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Background: Introgression has repeatedly been shown to play an important role in the adaptation of species to extreme environments, yet how introgression enables rodents with specialized subterranean lifestyle to acclimatize to high altitudes is still unclear. Myospalacinae is a group of subterranean rodents, among which the high-altitude plateau zokors (Eospalax baileyi) and the low-altitude Gansu zokors (E. cansus) are sympatrically distributed in the grassland ecosystems of the Qinghai-Tibet Plateau (QTP). Together, they provide a model for the study of the role of introgression in the adaptation of low-altitude subterranean rodents to high altitudes. Results: Applying low-coverage whole-genome resequencing and population genetics analyses, we identified evidence of adaptive introgression from plateau zokors into Gansu zokors, which likely facilitated the adaptation of the latter to the high-altitude environment of the QTP. We identified positively selected genes with functions related to energy metabolism, cardiovascular system development, calcium ion transport, and response to hypoxia which likely made critical contributions to adaptation to the plateau environment in both plateau zokors and high-altitude populations of Gansu zokors. Conclusions: Introgression of genes associated with hypoxia adaptation from plateau zokors may have played a role in the adaptation of Gansu zokors to the plateau environment. Our study provides new insights into the understanding of adaptive evolution of species on the QTP and the importance of introgression in the adaptation of species to high-altitude environments. [ABSTRACT FROM AUTHOR]

Background: The tribe Ampelopsideae plants are important garden plants with both medicinal and ornamental values. The study of codon usage bias (CUB) facilitates a deeper comprehension of the molecular genetic evolution of species and their adaptive strategies. The joint analysis of CUB in chloroplast genomes (cpDNA) offers valuable insights for in-depth research on molecular genetic evolution, biological resource conservation, and elite breeding within this plant family. Results: The base composition and codon usage preferences of the eighteen chloroplast genomes were highly similar, with the GC content of bases at all positions of their codons being less than 50%. This indicates that they preferred A/T bases. Their effective codon numbers were all in the range of 35–61, which indicates that the codon preferences of the chloroplast genomes of the 18 Ampelopsideae plants were relatively weak. A series of analyses indicated that the codon preference of the chloroplast genomes of the 18 Ampelopsideae plants was influenced by a combination of multiple factors, with natural selection being the primary influence. The clustering tree generated based on the relative usage of synonymous codons is consistent with some of the results obtained from the phylogenetic tree of chloroplast genomes, which indicates that the clustering tree based on the relative usage of synonymous codons can be an important supplement to the results of the sequence-based phylogenetic analysis. Eventually, 10 shared best codons were screened on the basis of the chloroplast genomes of 18 species. Conclusion: The codon preferences of the chloroplast genome in Ampelopsideae plants are relatively weak and are primarily influenced by natural selection. The codon composition of the chloroplast genomes of the eighteen Ampelopsideae plants and their usage preferences were sufficiently similar to demonstrate that the chloroplast genomes of Ampelopsideae plants are highly conserved. This study provides a scientific basis for the genetic evolution of chloroplast genes in Ampelopsideae species and their suitable strategies. [ABSTRACT FROM AUTHOR]

Cancer therapy is facing increasingly significant challenges, marked by a wide range of techniques and research efforts centered around somatic mutations, precision oncology, and the vast amount of big data. Despite this abundance of information, the quest to cure cancer often seems more elusive, with the "war on cancer" yet to deliver a definitive victory. A particularly pressing issue is the development of tumor treatment resistance, highlighting the urgent need for innovative approaches. Evolutionary, Quantum Biology and System Biology offer a promising framework for advancing experimental cancer research. By integrating theoretical studies, translational methods, and flexible multidisciplinary clinical research, there's potential to enhance current treatment strategies and improve outcomes for cancer patients. Establishing stronger links between evolutionary, quantum, entropy and chaos principles and oncology could lead to more effective treatments that leverage an understanding of the tumor's evolutionary dynamics, paving the way for novel methods to control and mitigate cancer. Achieving these objectives necessitates a commitment to multidisciplinary and interprofessional collaboration at the heart of both research and clinical endeavors in oncology. This entails dismantling silos between disciplines, encouraging open communication and data sharing, and integrating diverse viewpoints and expertise from the outset of research projects. Being receptive to new scientific discoveries and responsive to how patients react to treatments is also crucial. Such strategies are key to keeping the field of oncology at the forefront of effective cancer management, ensuring patients receive the most personalized and effective care. Ultimately, this approach aims to push the boundaries of cancer understanding, treating it as a manageable chronic condition, aiming to extend life expectancy and enhance patient quality of life. [ABSTRACT FROM AUTHOR]

Lymphocyte receptors independently evolved in both jawed and jawless vertebrates with similar adaptive immune responses. However, the diversity of functional subtypes and molecular architecture in jawless vertebrate lymphocytes, comparable to jawed species, is not well defined. Here, we profile the gills, intestines, and blood of the lamprey, Lampetra morii, with single-cell RNA sequencing, using a full-length transcriptome as a reference. Our findings reveal higher tissue-specific heterogeneity among T-like cells in contrast to B-like cells. Notably, we identify a unique T-like cell subtype expressing a homolog of the nonlymphoid hematopoietic growth factor receptor, MPL-like (MPL-L). These MPL-L+ T-like cells exhibit features distinct from T cells of jawed vertebrates, particularly in their elevated expression of hematopoietic genes. We further discovered that MPL-L+ VLRA+ T-like cells are widely present in the typhlosole, gill, liver, kidney, and skin of lamprey and they proliferate in response to both a T cell mitogen and recombinant human thrombopoietin. These findings provide new insights into the adaptive immune response in jawless vertebrates, shedding new light on the evolution of adaptive immunity. Lymphocyte subsets remain inadequately understood in jawless vertebrates, relative to jawed vertebrates. In this study, the authors combine single-cell RNA and whole-transcriptome sequencing to demonstrate that the lamprey, Lampreta morii, harbours specialised T-like cells that are distinct from those found in jawed vertebrates. [ABSTRACT FROM AUTHOR]

Bas van Fraassen's Darwinian explanation for the success of science has sparked four decades of discussion, with scientific realists and antirealists alike using biologically inspired reasoning to support their points of view. Based on critical engagement with van Fraassen's proposal itself and later contributions by Stathis Psillos and K. Brad Wray, we claim that central arguments on both sides of this controversy suffer from an insufficient understanding of Darwinism and its underlying biological concepts. Adding the necessary biological background turns out to subvert the argumentative force of viewing the success of scientific theories as analogous to the behaviour of biotic entities. In conclusion, we sketch more productive ways of viewing the relationship between biology and scientific realism. [ABSTRACT FROM AUTHOR]

The document "Contributors" from Curtis's Botanical Magazine provides brief biographical information about various researchers and professionals in the field of botany, horticulture, and botanical art. The contributors come from diverse backgrounds and institutions in Japan, Spain, the United Kingdom, and Singapore, showcasing a wide range of expertise in areas such as fern and lycophyte flora, plant systematics, ecological research, and botanical illustration. Their research interests include evolutionary history, plant diversity, conservation, and biological interactions, contributing valuable knowledge to the botanical community. [Extracted from the article]

This article explores various methods for tracing the geographic origin of illegally traded wildlife. It discusses the use of trade records, elemental signatures, and molecular genetics analysis as means to determine the source of confiscated animals and their products. The article emphasizes the importance of combining these approaches and establishing comprehensive databases to improve traceability and combat illegal trade. It also suggests the need for global action programs to reduce consumer demand, strengthen law enforcement measures, and promote sustainable alternatives to wildlife products in order to prevent the illegal wildlife trade and conserve biodiversity. [Extracted from the article]

