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Gene expression can be highly plastic in response to environmental variation. However, we know little about how expression plasticity is shaped by natural selection and evolves in wild and domesticated species. We used genotypic selection analysis to characterize selection on drought-induced plasticity of over 7,500 leaf transcripts of 118 rice accessions (genotypes) from different environmental conditions grown in a field experiment. Gene expression plasticity was neutral for most gradually plastic transcripts, but transcripts with discrete patterns of expression showed stronger selection on expression plasticity. Whether plasticity was adaptive and co-gradient or maladaptive and counter-gradient varied among varietal groups. No transcripts that experienced selection for plasticity across environments showed selection against plasticity within environments, indicating a lack of evidence for costs of adaptive plasticity that may constrain its evolution. Selection on expression plasticity was influenced by degree of plasticity, transcript length and gene body methylation. We observed positive selection on plasticity of co-expression modules containing transcripts involved in photosynthesis, translation and responsiveness to abiotic stress. Taken together, these results indicate that patterns of selection on expression plasticity were context-dependent and likely associated with environmental conditions of varietal groups, but that the evolution of adaptive plasticity would likely not be constrained by opposing patterns of selection on plasticity within compared to across environments. These results offer a genome-wide view of patterns of selection and ecological constraints on gene expression plasticity and provide insights into the interplay between plastic and evolutionary responses to drought at the molecular level.

Religion, a shared social system that connects people with a supernatural power, exists in human populations worldwide. Scientists have long debated whether religion is a cultural or evolutionary phenomenon; that is, whether religion is a learned set of values, beliefs, and behaviors, or instead the result of gene variants that have increased in frequency over time. In this paper, I argue that natural selection, the process by which the frequency of certain genes increases over generations due to their reproductive benefit, has played a role in the persistence of religion. I begin by providing background on the definitions of religion, biological evolution, and adaptation, which are necessary to clarify before analyzing the role of biological evolution and adaptivity in religion. I then explain and provide evidence for how religion meets the three conditions of natural selection. Finally, I present multiple adaptive hypotheses to explain how religion might increase fitness. This work clarifies scientific understanding of how natural selection impacts religion and expands on existing adaptive hypotheses that explain how religion might increase biological fitness.

We study the dynamics of the end monomers of a real chain confined in a spherical cavity to search for a small target on the cavity surface using Langevin dynamics simulation. The results are compared and contrasted with those of a Rouse chain to understand the influence of excluded volume interactions on the search dynamics, as characterized by the first passage time (FPT). We analyze how the mean FPT depends on the cavity size Rb, the target size a, and the degree of confinement quantified by Rg/Rb, with Rg being the polymer radius of gyration in free space. As a basic finding, the equilibrium distribution of the end monomers of a real chain in a closed spherical cavity differs from that of a Rouse chain at a given Rg/Rb, which leads to the differences between the mean FPTs of real and Rouse chains. Fitting the survival probability S(t) by a multi-exponential form, we show that the S(t) of real chains exhibits multiple characteristic times at large Rg/Rb. Our simulation results indicate that the search dynamics of a real chain exhibit three characteristic regimes as a function of Rg/Rb, including the transition from the Markovian to non-Markovian process at Rg/Rb ≈ 0.39, along with two distinct regimes at 0.39 < Rg/Rb < 1.0 and Rg/Rb > 1.0, respectively, where S(t) exhibits a single characteristic time and multiple characteristic times. [ABSTRACT FROM AUTHOR]

Impalas are unusual among bovids because they have remained morphologically similar over millions of years—a phenomenon referred to as evolutionary stasis. Here, we sequenced 119 whole genomes from the two extant subspecies of impala, the common (Aepyceros melampus melampus) and black‐faced (A. m. petersi) impala. We investigated the evolutionary forces working within the species to explore how they might be associated with its evolutionary stasis as a taxon. Despite being one of the most abundant bovid species, we found low genetic diversity overall, and a phylogeographic signal of spatial expansion from southern to eastern Africa. Contrary to expectations under a scenario of evolutionary stasis, we found pronounced genetic structure between and within the two subspecies with indications of ancient, but not recent, gene flow. Black‐faced impala and eastern African common impala populations had more runs of homozygosity than common impala in southern Africa, and, using a proxy for genetic load, we found that natural selection is working less efficiently in these populations compared to the southern African populations. Together with the fossil record, our results are consistent with a fixed‐optimum model of evolutionary stasis, in which impalas in the southern African core of the range are able to stay near their evolutionary fitness optimum as a generalist ecotone species, whereas eastern African impalas may struggle to do so due to the effects of genetic drift and reduced adaptation to the local habitat, leading to recurrent local extinction in eastern Africa and re‐colonisation from the South. [ABSTRACT FROM AUTHOR]

