applying evolutionary theories to sport contexts. Embracing our species' evolutionary history has the potential to inform ongoing debates in athlete development and performance, among other areas of sport science.

A cultural evolution theory for contemporary polarization trends in moral opinions

While existing theories of political polarization tend to suggest that the opinions of liberals and conservatives move in opposite directions, available data indicate that opinions on a wide range of moral issues move in the liberal direction among both liberals and conservatives. Moreover, some political scientists have hypothesized that this movement follows an S-shaped curve among liberals and a similar, but later, S-shaped curve among conservatives, so that polarization on a given issue first increases (as opinions at an initial stage move faster among liberals) and then decreases (as opinions at a later stage move faster among conservatives). Here we show that these dynamics are explained by Moral Argument Theory, a cultural evolution theory positing that opinion shifts on moral issues arise from a certain content bias in social opinion transmission. This theory also yields several other specific predictions about trends and polarization in moral opinions, which we test against longitudinal data on 55 moral issues from the General Social Survey (sample sizes between 1798 and 57,809 per issue). The predictions are generally confirmed. We conclude that a cultural evolution perspective can provide valuable insights for social science in understanding contemporary societal changes.

DNA Barcodes and Morphology Reveal Two New Species of the Genus Prochas Walkley, 1959 (Ichneumonidae, Campopleginae), from China

DNA barcoding is an effective modern tool in taxonomy, evolutionary biology, and biodiversity research. Many new species have been discovered and described with DNA barcodes as part of their diagnostic features. We combined morphological examination and molecular species delimitation of the mitochondrial cytochrome c oxidase 1 (COI) gene using the automatic barcode gap discovery (ABGD) to investigate species boundaries. The genus Prochas Walkley (Hymenoptera, Ichneumonidae, Campopleginae) was first reported from China and is new for the Oriental and Eastern Palearctic regions. Using an integrative taxonomy method, two new species P. rugipunctata sp. nov. and P. striata sp. nov. are hereby described and illustrated. A key to the world species and a distribution map are provided.

Quadripartite Evolutionary Game of Incentives for Green Retrofitting of Historical Buildings

Green retrofitting is a potent strategy to improve energy efficiency and support the cultural conservation of historical buildings. China has many historical buildings with significant potential for green retrofitting. Nevertheless, the Chinese green retrofit industry remains in its early stages due to the lack of a comprehensive promotion mechanism. Drawing upon evolutionary game theory, an evolutionary game model was formulated to analyze the interplay among governmental regulators, Energy Service Companies (ESCOs), the owners of historical buildings, and tourists. At an extreme disturbance intensity of 100%, a striking decline is observed in the likelihood of ESCOs maintaining the “green retrofit” strategy, with the probability dropping to a minimum of 24.68%. Under specific conditions however this interplay attains an optimal equilibrium state, denoted as (1,1,1,1). It is concluded that governmental regulators exhibit a greater degree of stability compared to other stakeholders, as they maintain their strategies despite external disturbances. Therefore, it is recommended that effective incentives and regulatory frameworks should consider the sensitivities of non-regulatory stakeholders to enhance the success of green retrofitting projects for historical buildings.

Inversions contribute disproportionately to parallel genomic divergence in dune sunflowers.

The probability of parallel genetic evolution is a function of the strength of selection and constraints imposed by genetic architecture. Inversions capture locally adapted alleles and suppress recombination between them, which limits the range of adaptive responses. In addition, the combined phenotypic effect of alleles within inversions is likely to be greater than that of individual alleles; this should further increase the contributions of inversions to parallel evolution. We tested the hypothesis that inversions contribute disproportionately to parallel genetic evolution in independent dune ecotypes of Helianthus petiolaris. We analysed habitat data and identified variables underlying parallel habitat shifts. Genotype-environment association analyses of these variables indicated parallel responses of inversions to shared selective pressures. We also confirmed larger seed size across the dunes and performed quantitative trait locus mapping with multiple crosses. Quantitative trait loci shared between locations fell into inversions more than expected by chance. We used whole-genome sequencing data to identify selective sweeps in the dune ecotypes and found that the majority of shared swept regions were found within inversions. Phylogenetic analyses of shared regions indicated that within inversions, the same allele typically was found in the dune habitat at both sites. These results confirm predictions that inversions drive parallel divergence in the dune ecotypes.