It remains debatable how many genes and how various the mechanisms are behind human adaptation to extreme environments, such as high altitudes. Despite extensive studies on Tibetans, Andeans and Ethiopians, new insights are expected to be provided with careful analysis of underrepresented highlanders living in a different geographical region, such as the Tajiks, who reside on the Pamir Plateau at an average altitude exceeding 4000 meters. Moreover, genetic admixture, as we observed in the current whole-genome deep-sequencing study of Xinjiang Tajiks (XJT), offers a unique opportunity to explore how admixture may facilitate adaptation to high-altitude environments. Compared with other extensively studied highlanders, XJT showed pronounced admixture patterns: most of their ancestry are derived from West Eurasians (34.5%–48.3%) and South Asians (21.4%–40.0%), and some minor ancestry from East Asians and Siberians (3.62%–17.5%). The greater genetic diversity in XJT than in their ancestral source populations provides a genetic basis for their adaptation to high-altitude environments. The admixture gain of functional adaptive components from ancestral populations could facilitate adaptation to high-altitude environments. Specifically, admixture-facilitated adaptation was strongly associated with skin-related candidate genes that respond to UV radiation (e.g. HERC2 and BNC2) and cardiovascular-system-related genes (e.g. MPI and BEST1). Notably, no adaptive variants of genes showing outstanding natural selection signatures in the Tibetan or Andean highlanders were identified in XJT, including EPAS1 and EGLN1 , indicating that a different set of genes contributed to XJT's survival on the Pamir Plateau, although some genes underlying natural selection in XJT have been previously reported in other highlanders. Our results highlight the unique genetic adaptations in XJT and propose that admixture may play a vital role in facilitating high-altitude adaptation. By introducing and elevating diversity, admixture likely induces novel genetic factors that contribute to the survival of populations in extreme environments like the highlands. [ABSTRACT FROM AUTHOR]

Intraspecific trait variation, essential to Darwin's mechanism of natural selection, has been widely examined for single characters. However, intraspecific variation of adaptive strategies which represent trade‐offs among multiple functional traits has received less attention, particularly for species that are globally distributed or invasive. Grime's competitor, stress tolerator and ruderal (CSR) scheme, well validated in the context of alien species invasions, provides both the theory and quantitative methodology to investigate adaptive strategies.Here, we quantified the intraspecific CSR strategy scores of a worldwide collection of 89 Phragmites australis genotypes which were cultivated in a common garden. We assessed the relationships between intraspecific variation in CSR strategy scores, genome size and climate of origin and tested whether the invasive and native lineages differ in CSR strategies.Substantial variation in intraspecific adaptive strategy, characterized mainly in C‐ and S‐selection, was observed. As expected, C‐, S‐ and R‐scores showed clear latitudinal clines and were strongly related to either genome size or climate of origin. Furthermore, invasive lineages were more stress adapted than native lineages.We conclude that the adaptive strategy of this perennial wetland grass varies globally, and its genotypes are surprisingly more stress tolerant in the invaded range where it was first detected ~150 years ago. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

In the present study, the physicochemical characteristics of 108 yoghurts purchased from the Greek market have been assessed. Generally, the range of the mean pH values of samples was 3.58–4.64, of fat 0–10.8%, of protein 3.29–10.05%, of total solids 10.75–25.18%, and of ash 0.5–1.17%. Samples were categorized as strained and non-strained (traditional with a crust or plain without a crust). The milk origin was classified as being from sheep, goats, cows, mixture of sheep–goat–cow milk, or cow–donkey milk combination. A significant effect of species origin was determined for yoghurt physicochemical attributes, whereas geographical origin, mainland or island, affected yoghurt acidity only. Discriminant analysis revealed MDA, pH, acidity, syneresis, fat, and protein content and color lightness and redness as the traits responsible for the discrimination of yoghurts into milk-type classes, whereas fat, protein, and ash content, pH, and syneresis attributes were responsible for the discrimination into fat content classes. Yoghurt samples were sufficiently clustered according to their fat content, whereas protein content and species origin discriminated yoghurts to a lesser extent. This first in-depth descriptive research on a wide range of samples of the renowned Greek yoghurt showed that several physicochemical characteristics can be used for sample discrimination. [ABSTRACT FROM AUTHOR]

Biological evolution has generated a vast array of natural compounds produced by organisms across all domains. Among these, secondary metabolites, selected to enhance an organism's competitiveness in its natural environment, make them a reservoir for discovering new compounds with cytotoxic activity, potentially useful as novel anticancer agents. Slime secretions, the first barrier between epithelial surfaces and the surrounding environment, frequently contain cytotoxic molecules to limit the growth of parasitic organisms. Planarians, freshwater Triclads, continuously secrete a viscous mucus with multiple physiological functions. The chemical composition of planarian mucus has been only partially elucidated, and there are no studies reporting its cytotoxic or cytostatic effects. In this study, we developed a protocol for collecting mucus from Dugesia japonica specimens and we demonstrated that it inhibits the growth of cancer cells by activating cytostatic and ROS-dependent cytotoxic mechanisms inducing lipid droplet accumulation and mitochondrial membrane reorganization. Although further research is needed to identify the specific chemicals responsible for the anticancer activity of planarian mucus, this work opens up numerous research avenues aimed at better understanding the mechanisms of action of this product for potential therapeutic applications. [ABSTRACT FROM AUTHOR]

Simple Summary: Adherence to smooth substrates is closely related to the morphology and distribution of adhesive structures on insects' legs, so it is hypothesized that the adhesive structures have been evolved as an adaption to smooth substrates in specific environments. However, the factors that promote the evolution of adhesive structures are still unclear. Using scanning electron microscopy, we compared the microstructure of the tarsi of five tiger beetle species, both male and female, belonging to two tribes living in arboreal and non-arboreal environments. We found that the different types of adhesive setae, including elongated spoon-like setae, elliptical setae, branched setae, filament-like setae, discoidal setae, spatulate setae and tapered setae, varied in different environments and genders. The adaptive evolution of these adhesive structures was probably driven by the selective pressures of both mating behavior and the presence of smooth substrates in the respective environments. The ability of many insects to adhere vertically or even upside down to smooth substrates is closely related to the morphology and distribution of the adhesive structures on their legs. During locomotion, the legs are in direct contact with different substrates, and it is hypothesized that the adhesive structures have been evolved as an adaption to smooth substrates in specific environments. To investigate whether there is a relationship between the presence of adhesive structures and the combined effects of different environments and mating behavior, we compared five species of tiger beetles belonging to two tribes living in arboreal and non-arboreal environments, respectively. In three non-arboreal species, we found a specific type of adhesive structure consisting of elongated spoon-like setae present on the protarsi of males but absent on the male meso- and metatarsi and on females. In Tricondyla pulchripes, an arboreal species living on stems, we found three types of adhesive setae on male protarsi, while only two types of setae were found on male meso- and metatarsi and on females. In Neocollyris linearis, an arboreal species living on leaves, we found three types of adhesive setae on male pro-, meso- and meta-tarsi but only two types of adhesive setae on females. The adaptive evolution of these adhesive structures was probably driven by the selective pressures of both mating behavior and the presence of smooth substrates in the respective environments. It is discussed that the adhesive structures in tiger beetles may be an adaptive evolutionary response to the plant surfaces and may play an important role in species differentiation. [ABSTRACT FROM AUTHOR]