The propensity of humans and non-human animals to discount future returns for short-term benefits is well established. This contrasts with the ability of organisms to unfold complex developmental sequences over months or years efficiently. Research has focused on various descriptive and predictive parameters of 'temporal discounting' in behavior, and researchers have proposed models to explain temporal preference in terms of fitness-maximizing outcomes. Still, the underlying ultimate cause of this phenomenon has not been deeply explored across taxa. Here, we propose an ultimate (i.e., evolutionary) causal explanation for the selection of temporal discounting largely conserved across taxa. We propose that preference for a short-term reward (e.g., heightened impulsivity) often is less than optimal and likely is the product of constraints imposed on natural selection with respect to predicting events in a temporal framework in the context of future uncertainty. Using a simple Newtonian model for time across a fitness landscape in which movement by organisms is only possible in one direction, we examine several factors that influence the ability of an organism to choose a distant reward over a more temporally proximate reward: including the temporal distance of the far reward, the relative value of the distant reward, and the effect of uncertainty about the value and presence of the distant reward. Our results indicate that an organism may choose a more distant reward, but only if it is not too far into the future and has a substantially higher-value fitness payoff relative to the short-term reward. Notably, any uncertainty about the distant reward made it extremely unlikely for an organism to choose the delayed reward strategy compared to choosing a closer reward, even if the distant reward had a much higher payoff because events that are uncertain are only partially visible to natural selection pressures. The results help explain why natural selection is constrained to promote more optimal behavioral strategies and why it has difficulty selecting a distant reward over a lower-value short-term reward. The degree of uncertainty is an especially salient ecological variable in promoting and preferencing short-term behavioral strategies across taxa. These results further help illustrate why, from an ultimate causal perspective, human and non-human taxa have difficulty making more optimal long-term decisions. [ABSTRACT FROM AUTHOR]

Large ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. While recent studies have used time-stratified aDNA for selection scans, most focus on single-locus methods. We conducted a multi-locus genotype scan on 708 samples spanning 7000 years of European history. We show that the G12 statistic, originally designed for unphased diploid data, can effectively detect selection in aDNA processed to create 'pseudo-haplotypes'. In simulations and at known positive control loci (e.g., lactase persistence), G12 outperforms the allele frequency-based selection statistic, SweepFinder2, previously used on aDNA. Applying our approach, we identified 14 candidate regions of selection across four time periods, with half the signals detectable only in the earliest period. Our findings suggest that selective events in European prehistory, including from the onset of animal domestication, have been obscured by neutral processes like genetic drift and demographic shifts such as admixture. Large-scale ancient DNA (aDNA) studies offer the chance to examine genomic changes over time, providing direct insights into human evolution. Here the authors use aDNA from 708 European samples to identify 14 regions of natural selection over 7,000 years. They find that many early signals of selection are lost in later periods due to neutral processes like genetic drift and admixture. [ABSTRACT FROM AUTHOR]

Each commentary on my article raises important points and new ideas for research on rhythmic processing in humans and other species. Here I respond to points concerning the role of social factors in the ontogeny of beat synchronization, the neural connectivity underlying beat synchronization, the evolution of this connectivity, and the mechanisms by which evolutionary changes in the strength of one white matter tract (driven by natural selection) can have knock-on effects on the structure of an adjacent tract. [ABSTRACT FROM AUTHOR]