A Methodology of Structural Incorporation for Model Transfer and Construction: The Case of Malthus’ and Darwin’s Models of Population

Abstract This paper proposes a methodology to investigate how the conceptual structure of a model may have borrowed from an already existing model in a different field. From a reverse perspective, it amounts to hypothesizing that an already existing model was somehow transferred to a new field and incorporated into a newly constructed model with the purpose of explaining some additional phenomena. We use two well-known theoretic models, Robert Malthus’ model of human population and Darwin’s model of organism population included in the theory of evolution by natural selection, to exemplify this “incorporation of a conceptual structure” methodology. By highlighting how the conceptual structure of Malthus’ model actually sits within that of Darwin’s model, we show how Darwin’s model may have been constructed, on the one hand, and how Malthus’ model may have been transferred, on the other hand. In order to show how the construction and transfer occur, we outline five epistemic strategies that could be underlying incorporation. Overall, this methodology can be viewed as a diadic and bijective perspective on models that can be applied to other similar cases, using “construction” and “transfer” as complementary handles to probe the available conceptual, structural, and historiographical material.

Rapid pyrolysis of paleo-oil pools recorded by fluid inclusions in an Ediacaran carbonate reservoir, southern China: Implications for the end-Guadalupian mass extinction

Thermogenic greenhouse gas emission associated with large igneous province emplacement has previously been hypothesized as a possible contributor to global warming that triggered mass extinctions in Earth’s history, yet this issue remains inadequately understood due to a lack of robust evidence. We present a well-preserved mineralogical, fluid inclusion, and geochemical record indicating a rapid pyrolysis of vast paleo-oil pools in an Ediacaran carbonate reservoir in the central Sichuan Basin (southern China) relating to the eruption of the Emeishan large igneous province that potentially contributed to the end-Guadalupian extinction (ca. 259 Ma). We conclude that the pyrolysis of the paleo-oil pools occurred at ca. 258.4 ± 7.3 Ma associated with the emplacement of the Emeishan large igneous province, causing a rapid increase of temperature and pressure with an estimated transient reservoir pressure of nearly twice that of the lithostatic pressure. A subsequent drop in the formation pressure occurred as the temperature continued to rise, indicating that massive over-pressured methane in the reservoir had been rapidly emitted into the atmosphere along faults or magmatic pipes, ultimately contributing to the end-Guadalupian extinction. Our study highlights the significance of massive emission of thermogenic methane related to large igneous provinces for climate change, carbon cycling, and biological evolution in Earth’s history.

A transphyletic study of metazoan β-catenin protein complexes

Beta-catenin is essential for diverse biological processes, such as body axis determination and cell differentiation, during metazoan embryonic development. Beta-catenin is thought to exert such functions through complexes formed with various proteins. Although β-catenin complex proteins have been identified in several bilaterians, little is known about the structural and functional properties of β-catenin complexes in early metazoan evolution. In the present study, we performed a comparative analysis of β-catenin sequences in nonbilaterian lineages that diverged early in metazoan evolution. We also carried out transphyletic function experiments with β-catenin from nonbilaterian metazoans using developing Xenopus embryos, including secondary axis induction in embryos and proteomic analysis of β-catenin protein complexes. Comparative functional analysis of nonbilaterian β-catenins demonstrated sequence characteristics important for β-catenin functions, and the deep origin and evolutionary conservation of the cadherin–catenin complex. Proteins that co-immunoprecipitated with β-catenin included several proteins conserved among metazoans. These data provide new insights into the conserved repertoire of β-catenin complexes.