Whole‐genome duplication (polyploidy) poses many complications but is an important driver for eukaryotic evolution. To experimentally study how many challenges from the cellular (including gene expression) to the life history levels are overcome in polyploid evolution, a system in which polyploidy can be reliably induced and sustained over generations is crucial. Until now, this has not been possible with animals, as polyploidy notoriously causes first‐generation lethality. The parasitoid wasp Nasonia vitripennis emerges as a stunningly well‐suited model. Polyploidy can be induced in this haplodiploid system through (1) silencing genes in the sex determination cascade and (2) by colchicine injection to induce meiotic segregation failure. Nasonia polyploids produce many generations in a short time, making them a powerful tool for experimental evolution studies. The strong variation observed in Nasonia polyploid phenotypes aids the identification of polyploid mechanisms that are the difference between evolutionary dead ends and successes. Polyploid evolution research benefits from decades of Nasonia research that produced extensive reference—omics data sets, facilitating the advanced studies of polyploid effects on the genome and transcriptome. It is also possible to create both inbred lines (to control for genetic background effects) and outbred lines (to conduct polyploid selection regimes). The option of interspecific crossing further allows to directly contrast autopolyploidy (intraspecific polyploidy) to allopolyploidy (hybrid polyploidy). Nasonia can also be used to investigate the nascent field of using polyploidy in biological control to improve field performance and lower ecological risk. In short, Nasonia polyploids are an exceptional tool for researching various biological paradigms. [ABSTRACT FROM AUTHOR]

Cycle‐cup oaks (Quercus section Cyclobalanopsis) are one of the principal components of forests in the tropical and subtropical climates of East and Southeast Asia. They have experienced relatively recent increases in the diversification rate, driven by changing climates and the Himalayan orogeny. However, the evolutionary history and adaptive mechanisms at the chloroplast genome level in cycle‐cup oaks remain largely unknown. Therefore, we studied this problem by conducting chloroplast genomics on 50 of the ca. 90 species. Comparative genomics and other analyses showed that Quercus section Cyclobalanopsis had a highly conserved chloroplast genome structure. Highly divergent regions, such as the ndhF and ycf1 gene regions and the petN—psbM and rpoB—trnC‐GCA intergenic spacer regions, provided potential molecular markers for subsequent analysis. The chloroplast phylogenomic tree indicated that Quercus section Cyclobalanopsis was not monophyletic, which mixed with the other two sections of subgenus Cerris. The reconstruction of ancestral aera inferred that Palaeotropics was the most likely ancestral range of Quercus section Cyclobalanopsis, and then dispersed to Sino‐Japan and Sino‐Himalaya. Positive selection analysis showed that the photosystem genes had the lowest ω values among the seven functional gene groups. And nine protein‐coding genes containing sites for positive selection: ndhA, ndhD, ndhF, ndhH, rbcL, rpl32, accD, ycf1, and ycf2. This series of analyses together revealed the phylogeny, evolutionary history, and ecological adaptation mechanism of the chloroplast genome of Quercus section Cyclobalanopsis in the long river of earth history. These chloroplast genome data provide valuable information for deep insights into phylogenetic relationships and intraspecific diversity in Quercus. [ABSTRACT FROM AUTHOR]

Macropsini is a tribe of Eurymelinae in the family Cicadellidae that is widely distributed worldwide. Still, its taxonomic status has been unstable, and the classification of certain clades at the genus level has been controversial. The aim of this study is to address the patterns and processes that explain the structure and the evolution of the mitogenomes of Macropsini, while contributing to the resolution of systematic issues involving five of their genera. To this task, the mitogenomes of 26 species of the tribe were sequenced and characterized, and their phylogenetic relationships were reconstructed. The results revealed that the nucleotide composition of mitochondrial genes in these 26 species was significantly skewed toward A and T. Codons ending with T or A in relative synonymous codon usage were significantly more prevalent than those ending with C or G. The parity plot, neutrality plot, and correspondence analysis revealed that mutation and selective pressure affect codon usage patterns. In the phylogenetic relationships of the Macropsini, the monophyly of Pedionis and Macropsis was well‐supported. Meanwhile, Oncopsis revealed paraphyletic regarding Pediopsoides. In conclusion, this research not only contributes the valuable data to the understanding of the mitogenome of the Macropsini but also provides a reference for future investigations on codon usage patterns, potential adaptive evolution, and the phylogeny of the mitogenome within the subfamily Eurymelinae. [ABSTRACT FROM AUTHOR]

Background: Xylitol, a five-carbon polyalcohol, is used in the food and pharmaceutical industries and as a building block in the synthesis of high-value chemicals. It can be sustainably produced from renewable sources through xylose assimilating microbe fermentation. Results: We screened microbial strains for xylitol production and identified Wickerhamomyces anomalus Z1 as a key xylitol producer. Utilizing lignocellulosic biomass hydrolysates for xylitol production poses challenges due to microbial sensitivity to inhibitors from biomass pre-treatment. In this study, an adaptive laboratory evolution (ALE) of W. anomalus Z1 was performed by culturing the yeast in a mineral medium supplemented with gradual increases of sugarcane bagasse hemicellulosic hydrolysate (SCHH) obtained by intensified steam explosion pretreatment. The performance of the adapted yeast, named Wickerhamomyces anomalus ALE, was assessed in comparison to the wild-type strain regarding its capacity to produce xylitol using SCHH. The evolved yeast reached a xylitol yield of 0.11 g xylitol/g xylose whereas the wild-type strain could not produce xylitol. Removing acetic acid from SCHH enhanced W. [ABSTRACT FROM AUTHOR]

Time-of-use pricing of electric energy, as an important part of the national policy of energy conservation and emission reduction, requires accurate electric energy data as support. However, due to various reasons, the electric energy data are often missing. To address this thorny problem, this paper constructs a CNN and GRU-based recovery model (RCNN-BiGRU) for electric energy data by taking the missing data as the output and the historical data of the neighboring moments as the input. Firstly, a convolutional network with a residual structure is used to capture the local dependence and periodic patterns of the input data, and then a bidirectional GRU network utilizes the extracted potential features to model the temporal relationships of the data. Aiming at the difficult selection of network structure parameters and training process parameters, an accelerated adaptive differential evolution (AADE) algorithm is proposed to optimize the electrical energy data recovery model. The algorithm designs an accelerated mutation operator and at the same time adopts an adaptive strategy to set the two key parameters. A large amount of real grid data are selected as samples to train the network, and the comparison results verify that the proposed combined model outperforms the related CNN and GRU networks. The comparison experimental results with other optimization algorithms also show that the AADE algorithm proposed in this paper has better data recovery performance on the training set and significantly better performance on the test set. [ABSTRACT FROM AUTHOR]

This paper introduces the improvements in natural-frequency-based SHM by applying bio-inspired optimization methods and a vision-based monitoring system for effective damage detection. This paper proposes a natural frequency extraction method using a motion magnification-based vision monitoring system with bio-inspired optimization techniques to estimate the damage location and depth in a cantilever beam. The proposed optimization techniques are inspired by natural processes and biological evolution including genetic algorithms, particle swarm optimization, sea lion optimization, and coral reefs optimization. To verify the performance of each bio-inspired optimization method, the eigenvalues of a two-bay truss structure are used for estimating the damaged elements. Then, using the proposed video motion magnification method, the natural frequency for each undamaged and damaged cantilever beam is extracted and compared with the LDV sensor to verify the proposed vision-based monitoring system. The performance of each bio-inspired optimizer in damage detection is compared. As a result, coral reefs optimization shows the lowest average error, around 1%, in damage detection using the natural frequency. [ABSTRACT FROM AUTHOR]