Background: Echolocation was a key development in toothed whale evolution, enabling their adaptation and diversification across various environments. Previous bioacoustic and morphological studies suggest that environmental pressures have influenced the evolution of echolocation in toothed whales. This hypothesis demands further investigation, especially regarding the molecular mechanisms involved in the adaptive radiation of toothed whales across multiple habitats. Here we show that the coding sequences of four hearing genes involved in echolocation (CDH23, prestin, TMC1, and CLDN14) have different signatures of molecular evolution among riverine, coastal, and oceanic dolphins, suggesting that the evolutionary constraints of these habitats shaped the underlying genetic diversity of the toothed whale sonar. Results: Our comparative analysis across 37 odontocete species revealed patterns of accelerated evolution within coastal and riverine lineages, supporting the hypothesis that shallow habitats pose specific selective pressures to sonar propagation, which are not found in the deep ocean. All toothed whales with genes evolving under positive selection are shallow coastal species, including three species that have recently diverged from freshwater lineages (Cephalorhynchus commersonii, Sotalia guianensis, and Orcaella heinsohni - CDH23), and three species that operate specialized Narrow Band High Frequency (NBHF) Sonars (Phocoena sinus - prestin, Neophocaena phocaenoides - TMC1 and Cephalorhynchus commersonii - CDH23). For river dolphins and deep-diving toothed whales, we found signatures of positive selection and molecular convergence affecting specific sites on CDH23, TMC1, and prestin. Positively selected sites (PSS) were different in number, identity, and substitution rates (dN/dS) across riverine, coastal, and oceanic toothed whales. Conclusion: Here we shed light on potential molecular mechanisms underlying the diversification of toothed whale echolocation. Our results suggest that toothed whale hearing genes changed under different selective pressures in coastal, riverine, and oceanic environments. [ABSTRACT FROM AUTHOR]

Identifying the mechanisms underlying the persistence of rare species has long been a motivating question for ecologists. Classical theory implies that community dynamics should be driven by common species, and that natural selection should not allow small populations of rare species to persist. Yet, a majority of the species found on Earth are rare. Consequently, several mechanisms have been proposed to explain their persistence, including negative density dependence, demographic compensation, vital rate buffering, asynchronous responses of subpopulations to environmental heterogeneity, and fine‐scale source‐sink dynamics. Persistence of seeds in a seed bank, which is often ignored in models of population dynamics, can also buffer small populations against collapse. We used integral projection models (IPMs) to examine the population dynamics of Oenothera coloradensis, a rare, monocarpic perennial forb, and determine whether any of five proposed demographic mechanisms for rare species persistence contribute to the long‐term viability of two populations. We also evaluate how including a discrete seed bank stage changes these population models. Including a seed bank stage in population models had a significantly increased modeled O. coloradensis population growth rate. Using this structured population model, we found that negative density‐dependence was the only supported mechanism for the persistence of this rare species. We propose that high micro‐site abundances within a spatially heterogeneous environment enables this species to persist, allowing it to sidestep the demographic and genetic challenges of small population size that rare species typically face. The five mechanisms of persistence explored in our study have been demonstrated as effective strategies in other species, and the fact that only one of them had strong support here supports the idea that globally rare species can employ distinct persistence strategies. This reinforces the need for customized management and conservation strategies that mirror the diversity of mechanisms that allow rare species persistence. [ABSTRACT FROM AUTHOR]

Summary Genome merging is a common phenomenon causing a wide range of consequences on phenotype, adaptation, and gene expression, yet its broader implications are not well‐understood. Two consequences of genome merging on gene expression remain particularly poorly understood: dosage effects and evolution of expression. We employed Chlamydomonas reinhardtii as a model to investigate the effects of asymmetric genome merging by crossing a diploid with a haploid strain to create a novel triploid line. Five independent clonal lineages derived from this triploid line were evolved for 425 asexual generations in a laboratory natural selection experiment. Utilizing fitness assays, flow cytometry, and RNA‐Seq, we assessed the immediate consequences of genome merging and subsequent evolution. Our findings reveal substantial alterations in genome size, gene expression, protein homeostasis, and cytonuclear stoichiometry. Gene expression exhibited expression‐level dominance and transgressivity (i.e. expression level higher or lower than either parent). Ongoing expression‐level dominance and a pattern of ‘functional dominance’ from the haploid parent was observed. Despite major genomic and nucleo‐cytoplasmic disruptions, enhanced fitness was detected in the triploid strain. By comparing gene expression across generations, our results indicate that proteostasis restoration is a critical component of rapid adaptation following genome merging in Chlamydomonas reinhardtii and possibly other systems. [ABSTRACT FROM AUTHOR]

The balance between chromosomal and plasmid DNAs determines the genomic plasticity of prokaryotes. Natural selections, acting on the level of organisms or plasmids, shape the abundances of plasmid DNAs in prokaryotic genomes. Despite the importance of plasmids in health and engineering, there have been rare systematic attempts to quantitatively model and predict the determinants underlying the strength of different selection forces. Here, we develop a metabolic flux model that describes the intracellular resource competition between chromosomal and plasmid-encoded reactions. By coarse graining, this model predicts a landscape of natural selections on chromosome/plasmid balance, which is featured by the tradeoff between phenotypic and non-phenotypic selection pressures. This landscape is further validated by the observed pattern of plasmid distributions in the vast collection of prokaryotic genomes retrieved from the NCBI database. Our results establish a universal paradigm to understand the prokaryotic chromosome/plasmid interplay and provide insights into the evolutionary origin of plasmid diversity. An intracellular resource competition model sheds light on the evolutionary forces that govern the balance between chromosomal and plasmid DNAs in prokaryotic genomes. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are post-transcriptional, non-coding regulatory RNAs that function coordinately with transcription factors (TFs) in gene regulatory networks. TFs and their targets are often co-regulated by miRNAs, forming composite feedforward circuits (cFFCs) with varying degrees of redundancy, primarily mediated by miRNAs. However, the maintenance of miRNA-mediated regulatory redundancy and its impact on gene expression evolution remain elusive. By integrating ChIP-seq data from ENCODE and miRNA targeting from TargetScanFly, we quantified miRNA-mediated cFFC redundancy in Drosophila melanogaster embryos and larvae, revealing more than three quarters of miRNA targets are involved in redundant cFFCs. Higher cFFC redundancy, where more miRNAs target the same gene within a cFFC, is correlated with stronger purifying selection, reduced expression divergence between species, and increased expression stability under heat shock stress. Redundant cFFCs primarily regulate older or broadly expressed young genes. These findings highlight the role of miRNA-mediated cFFC redundancy in enhancing gene expression robustness through natural selection. Network analysis reveals miRNAs mediate high redundancy of composite feedforward circuits (cFFCs) in Drosophila, correlating with strong purifying selection, reduced interspecies expression divergence, and increased stability under stress. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Taxa Methods Results Main Conclusions The combined influences of demographic dynamics and gene flow on local adaptation in plants is still poorly understood. Here, we used a genome scan approach on three closely related Neotropical palms, Acrocomia aculeata, A. intumescens and A. totai, to identify the evolutionary processes generating shared and lineage‐specific patterns of differentiation and selection across the genomic landscape.Amazonia, Atlantic Forest, Cerrado and Caatinga ecoregions of Brazil.Arecaceae.We used target sequence capture and analysis of climatic correlation, detection of selective sweeps, balancing selection, and spatial and non‐spatial models to identify signatures of natural selection and admixture. We also determined temporal dynamics in spatial distribution and demographic changes.We found a higher number of lineage‐specific than shared adaptive sites (SNPs) and no evidence of selective sweeps in shared genes, suggesting lineage specific natural selection across species. Further, evidence of balancing selection in several genes was also identified in the three species. Niche‐based and coalescent models suggest that shifts in spatial range during the Quaternary caused overlapping distributions between species, leading to hybridisation between parapatric localities.Interspecific hybridisation may have spread both neutral and adaptive SNPs, which may explain the shared adaptive genes between species. Taken together, we show how genomic adaptation can occur despite introgression, through evolutionary processes that likely drive similar patterns of adaptation in other organisms. [ABSTRACT FROM AUTHOR]

The WRKY transcription factor gene family in soybean [Glycine max (L.) Merr.] (GmWRKY) is critical for the plant's development and stress responses. This study examines the evolutionary dynamics of the GmWRKY gene family, focusing on its synonymous codon usage bias (CUB) in a comprehensive set of 179 coding sequences. CUB was analyzed using various indices, revealing a preference for A/T-ending codons and relatively low codon bias. Codon adaptation index (CAI) analysis suggested that these genes are optimized for efficient translation despite relatively low bias, reflecting a balance between codon diversity and translation efficiency. Neutrality and NC plots indicated that selective forces dominate over mutational forces in shaping codon usage, while selection signature analysis showed purifying selection being prevalent across the gene family. However, episodic positive selection was also detected in certain clades, highlighting potential adaptive diversification in response to environmental stress. Additionally, promoter binding site analysis uncovered correlations between codon usage and transcriptional regulation, indicating a context-dependent relationship between CUB and gene expression. Phylogenetic analysis identified 11 well-supported clades in the modern GmWRKY gene family and ancestral sequence reconstruction revealed more relaxed codon preferences and reduced selection constraints in modern GmWRKY genes, potentially linked to neofunctionalization and adaptation to environmental changes. These findings provide a framework for optimizing gene expression in transgenic soybean crops with resilience. Further functional validation of positively selected genes is recommended to elucidate their role in stress responses. [ABSTRACT FROM AUTHOR]