Simple Summary: This review challenges the current ESGO/ESTRO/ESP guidelines on endometrial cancer risk classification, emphasizing the need to have more extensive and differentiated patient cohorts and to carefully consider the length of follow-up evaluation. Since the new guidelines for endometrial cancer risk classification have been released, many reviews have proposed a critical re-evaluation. In this review, we look back to how the molecular classification system has been built and its evolution in time. Since the new guidelines for endometrial cancer risk classification have been published, many reviews have proposed a critical re-evaluation. In this review, we look back to how the molecular classification system was built and its evolution in time to highlight the major flaws, particularly the biases stemming from the inherent limitations of the cohorts involved in the discoveries. A significant drawback in some cohorts is the inclusion criteria, as well as the retrospective nature and the notably sparse numbers, especially in the POLEmut (nonsynonymous mutation in EDM domain of POLE) risk groups, all of which impact the reliability of outcomes. Additionally, a disregard for variations in follow-up duration leads to a non-negligible bias, which raises a substantial concern in data interpretation and guideline applicability. Finally, according to the results that we obtained through a re-analysis of the confirmation cohort, the p53abn (IHC positive for p53 protein) subgroup, which is predominant in non-endometrioid histology (73–80%), loses its predictivity power in the endometrioid cohort of patients. The exclusion of non-endometrioid subtypes from the cohort led to a complete overlap of three molecular subgroups (all except POLEmut) for both overall and progression-free survival outcomes, suggesting the need for a more histotype-specific approach. In conclusion, this review challenges the current ESGO/ESTRO/ESP guidelines on endometrial cancer risk classification and highlights the limitations that must be addressed to better guide the clinical decision-making process. [ABSTRACT FROM AUTHOR]

Observations of genetically repeated evolution (repeatability) in complex organisms are incongruent with the Fisher–Orr model, which implies that repeated use of the same gene should be rare when mutations are pleiotropic (i.e. affect multiple traits). When spatially divergent selection occurs in the presence of migration, mutations of large effect are more strongly favored, and hence, repeatability is more likely, but it is unclear whether this observation is limited by pleiotropy. Here, we explore this question using individual-based simulations of a two-patch model incorporating multiple quantitative traits governed by mutations with pleiotropic effects. We explore the relationship between fitness trade-offs and repeatability by varying the alignment between mutation effect and spatial variation in trait optima. While repeatability decreases with increasing trait dimensionality, trade-offs in mutation effects on traits do not strongly limit the contribution of a locus of large effect to repeated adaptation, particularly under increased migration. These results suggest that repeatability will be more pronounced for local rather than global adaptation. Whereas pleiotropy limits repeatability in a single-population model, when there is local adaptation with gene flow, repeatability can occur if some loci are able to produce alleles of large effect, even when there are pleiotropic trade-offs. [ABSTRACT FROM AUTHOR]

How sex chromosomes evolve compared to autosomes remains an unresolved question in population genetics. Most studies focus on only a handful of taxa, resulting in uncertainty over whether observed patterns reflect general processes or idiosyncrasies in particular clades. For example, in female heterogametic (ZW) systems, bird Z chromosomes tend to evolve quickly but not adaptively, while in Lepidopterans they evolve adaptively, but not always quickly. To understand how these observations fit into broader evolutionary patterns, we explore Z chromosome evolution outside of these two well-studied clades. We utilize a publicly available genome, gene expression, population, and outgroup data in the salmon louse Lepeophtheirus salmonis , an important agricultural pest copepod. We find that the Z chromosome is faster evolving than autosomes, but that this effect is driven by increased drift rather than adaptive evolution. Due to high rates of female reproductive failure, the Z chromosome exhibits a slightly lower effective population size than the autosomes which is nonetheless to decrease efficiency of hemizygous selection acting on the Z. These results highlight the usefulness of organismal life history in calibrating population genetic expectations and demonstrate the value of the ever-expanding wealth of publicly available data to help resolve outstanding evolutionary questions. [ABSTRACT FROM AUTHOR]

Premise of research. Species-level variation in interactions with root-associated microbial communities has its evolutionary origins within species, where dissection of the mechanistic basis of plant divergence is also tractable. We use montane annual and coastal perennial populations (ecotypes) of Mimulus guttatus (yellow monkeyflower) to ask whether and how plant-microbe-soil interactions have diverged between populations with distinct life histories. Methodology. We characterized fungal communities in representative montane annual (Iron Mountain) and dune perennial (Florence dunes) habitats in Oregon, where previous reciprocal transplants revealed local adaptation. We then investigated how plant ecotype, microbial source, and soil origin affected plant performance and root-associated fungal communities in a full-factorial greenhouse experiment using plants, soils, and nested inocula (sterilized, filtered to remove arbuscular mycorrhizal fungi, and whole) from the two sites. Pivotal results. In the field, coastal perennial and montane annual monkeyflowers harbored distinct fungal communities, and perennial roots were enriched for mutualistic taxa relative to local soils. In the greenhouse common garden, microbial effects were largely negative (particularly in the annual ecotype), and there was no evidence of plant local adaptation to belowground conditions. However, the coastal perennial ecotype was more colonized by arbuscular mycorrhizal fungi than the montane annual ecotype, and it preferentially recruited local arbuscular mycorrhizal fungi taxa even when inoculated from the montane source. Conclusions. Our results suggest that population divergence in life history and related traits shapes plant responsiveness to soil microbes and the specificity of their associations with root endophytic fungi, such as arbuscular mycorrhizal fungi. Complex belowground effects on plant performance do not fit a simple pattern of local adaptation but may be by-products of other drivers of plant divergence. This work advances the study of heritable variation in plant-soil-microbe interactions in a model species for understanding the genomics of plant adaptation. [ABSTRACT FROM AUTHOR]

In a complex environment with multiple feasible paths, planning a globally optimal path and performing dynamic path planning for robots is challenging. Therefore, this paper proposed a new adaptive Differential Evolution algorithm combined with K-modes clustering, BP neural network, and other strategies (KBPDE) to overcome this issue. The proposed KBPDE algorithm applies a new population initialization strategy based on K-modes clustering and a two-population strategy to enhance the population diversity and prevent the algorithm from falling into local optima. A BP neural network model is developed to obtain the appropriate mutation scale factor F at each generation G. Based on the positional relationships among individuals in the current generation, a novel mutation strategy is presented. Finally, an adaptive population size strategy is introduced to raise the algorithm's efficiency. In a complicated environment with several feasible paths, the experimental results demonstrate that KBPDE can obtain the globally optimal path in contrast to GA, DE, and the excellent versions of DE. In a partially known environment, the EKBPDE can plan the path successfully. [ABSTRACT FROM AUTHOR]

I endorse five central themes of Charlotte Witt's Social Goodness: the pervasiveness and irreducibility of social roles and norms; normative externalism; the artisanal model; a richer social ontology; and the possible critical transformation of social norms from within. I reframe these themes within the biological account of the evolution and development of human ways of life in Joseph Rouse's Social Practices as Biological Niche Construction. Witt's social analysis attends to human bodies as loci of artisanal skills and social salience as gendered, sexed, and raced, but not to bodies as vulnerable, dependent organisms in social environments. A broader, biological conception of normativity shifts from Witt's focus on social roles and norms to the dynamics of social practices as shaping people's developmental environments. This more complex account of social dynamics enriches Witt's conservative account of how practices are transmitted and sustained. It thereby surpasses limitations in her account of how hierarchical social norms can be both obligating and open to critical challenge from within. It does so in three ways: by emphasizing normative conflicts within practices, by shifting from individual know-how to discursive practices as loci of artisanal authority, and by an account of power relations as intertwined with biosocial normativity. [ABSTRACT FROM AUTHOR]

Adaptive radiations highlight the mechanisms by which species and traits diversify and the extent to which these patterns are predictable. We used 1,110 high-speed videos of suction feeding to study functional and morphological diversification in 300 cichlid species from three African Great Lake radiations of varying ages (Victoria, Malawi, and Tanganyika) and an older, spatially dispersed continental radiation in the Neotropics. Among African radiations, standing diversity was reflective of time. Morphological and functional variance in Lake Victoria, the youngest radiation, was a subset of that within Lake Malawi, which itself was nested within the older Tanganyikan radiation. However, functional diversity in Neotropical cichlids was often lower than that in Lake Tanganyika, despite being much older. These two radiations broadly overlapped, but each diversified into novel trait spaces not found in the youngest lake radiations. Evolutionary rates across radiations were inversely related to age, suggesting extremely rapid trait evolution at early stages, particularly in lake radiations. Despite this support for early bursts, other patterns of trait diversity were inconsistent with expectations of adaptive radiations. This work suggests that cichlid functional evolution has played out in strikingly similar fashion in different radiations, with contingencies eventually resulting in lineage-specific novelties. [ABSTRACT FROM AUTHOR]