The best-known example of episodic memory in animals came from food-storing birds. One of the beauties of the food-storing system was that inherent in the behaviour were the elements that (at the time) made up episodic memory: what, where and when. While there were then already plenty of data on animals' ability to put together what and where, the addition of the time element in animals' memory and its testing was one that was both new and experimentally challenging. It has, however, led to an increasing variety of examples showing that animals can put together all three informational components. If episodic memories can be described as those memories that make any one of us who we are, why should non-human animals have such memories? Here, we argue that episodic memories play a significant functional role in the lives of real animals, in particular, enabling them to make decisions about how they might or should act in their future. We support our argument with data from a range of examples, focussing on data from the field. This article is part of the theme issue 'Elements of episodic memory: lessons from 40 years of research'. [ABSTRACT FROM AUTHOR]

The high-altitude, low-oxygen environment of the Qinghai-Tibet Plateau poses significant challenges for the introduction of superior livestock breeds. However, local plateau species have adapted to thrive and reproduce under these harsh conditions. Understanding the molecular mechanisms behind plateau animals' adaptation to low-oxygen environments is essential for breeding livestock suited to high-altitude regions. Tibetan pigs, which have undergone long-term natural selection and artificial breeding, have developed the ability to survive and reproduce in hypoxic environments. In this study, we conducted whole-genome resequencing of 30 Tibetan pigs from high-altitude regions and 30 Diannan small-ear pigs from low-altitude areas, to identify candidate genes that support Tibetan pigs' adaptation to hypoxic conditions through selection signal analysis. Additionally, we performed transcriptome sequencing on five tissues (heart, liver, spleen, lung, and bone marrow) from both Tibetan pigs and Diannan small-ear pigs to identify genes with significant differential expression between the two breeds. We then integrated the genomic and transcriptomic data by examining the expression of candidate genes identified in selection signal analysis across different tissues. The selection signal analysis identified 10 genes— HES 4, ANGPT 1, HIF3 A, SPHK 2, PCK 2, RCN 3, HIGD2 A, DNM 2, IRF 9, and SRF —that were under positive selection in the Tibetan pig population and are associated with hypoxia adaptation. When combined with transcriptome data, we found that five of these genes— HIF3 A, RCN 3, HIGD2 A, PCK 2, and IRF 9—exhibited differential expression. Through an integrated approach of selection signal and transcriptome analysis, we identified five key functional genes that contribute to the adaptation of Tibetan pigs to hypoxic environments. These findings offer new insights into the adaptability of plateau animals. [ABSTRACT FROM AUTHOR]

Background and Aims Diversity in pappus shapes and size in Asteraceae suggests an adaptive response to dispersion challenges adjusting diaspores to optimal phenotypic configurations. Here, by analysing the relationship among pappus–cypsela size relationships, flight performance and pappus types in an evolutionary context, we evaluate the role of natural selection acting on the evolution of diaspore configuration at a macro-ecological scale in the daisy family. Methods To link pappus–cypsela size relationships with flight performance we collected published data on these traits from 82 species. This allowed us to translate morphometric traits in flight performance for 150 species represented in a fully resolved backbone phylogeny of the daisy family. Through ancestral reconstructions and evolutionary model selection, we assessed whether flight performance was associated with and constrained by different pappus types. Additionally, we evaluated, through phylogenetic regressions, whether species with different pappus types exhibited evolutionary allometric pappus–cypsela size relationships. Results The setose pappus type had the highest flight performances and represented the most probable ancestral state in the family. Stepwise changes in pappus types independently led from setose to multiple instances of pappus loss with associated reduction in flight performance. Flight performance evolution was best modelled as constrained by five adaptive regimes represented by specific pappus types which correspond to specific optimal diaspore configurations that are distinct in pappus–cypsela allometric relationships. Conclusions Evolutionary modelling suggests natural selection as the main factor of diaspore configuration changes which proceeded towards five optima, often overcoming constraints imposed by allometric relationships and favouring evolution in certain directions. With the perspective that natural selection is the main process driving the observed patterns, various biotic and abiotic are suggested as principal drivers of transitions in diaspore configurations along space and time in the daisy family history. The results also allow discussion of evolutionary changes in a historical context. [ABSTRACT FROM AUTHOR]

An expanding body of research aims to identify culture in cetaceans, often positing killer whales as an exemplar species. To this end, gene-culture coevolutionary theory provides a conceptual language with which whales are discussed in raciological terms. It renders killer whale ecotypes as discrete cultures that are intrinsically xenophobic and evolutionarily divergent. Such research on whale culture intends to substantiate theories of divergent natural selection between human cultures as well. This effort furthers the essentialism, simultaneously biological and cultural, that has long impelled colonial technoscientific projects of racial typologization. The exchange between the raciologies of humans and killer whales is facilitated by the infrahumanizing frameworks of gene-culture coevolutionary theory that locate whale populations alongside indigenous peoples on a spectrum of cultural simplicity and complexity. At this convergence of the animal and the human, gene-culture coevolutionary theory posits indigenous peoples and killer whales as evidence for social Darwinist theories that dehistoricize and naturalize intercultural conflict and ethnicization. The extension of raciology beyond the human species signals an urgent need to decolonize the biological sciences. [ABSTRACT FROM AUTHOR]

Jujube (Ziziphus jujuba Mill.), renowned for its nutritional value and health benefits, is believed to have originated in the middle and lower reaches of the Yellow River in China, where it underwent domestication from wild jujube. Nonetheless, the evolutionary trajectory and species differentiation between wild jujube and cultivated jujube still require further elucidation. The chloroplast genome (plastome), characterized by its relatively lower mutation rate compared to the nuclear genome, serves as an excellent model for evolutionary and comparative genomic research. In this study, we analyzed 326 nonredundant plastomes, encompassing 133 jujube cultivars and 193 wild jujube genotypes distributed throughout China. Noteworthy variations in the large single copy region primarily account for the size differences among these plastomes, impacting the evolution from wild jujube to cultivated varieties. Horizontal gene transfer (HGT) unveiled a unique chloroplast‐to‐nucleus transfer event, with transferred fragments predominantly influencing the evolution of the nuclear genome while leaving the plastome relatively unaffected. Population genetics analysis revealed two distinct evolutionary pathways from wild jujube to cultivated jujube: one driven by natural selection with minimal human interference, and the other resulting from human domestication and cultivation. Molecular dating, based on phylogenetic analysis, supported the likelihood that wild jujube and cultivated jujube fall within the same taxonomic category, Z. jujuba. In summary, our study comprehensively examined jujube plastome structures and HGT events, simultaneously contributing novel insights into the intricate processes that govern the evolution and domestication of jujube species. [ABSTRACT FROM AUTHOR]

This study developed a structured fruit cube (FC) snack using only natural ingredients, specifically red grape and apple, without hydrocolloids and sucrose. After development, physicochemical characterization and analysis of phenolic compounds (PCs), including anthocyanins, flavonols, and hydroxycinnamic acid derivatives, using HPLC-DAD-ESI-MS/MS, were conducted. Sensory quality was also assessed through an acceptance and sensory profile analysis using the rate-all-that-apply methodology. The results showed that the FC had physicochemical characteristics similar to other structured fruits that use hydrocolloids. Additionally, they presented a complex composition of PCs, predominantly including anthocyanins derived from malvidin (tri-substituted methoxylated anthocyanins), notably cumarylated ones. Flavonols compounds comprised the 3-glucoside series of myricetin, quercetin, laricitrin, kaempferol, isorhamnetin, and syringetin; the 3-galactoside series of myricetin and quercetin; and the 3-glucuronic acid series of myricetin and quercitin, along with rutin. The presence of caftaric acid, coutaric acid, fertaric acid, and p-coumaroyl-glucose was also detected, alongside caffeic acid-O-glucoside 1, caffeic acid-O-glucoside 2, chlorogenic acid, 4-O-p-coumaroylquinic acid, and dicaffeoylquinic acid. In conclusion, the selection of natural ingredients was technologically suitable for obtaining an FC. Despite using conventional drying at 60 °C, the product showed notable concentrations of PCs and also achieved great sensory acceptance. [ABSTRACT FROM AUTHOR]