Economics and biology have long been overlapping and mutually enriching fields. We contribute to this cross-fertilization by spelling out the implications for economic theory of some recent insights from evolutionary neurobiology. We note that dynamic homeostasis, a core feature of life processes, has shaped social interactions at varied stages of evolution – from the patterns of competition and cooperation among early life forms to the complex process of human cultures. The resulting homeostatic perspective is not compatible with several leading economic theories but does provide a biological footing for promising concepts such as ecological rationality, heuristics, heterogeneity of economic agents, and complex, self-organizing dynamics. [ABSTRACT FROM AUTHOR]

Animals interact both within and between species, sharing common spaces. Animals exhibit cultural behaviours. Animals can influence and learn from each other, including interactions with other species. The co-culture concept suggests that two populations of different species can influence each other's cultures through synchronised activities. Co-culture emphasises cultural adaptations within ecological niches. The concept of 'co-culture' is introduced as a novel framework for understanding the mutual cultural evolution between animal species, including, but not only, humans. It explores the dynamics of interspecies interactions, particularly in how different species influence each other's behavioural and cognitive adaptations. Various instances of interspecies cultural exchange are highlighted, such as the acquisition of medicinal plants from animals resulting in a shared medicinal culture, adaptive behaviours of urban wildlife, and cooperative behaviours between animal species. Co-culture challenges the notion of species-specific culture, underscoring the complexity and interconnectedness of human and animal societies, and between animal societies. Further research into co-culture is advocating and emphasising its implications for conservation, urban planning, and a deeper understanding of animal cognition and behaviour. [ABSTRACT FROM AUTHOR]

Antagonistic coevolution, arising from genetic conflict, can drive rapid evolution and biological innovation. Conflict can arise both between organisms and within genomes. This review focuses on budding yeasts as a model system for exploring intra- and inter-genomic genetic conflict, highlighting in particular the 2-micron (2μ) plasmid as a model selfish element. The 2μ is found widely in laboratory strains and industrial isolates of Saccharomyces cerevisiae and has long been known to cause host fitness defects. Nevertheless, the plasmid is frequently ignored in the context of genetic, fitness, and evolution studies. Here, I make a case for further exploring the evolutionary impact of the 2μ plasmid as well as other selfish elements of budding yeasts, discuss recent advances, and, finally, future directions for the field. [ABSTRACT FROM AUTHOR]

Basing on logical assumptions and necessary steps of complexification along biological evolution, we propose here an evolutionary path from molecules to cells presenting four ages and three major transitions. At the first age, the basic biomolecules were formed and become abundant. The first transition happened with the event of a chemical symbiosis between nucleic acids and peptides worlds, which marked the emergence of both life and the process of organic encoding. FUCA, the first living process, was composed of self-replicating RNAs linked to amino acids and capable to catalyze their binding. The second transition, from the age of FUCA to the age of progenotes, involved the duplication and recombination of proto-genomes, leading to specialization in protein production and the exploration of protein to metabolite interactions in the prebiotic soup. Enzymes and metabolic pathways were incorporated into biology from protobiotic reactions that occurred without chemical catalysts, step by step. Then, the fourth age brought origin of organisms and lineages, occurring when specific proteins capable to stackle together facilitated the formation of peptidic capsids. LUCA was constituted as a progenote capable to operate the basic metabolic functions of a cell, but still unable to interact with lipid molecules. We present evidence that the evolution of lipid interaction pathways occurred at least twice, with the development of bacterial-like and archaeal-like membranes. Also, data in literature suggest at least two paths for the emergence of DNA biosynthesis, allowing the stabilization of early life strategies in viruses, archaeas and bacterias. Two billion years later, the eukaryotes arouse, and after 1,5 billion years of evolution, they finally learn how to evolve multicellularity via tissue specialization. [ABSTRACT FROM AUTHOR]

Evolution is the integrative framework of the life sciences. Even though the topic is often not formally introduced before high school, young children already have various ideas about evolutionary principles (variation, inheritance, and selection) and their underlying key concepts (e.g., differential fitness, reproduction, and speciation). Describing and refining those ideas has increasingly received attention over the last two decades. However, we see two scopes of improvement in the field: (1) There is a need to examine children's ideas about evolutionary concepts holistically rather than focusing at specific aspects. (2) Although research has shown that older students have different ideas about animal and plant evolution, there is little data on children's ideas about plant evolution to compare with their ideas about animal evolution. All of this results in an incomplete record of children's pre‐existing ideas that would help to design assessments or interventions. Consequently, we developed a set of questions, about the evolutionary principles and interviewed 24 kindergarten children. Most children had basic ideas about individual variation in animals and plants but experienced a lack of knowledge about the origin of variation. Most children seemed to acknowledge plants as living beings and reasoned equally about animals and plants for most concepts. However, many children failed to reason about reproduction and inheritance in plants because they believed plants would not reproduce sexually. Confronted with a selection scenario, most children struggled applying concepts previously shown on an individual level to a population level. Considering our findings, we propose ideas about how to measure and foster children's pre‐existing ideas about evolution. [ABSTRACT FROM AUTHOR]

Consolidated bioprocessing candidate, Clostridium thermocellum, is a cellulose hydrolysis specialist, with the ability to ferment the released sugars to produce bioethanol. C. thermocellum is generally studied with model substrates Avicel and cellobiose to understand the metabolic pathway leading to ethanol. In the present study, adaptive laboratory evolution, allowing C. thermocellum DSM 1237 to adapt to growth on glucose, fructose, and sorbitol, with the prospect that some strains will adapt their metabolism to yield more ethanol. Adaptive growth on glucose and sorbitol resulted in an approximately 1 mM and 2 mM increase in ethanol yield per millimolar glucose equivalent, respectively, accompanied by a shift in the production of the other expected fermentation end products. The increase in ethanol yield observed for sorbitol adapted cells was due to the carbon source being more reduced compared to cellobiose. Glucose and cellobiose have similar oxidation states thus the increase in ethanol yield is due to the rerouting of electrons from other reduced metabolic products excluding H2 which did not decrease in yield. There was no increase in ethanol yield observed for fructose adapted cells, but there was an unanticipated elimination of formate production, also observed in sorbitol adapted cells suggesting that fructose has regulatory implications on formate production either at the transcription or protein level. [ABSTRACT FROM AUTHOR]

Aim: Genetic diversity is crucial for species adaptability. Understanding the mechanisms behind its formation and maintenance is essential for effective conservation. Recent studies have demonstrated that despite experiencing severe population bottlenecks, Muntiacus reevesi retains high genetic diversity and continues its northward migration, indicative of ongoing adaptive evolution. However, our comprehension of this phenomenon remains incomplete. The objective of this study is to explore the mechanisms underlying the formation of high genetic diversity and the genomic characteristics associated with local adaptation, using M. reevesi as a case study. Location: Southern China. Methods: We analysed resequencing data from 62 genomes and identified 29,124,081 high‐quality single‐nucleotide polymorphisms (SNPs). We used population genetics, demographic history, population differentiation, gene flow analysis software, and genotype‐environment association (GEA) models to assess the factors that have contributed to high genetic diversity and environmental adaptability in the historical climate and geographical context. Results: The study identified that during Pleistocene climatic fluctuations, M. reevesi diverged into eastern (DB and WJW populations) and western lineages (WL, BA, and QL populations), all displayed high genetic diversity. Historically, M. reevesi maintained large effective populations, but contemporary human‐induced threats have led to a significant decline. Population differentiation models suggest distinct expansion pathways for eastern and western lineages, resulting in population admixture, with mountain corridors facilitating gene flow and maintaining high genetic diversity. Additionally, environmental‐genotype analysis revealed local adaptation in the QL‐BA population, highlighting candidate adaptive genes (ME3 and PRKG1) potentially linked to cold adaptation and foraging behaviour. Conclusion: This study enhances our understanding of the mechanisms behind the high genetic diversity and environmental adaptability of M. reevesi, offering insights into how bottleneck populations maintain diversity, crucial for biogeographic research and conservation strategies for similar species. [ABSTRACT FROM AUTHOR]