The water lily aphid, Rhopalosiphum nymphaeae, is the only known aphid that can live in both terrestrial and aquatic conditions. In this study, the complete mitochondrial genome of R. nymphaeae was generated using Illumina sequencing technology. The typical circular DNA mitochondrial genome of R. nymphaeae is 15,772 bp in length, with a high A+T content (84.34%). It contains 37 coding genes (13 protein-coding genes, 22 transport RNAs, and two ribosomal RNAs) and two non-coding regions (one control region and one repeat region). Enc-plot, PR2-bias, and neutrality plot analysis indicated that the codon usage of the protein-coding genes is mainly affected by natural selection. The evolution rate analysis (the ratio of nonsynonymous to synonymous, Ka/Ks) indicated that all the PCGs in R. nymphaeae are under a strong purifying selection. The control region has conserved structure elements, and two types of tandem repeat units exist. The length and sequence of the aphid-unique repeat region has high similarity with closely related species. Phylogenetic analyses determined by both maximum likelihood and Bayesian inference support the monophyly of Aphidinae, Aphidini, Aphidina, and Rhopalosiphina. However, the monophyly of the genera in Rhopalosiphina, such as Rhopalosiphum, is still not resolved. This study may help us to understand the phylogenetic relationship of aphids, and much more aphid data are needed in future studies. [ABSTRACT FROM AUTHOR]

Predator and prey traits are important determinants of the outcomes of trophic interactions. In turn, the outcomes of trophic interactions shape predator and prey trait evolution. How species' traits respond to selection from trophic interactions depends crucially on whether and how heritable species' traits are and their genetic correlations. Of the many traits influencing the outcomes of trophic interactions, body size and movement traits have emerged as key traits. Yet, how these traits shape and are shaped by trophic interactions is unclear, as few studies have simultaneously measured the impacts of these traits on the outcomes of trophic interactions, their heritability, and their correlations within the same system.We used outcrossed lines of the ciliate protist Paramecium caudatum from natural populations to examine variation in morphology and movement behaviour, the heritability of that variation, and its effects on Paramecium susceptibility to predation by the copepod Macrocyclops albidus.We found that the Paramecium lines exhibited heritable variation in body size and movement traits. In contrast to expectations from allometric relationships, body size and movement speed showed little covariance among clonal lines. The proportion of Paramecium consumed by copepods was positively associated with Paramecium body size and velocity but with an interaction such that greater velocities led to greater predation risk for large body‐sized paramecia but did not alter predation risk for smaller paramecia. The proportion of paramecia consumed was not related to copepod body size. These patterns of predation risk and heritable trait variation in paramecia suggest that copepod predation may act as a selective force operating independently on movement and body size and generating the strongest selection against large, high‐velocity paramecia.Our results illustrate how ecology and genetics can shape potential natural selection on prey traits through the outcomes of trophic interactions. Further simultaneous measures of predation outcomes, traits, and their quantitative genetics will provide insights into the evolutionary ecology of species interactions and their eco‐evolutionary consequences. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

The G matrix is the matrix of additive genetic variances and covariances for a vector of phenotypes. Here we apply the classical theory for the balance among selection, genetic drift, and mutations to find the contributions to G from each locus for populations at stasis. The fitness is approximated by a linear function of phenotypes, with coefficients affected by environmental fluctuations. We show that the G matrix can be decomposed into four additive components generated by selection, drift, mutations, and environmental fluctuations. Selection is on average counteracted by the other three processes included in Fisher's concept of deterioration of the environment, generating considerable changes in mean phenotypes. The theory illustrates that neither Fisher's fundamental theorem nor Lande's classical gradient formula is sufficient for assessing adaptive changes through time unless the deteriorations are corrected for. This applies for populations at stasis, but also for populations that are subject to long-term evolutionary changes. The theory also indicates several possible comparative studies for investigations of deteriorating effects. Our analyses also suggest that the factor loadings to the eigenvector of the G matrix with the lowest eigenvalue will rather accurately indicate the relative contributions from different phenotype components to fitness. This is information notoriously difficult to obtain in natural populations. [ABSTRACT FROM AUTHOR]