Microalgae have great potential as a future source to meet the increasing global demand for foods. Several microalgae are permitted as safety sources in different countries and regions, and processed as commercial products. However, edible safety, economic feasibility, and acceptable taste are the main challenges for microalgal application in the food industry. Overcome such challenges by developing technology accelerates transition of microalgae into sustainable and nutritious diets. In this review, edible safety of Spirulina, Chlamydomonas reinhardtii, Chlorella, Haematococcus pluvialis, Dunaliella salina, Schizochytrium and Nannochloropsis is introduced, and health benefits of microalgae-derived carotenoids, amino acids, and fatty acids are discussed. Technologies of adaptive laboratory evolution, kinetic model, bioreactor design and genetic engineering are proposed to improve the organoleptic traits and economic feasibility of microalgae. Then, current technologies of decoloration and de-fishy are summarized to provide options for processing. Novel technologies of extrusion cooking, delivery systems, and 3D bioprinting are suggested to improve food quality. The production costs, biomass values, and markets of microalgal products are analyzed to reveal the economic feasibility of microalgal production. Finally, challenges and future perspectives are proposed. Social acceptance is the major limitation of microalgae-derived foods, and further efforts are required toward the improvement of processing technology. [ABSTRACT FROM AUTHOR]

Phages adapt to stressful environments by modulating reproductive strategies, infection efficiency, host ranges, and migration patterns. Phages can enhance microbiome adaptability by encoding auxiliary metabolic genes (AMGs) related to stress resistance and promoting biofilm formation. Phages drive a vital 'viral shunt', retaining organic matter and promoting nutrient cycling in resource-limited environments. Through the expression of AMGs, phages modulate microbial nutrient metabolism, influencing biogeochemical cycles in stressful conditions. Bacterial antiviral systems modulate the trade-off of detrimental cell lysis and beneficial horizontal gene transfer mediated by phages in stressful environments. Bacteriophages (phages) play a vital role in ecosystem functions by influencing the composition, genetic exchange, metabolism, and environmental adaptation of microbial communities. With recent advances in sequencing technologies and bioinformatics, our understanding of the ecology and evolution of phages in stressful environments has substantially expanded. Here, we review the impact of physicochemical environmental stress on the physiological state and community dynamics of phages, the adaptive strategies that phages employ to cope with environmental stress, and the ecological effects of phage–host interactions in stressful environments. Specifically, we highlight the contributions of phages to the adaptive evolution and functioning of microbiomes and suggest that phages and their hosts can maintain a mutualistic relationship in response to environmental stress. In addition, we discuss the ecological consequences caused by phages in stressful environments, encompassing biogeochemical cycling. Overall, this review advances an understanding of phage ecology in stressful environments, which could inform phage-based strategies to improve microbiome performance and ecosystem resilience and resistance in natural and engineering systems. [ABSTRACT FROM AUTHOR]

The evolutionary dynamics of the ecoregions of southern South America and the species that inhabit them have been poorly studied, and few biogeographic hypotheses have been proposed and tested. Quaternary climatic oscillations are among the most important processes that have led to the current distribution of genetic variation in different regions of the world. In this work, we studied the evolutionary history and distribution of the Córdoba vesper mouse (Calomys venustus), a characteristic rodent of the region of which little is known about its natural history. Since the population dynamics of this species are influenced by climatic factors, this rodent is a suitable model to study the effects of Quaternary climatic oscillations in central Argentina. The mitochondrial cytochrome b gene was sequenced to analyze the phylogeography of C. venustus, and ecological niche modeling tools were used to map its potential distributions. The results of these approaches were combined to provide additional spatially explicit information about this species' past. Our results suggest that the Espinal was the area of origin of this species, which expanded demographically and spatially during the last glacial period. A close relationship was found between the Espinal and the Mountain Chaco. These results are consistent with previous studies and emphasize the role of the Espinal in the biogeographic history of southern South America as an area of origin of several species. [ABSTRACT FROM AUTHOR]

The marine environment presents challenges for wound healing in cetaceans, despite their remarkable recovery abilities with minimal infections or complications. However, the molecular mechanism underlying this efficient wound healing remains underexplored. To better understand the molecular mechanisms behind wound healing in cetaceans, we investigated the evolutionary patterns of 37 wound healing‐related genes in representative mammals. We found wound healing‐related genes experience adaptive evolution in cetaceans: (1) Three extrinsic coagulation pathway‐related genes—tissue factor (F3), coagulation factor VII (F7), and coagulation factor X (F10)—are subject to positive selection in cetaceans, which might promote efficient hemostasis after injury; positive selection in transforming growth factor‐beta 2 (TGF‐β2), transforming growth factor‐beta 3 (TGF‐β3), and platelet‐derived growth factor D (PDGFD), which play immunological roles in wound healing, may help cetaceans enhance inflammatory response and tissue debridement. (2) Coagulation factor XII (F12) is the initiation factor in the intrinsic coagulation pathway. It had a premature stop codon mutation and was subjected to selective stress relaxation in cetaceans, suggesting that the early termination of F12 may help cetaceans avoid the risk of vascular blockage during diving. (3) Fibrinogen alpha chain (FGA) and FIII, which were detected to contain the specific amino acid substitutions in marine mammals, indicating similar evolutionary mechanisms might exist among marine mammals to maintain strong wound‐healing ability. Thus, our research provides further impetus to study the evolution of the wound healing system in cetaceans and other marine mammals, extending knowledge of preventing coagulation disorder and atherosclerosis in humans. [ABSTRACT FROM AUTHOR]

The role of plumage ornamentation as a signal of parasite infection is a key issue in the evolution of animal behaviour. Despite the undeniable role of host–parasite interactions in sexual selection, it is still unclear how parasites influence the variance in the expression of females displaying multiple ornaments. Here, by taking advantage of a long-term and individual-based, monitored population of pied flycatchers, Ficedula hypoleuca , in a Mediterranean area, we investigated the variation in the expression of wing patch (size) and forehead patch (occurrence and size) in relation to infections with haemosporidian parasites in breeding adult females. Haemosporidian infection was related to wing patch size, and this association varied in direction and magnitude depending on the origin of birds (locally born versus immigrant) and the type of breeding habitat (oakwood versus pine plantation). Specifically, differences in wing patch size were most evident among immigrant females breeding in the pine plantation, with noninfected females expressing larger wing patches than infected ones. Regarding the forehead patch, its occurrence was also modulated by haemosporidian infection through two-way interactions with bird origin (lower occurrence in locally born females) and breeding habitat type (lower occurrence among infected than uninfected females in the oakwood, whereas the opposite was true in the pine plantation). Only bird age predicted forehead patch size. Therefore, in addition to haemosporidian infection, the expression of these ornaments was related to extrinsic (breeding habitat) and intrinsic (age, origin) factors, which suggests the existence of trade-offs between physiological responses to infection and the expression of secondary sexual traits. Overall, our results suggest that plumage ornaments provide independent and reliable information on the haemosporidian infection status of female pied flycatchers. • Whether plumage ornaments are a sign of parasitic infections in females is unclear. • We assessed the links between two female ornaments and haemosporidian infection. • The expression of both ornaments was related to infection, origin, habitat and age. • However, the correlations between these factors differed depending on the ornament. • This suggests different signals for ornamentation – infection response trade-offs. [ABSTRACT FROM AUTHOR]

Motivated by biological evolution, this paper explains the rationality of Vision Transformer by analogy with the proven practical evolutionary algorithm (EA) and derives that both have consistent mathematical formulation. Then inspired by effective EA variants, we propose a novel pyramid EATFormer backbone that only contains the proposed EA-based transformer (EAT) block, which consists of three residual parts, i.e., Multi-scale region aggregation, global and local interaction, and feed-forward network modules, to model multi-scale, interactive, and individual information separately. Moreover, we design a task-related head docked with transformer backbone to complete final information fusion more flexibly and improve a modulated deformable MSA to dynamically model irregular locations. Massive quantitative and quantitative experiments on image classification, downstream tasks, and explanatory experiments demonstrate the effectiveness and superiority of our approach over state-of-the-art methods. E.g., our Mobile (1.8 M), Tiny (6.1 M), Small (24.3 M), and Base (49.0 M) models achieve 69.4, 78.4, 83.1, and 83.9 Top-1 only trained on ImageNet-1K with naive training recipe; EATFormer-Tiny/Small/Base armed Mask-R-CNN obtain 45.4/47.4/49.0 box AP and 41.4/42.9/44.2 mask AP on COCO detection, surpassing contemporary MPViT-T, Swin-T, and Swin-S by 0.6/1.4/0.5 box AP and 0.4/1.3/0.9 mask AP separately with less FLOPs; Our EATFormer-Small/Base achieve 47.3/49.3 mIoU on ADE20K by Upernet that exceeds Swin-T/S by 2.8/1.7. Code is available at https://github.com/zhangzjn/EATFormer. [ABSTRACT FROM AUTHOR]

Background and Aims Carex breviculmis is a perennial herb with good resistance and is widely used for forage production and turf management. It is important in ecology, environmental protection and biodiversity conservation, but faces several challenges due to human activities. However, the absence of genome sequences has limited basic research and the improvement of wild plants. Methods We annotated the genome of C. breviculmis and conducted a systematic analysis to explore its resistance to harsh environments. We also conducted a comparative analysis of Achnatherum splendens , which is similarly tolerant to harsh environments. Key Results The assembled the genome comprises 469.01 Mb, revealing 37 372 genes with a BUSCO completeness score of 99.0 %. The genome has 52.03 % repetitive sequences, primarily influenced by recent LTR insertions that have contributed to its expansion. Phylogenetic analysis suggested that C. breviculmis diverged from C. littledalei ~6.61 million years ago. Investigation of repetitive sequences and expanded gene families highlighted a rapid expansion of tandem duplicate genes, particularly in areas related to sugar metabolism, synthesis of various amino acids, and phenylpropanoid biosynthesis. Additionally, our analysis identified crucial genes involved in secondary metabolic pathways, such as glycolysis, phenylpropanoid biosynthesis and amino acid metabolism, which have undergone positive selection. We reconstructed the sucrose metabolic pathway and identified significant gene expansions, including 16 invertase, 9 sucrose phosphate synthase and 12 sucrose synthase genes associated with sucrose metabolism, which showed varying levels of expansion. Conclusions The expansion of these genes, coupled with subsequent positive selection, contributed to the ability of C. breviculmis to adapt to environmental stressors. This study lays the foundation for future research on the evolution of Carex plants, their environmental adaptations, and potential genetic breeding. [ABSTRACT FROM AUTHOR]

Background and Aims Latitudinal diversity gradients have been intimately linked to the tropical niche conservatism hypothesis, which posits that there has been a strong filter due to the challenges faced by ancestral tropical lineages to adapt to low temperatures and colonize extra-tropical regions. In liverworts, species richness is higher towards the tropics, but the centres of diversity of the basal lineages are distributed across extra-tropical regions, pointing to the colonization of tropical regions by phylogenetically clustered assemblages of species of temperate origin. Here, we test this hypothesis through analyses of the relationship between macroclimatic variation and phylogenetic diversity in Chinese liverworts. Methods Phylogenetic diversity metrics and their standardized effect sizes for liverworts in each of the 28 regional floras at the province level in China were related to latitude and six climate variables using regression analysis. We conducted variation partitioning analyses to determine the relative importance of each group of climatic variables. Key Results We find that the number of species decreases with latitude, whereas phylogenetic diversity shows the reverse pattern, and that phylogenetic diversity is more strongly correlated with temperature-related variables compared with precipitation-related variables. Conclusions We interpret the opposite patterns observed in phylogenetic diversity and species richness in terms of a more recent origin of tropical diversity coupled with higher extinctions in temperate regions. [ABSTRACT FROM AUTHOR]

Until the mid-nineteenth century, "physiology" was a comprehensive theory of life, expounded and shaped by Johannes P. Müller (1801–1858). Biologists and medical doctors still refer to him today. In the summer term of 1851, Müller gave a lecture on the Comparative Anatomy of animals. This lecture was attended and recorded by Ernst Zeller (1830–1902), a future physician and zoologist, and has recently been published together with a German transcript. In this paper, we situate Johannes Müller within the intellectual history of his time. Through his "empirical idealism," we show how he opposed the speculative tendencies of the romantic understanding of nature, the emerging evolutionism, and the growing splits in the natural sciences. Müller focused on recognizing living nature as a whole and realizing ideal "phenomena" through his empirical research. He considered the notion of the soul of the world. Müller's lecture transcript serves as a poignant testament to German scientific culture in the mid-nineteenth century, a few years before the publication of Darwin's Origin of Species. It also provides valuable insights into the self-contained epistemological foundations of morphology. [ABSTRACT FROM AUTHOR]

In honour of the two hundredth birthday of naturalist Alfred Russel Wallace (1823–1913) we present a transcription and analysis of the plan for Wallace's unrealized final book. Recently come to light, Darwin and Wallace was to have been a volume of eight chapters published by the well-known London publishing house of John Murray in the spring of 1915, a project derailed by Wallace's death at the age of 90 in November 1913. Drawing on letters, manuscripts and contemporary published works, we show how the chapter outlines illuminate Wallace's late-life thinking about his and Darwin's working methods, the factors contributing to their independent discovery of natural selection and contemporary challenges to Darwin–Wallace evolutionary gradualism and natural selection by the neo-Lamarckian, mutationist and early Mendelian schools during the period dubbed the 'eclipse of Darwinism'. Wallace's planned book provides insight into how the co-founder of modern evolutionary biology saw his legacy in relation to Darwin's, and his role as fierce and eloquent defender of his and Darwin's theory during a fascinating period in the history of evolutionary biology. In the emergence of neo-Darwinism in the 'Modern Synthesis' period, Wallace's contributions were largely omitted, an oversight that Darwin and Wallace may have prevented had it been realized. [ABSTRACT FROM AUTHOR]

Assessing the effects of multigenerational exposure of aquatic animal populations to chemical contamination is essential for ecological risk assessment. However, beyond rare examples reporting the sporadic emergence of a toxicological tolerance within populations that persist in contaminated environments, conclusive results are even more limited from field studies when it comes to the alteration of life-history traits. Here, we investigated whether long-term exposure to cadmium (Cd) influences size-related life-history traits (i.e., size at puberty, median adult size, maximum size) in Gammarus fossarum, a keystone species of European stream ecosystems. We studied 13 field populations of G. fossarum (cryptic lineage B) living in headwater rivers located in natural areas scattered at a large geographical scale and exposed to contrasted bioavailable Cd contamination levels due to different local geochemical backgrounds. We achieved a detailed description of the physical and physicochemical conditions of the river reaches investigated. Land-use parameters, hydrological characteristics (flow, slope, river width, flow structure, mosaic of substrates), and physicochemical conditions (temperature, conductivity, dissolved oxygen) were measured. Metallic bioavailable contamination was assessed using a standardized active biomonitoring procedure (Gammarus caging). Based on the field demographic census of the 13 populations, our results demonstrated that chronic Cd contamination significantly influences life-history in the G. fossarum species, with a significant reduction in all size traits of populations (size at puberty, median adult size, maximum size). In addition, we confirmed Cd-tolerance in contaminated populations during exposure tests in the laboratory. Various hypotheses can be then put forward to explain the modification of size-related life-history traits: a direct toxic effect of Cd, a cost of Cd-tolerance, or an adaptive evolution of life-history exposed to toxic pressure. Highlights: Characterization of Cd-exposure, Cd-tolerance, and size distribution of 13 Gammarus field populations. Occurrence of natural high levels of Cd exposure in headwater rivers. Reduced size at puberty, reduced mean and maximal body size in Cd-exposed populations. Cost of tolerance versus life-history adaptation as underlying evolutionary mechanisms. [ABSTRACT FROM AUTHOR]

Because aging and internally determined lifespan vary greatly between similar species it is now widely accepted that aging is an evolved trait, resulting in two classes of evolutionary aging theories: aging is programmed by complex biological mechanisms, and aging is not programmed. As recently as 2002 programmed aging is thought to be theoretically impossible. However, genetics discoveries, results of selective breeding, and other direct evidence strongly support the idea that aging creates an evolutionary advantage and that therefore complex biological mechanisms evolved that control aging in mammals and other multiparous organisms. Like life‐cycle programs that control reproduction, growth, and menopause the aging program can adjust the aging trait during an individual's life to compensate for temporary or local changes in external conditions that alter the optimum lifespan for a particular species population. Genetics discoveries also strongly support the evolvability concept to the effect that sexually reproducing species can evolve design features that increase their ability to evolve, and that aging is one such feature. Genetics discoveries also prove that biological inheritance involves transmission of organism design information in digital form between parent and descendant of any organism. This has major implications for the evolution process. [ABSTRACT FROM AUTHOR]

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Health assessment is necessary to ensure that lithium-ion batteries operate safely and dependably. Nonetheless, there are the following two common problems with the health assessment models for lithium-ion batteries that are currently in use: inability to comprehend the assessment results and the uncertainty around the chemical reactions occurring inside the battery. A rule-based modeling strategy that can handle ambiguous data in health state evaluation is the belief rule base (BRB). In existing BRB studies, experts often provide parameters such as the initial belief degree, but the parameters may not match the current data. In addition, random global optimization methods may undermine the interpretability of expert knowledge. Therefore, this paper proposes a lithium-ion battery health assessment method based on the double optimization belief rule base with interpretability (DO-BRB-I). First, the belief degree is optimized according to the data distribution. Then, to increase accuracy, belief degrees and other parameters are further optimized using the projection covariance matrix adaptive evolution strategy (P-CMA-ES). At the same time, four interpretability constraint strategies are suggested based on the features of lithium-ion batteries to preserve interpretability throughout the optimization process. Finally, to confirm the efficacy of the suggested approach, a sample of the health status assessment of the B0006 lithium-ion battery is provided. [ABSTRACT FROM AUTHOR]

Horseshoe bats (genus Rhinolophus, family Rhinolophidae) represent an important group within chiropteran phylogeny due to their distinctive traits, including constant high-frequency echolocation, rapid karyotype evolution, and unique immune system. Advances in evolutionary biology, supported by highquality reference genomes and comprehensive whole-genome data, have significantly enhanced our understanding of species origins, speciation mechanisms, adaptive evolutionary processes, and phenotypic diversity. However, genomic research and understanding of the evolutionary patterns of Rhinolophus are severely constrained by limited data, with only a single published genome of R. ferrumequinum currently available. In this study, we constructed a high-quality chromosome-level reference genome for the intermediate horseshoe bat (R. affinis). Comparative genomic analyses revealed potential genetic characteristics associated with virus tolerance in Rhinolophidae. Notably, we observed expansions in several immune-related gene families and identified various genes functionally associated with the SARS-CoV- 2 signaling pathway, DNA repair, and apoptosis, which displayed signs of rapid evolution. In addition, we observed an expansion of the major histocompatibility complex class II (MHC-II) region and a higher copy number of the HLADQB2 gene in horseshoe bats compared to other chiropteran species. Based on whole-genome resequencing and population genomic analyses, we identified multiple candidate loci (e.g., GLI3) associated with variations in echolocation call frequency across R. affinis subspecies. This research not only expands our understanding of the genetic characteristics of the Rhinolophus genus but also establishes a valuable foundation for future research. [ABSTRACT FROM AUTHOR]

Recent findings from comparative and evolutionary physiologists reveal novel insights into the regulation of inflammation and immune function under conditions of chronic-sustained and intermittent hypoxia. Comparative approaches provide a valuable gateway for discovering essential principals of physiology and adaptive molecular strategies utilized in nature that protect against clinically relevant stressors, which can guide therapeutic developments in biomedical science.

The basic plan of the retina is conserved across vertebrates, yet species differ profoundly in their visual needs1. Retinal cell types may have evolved to accommodate these varied needs, but this has not been systematically studied. Here we generated and integrated single-cell transcriptomic atlases of the retina from 17 species: humans, two non-human primates, four rodents, three ungulates, opossum, ferret, tree shrew, a bird, a reptile, a teleost fish and a lamprey. We found high molecular conservation of the six retinal cell classes (photoreceptors, horizontal cells, bipolar cells, amacrine cells, retinal ganglion cells (RGCs) and Müller glia), with transcriptomic variation across species related to evolutionary distance. Major subclasses were also conserved, whereas variation among cell types within classes or subclasses was more pronounced. However, an integrative analysis revealed that numerous cell types are shared across species, based on conserved gene expression programmes that are likely to trace back to an early ancestral vertebrate. The degree of variation among cell types increased from the outer retina (photoreceptors) to the inner retina (RGCs), suggesting that evolution acts preferentially to shape the retinal output. Finally, we identified rodent orthologues of midget RGCs, which comprise more than 80% of RGCs in the human retina, subserve high-acuity vision, and were previously believed to be restricted to primates2. By contrast, the mouse orthologues have large receptive fields and comprise around 2% of mouse RGCs. Projections of both primate and mouse orthologous types are overrepresented in the thalamus, which supplies the primary visual cortex. We suggest that midget RGCs are not primate innovations, but are descendants of evolutionarily ancient types that decreased in size and increased in number as primates evolved, thereby facilitating high visual acuity and increased cortical processing of visual information.

Steranes preserved in sedimentary rocks serve as molecular fossils, which are thought to record the expansion of eukaryote life through the Neoproterozoic Era ( ~ 1000-541 Ma). Scientists hypothesize that ancient C27 steranes originated from cholesterol, the major sterol produced by living red algae and animals. Similarly, C28 and C29 steranes are thought to be derived from the sterols of prehistoric fungi, green algae, and other microbial eukaryotes. However, recent work on annelid worms-an advanced group of eumetazoan animals-shows that they are also capable of producing C28 and C29 sterols. In this paper, we explore the evolutionary history of the 24-C sterol methyltransferase (smt) gene in animals, which is required to make C28+ sterols. We find evidence that the smt gene was vertically inherited through animals, suggesting early eumetazoans were capable of C28+ sterol synthesis. Our molecular clock of the animal smt gene demonstrates that its diversification coincides with the rise of C28 and C29 steranes in the Neoproterozoic. This study supports the hypothesis that early eumetazoans were capable of making C28+ sterols and that many animal lineages independently abandoned its biosynthesis around the end-Neoproterozoic, coinciding with the rise of abundant eukaryotic prey.