Sand rice (Agriophyllum squarrosum (L.) Moq.), an annual psammophyte, is a promising wild plant for de novo domestication. Although many related studies have been documented recently, a basic phenological scale describing its growth stages is lacking. To address this gap, we have defined nine principal growth stages, each subdivided into several secondary stages according the international BBCH coding system. The growth stages mainly include seedling emergence, leaf development, formation of the primary branches, main stem elongation, inflorescence emergence, flowering, fruit development, ripening and senescence. Importantly, the growth sequence of sand rice reveals a distinctive stage, coded as BBCH21, characterized by the elongation of the first pair of primary branches, which occurs prior to main stem visible (BBCH30). This branch priority phenotype in sand rice strongly challenges the generally recognized growth pattern of 'apical dominance' in dicotyledons. The sequential and chronological progression of principal growth stages of sand rice was further determined in an experimental field with a representative genotype from the Tengger desert of Northwest China in 2023. The establishment of BBCH scale of sand rice lays a methodological foundation for morphological assessment among different germplasms and between wild‐type and mutant plants. This will accelerate the de novo domestication process of sand rice using natural selection and artificial mutagenesis. [ABSTRACT FROM AUTHOR]

DNA methylation has been proposed to be an important mechanism that allows plants to respond to their environments sometimes entirely uncoupled from genetic variation. To understand the genetic basis, biological functions and climatic relationships of DNA methylation at a population scale in Arabidopsis thaliana, we performed a genome‐wide association analysis with high‐quality single nucleotide polymorphisms (SNPs), and found that ~56% on average, especially in the CHH sequence context (71%), of the differentially methylated regions (DMRs) are not tagged by SNPs. Among them, a total of 3235 DMRs are significantly associated with gene expressions and potentially heritable. 655 of the 3235 DMRs are associated with climatic variables, and we experimentally verified one of them, HEI10 (HUMAN ENHANCER OF CELL INVASION NO.10). Such epigenetic loci could be subjected to natural selection thereby affecting plant adaptation, and would be expected to be an indicator of accessions at risk. We therefore incorporated these climate‐related DMRs into a gradient forest model, and found that the natural A. thaliana accessions in Southern Europe that may be most at risk under future climate change. Our findings highlight the importance of integrating DNA methylation that is independent of genetic variations, and climatic data to predict plants' vulnerability to future climate change. [ABSTRACT FROM AUTHOR]

A wide diversity of Mobile Genetic Elements (MGEs) are able to transfer host DNA. MGE-mediated 'sex' can be of significant influence on host evolution. Many instances of host DNA transfer are likely to be transient and non-adaptive. Evidence of MGE domestication suggests that host benefits of MGE-mediated sex could exist. The prokaryote world is replete with mobile genetic elements (MGEs) – self-replicating entities that can move within and between their hosts. Many MGEs not only transfer their own DNA to new hosts but also transfer host DNA located elsewhere on the chromosome in the process. This could potentially lead to indirect benefits to the host when the resulting increase in chromosomal variation results in more efficient natural selection. We review the diverse ways in which MGEs promote the transfer of host DNA and explore the benefits and costs to MGEs and hosts. In many cases, MGE-mediated transfer of host DNA might not be selected for because of a sex function, but evidence of MGE domestication suggests that there may be host benefits of MGE-mediated sex. [ABSTRACT FROM AUTHOR]

In order to describe large-scale spatial structure of sockeye salmon on the Asian part of the range, the variability of 45 SNP loci was analyzed in 22 samples from the Northwest coast of the Pacific Ocean. Three large regional population complexes were identified: Southwest Kamchatka, Kamchatka River basin, and the Northeast (comprising stocks from Koryak Highlands). Populations within the identified complexes are connected by gene migration and have a common origin, close geographic proximity, comparable climatic, landscape, and environmental conditions in the freshwater and early marine periods of sockeye salmon life. Populations confined to watersheds of the North coast of the Sea of Okhotsk (Palana and Okhota rivers), along with island populations, displayed distinctions from the isolated population complexes. It is hypothesized that the marked divergence observed in island populations is primarily caused by genetic drift occurring during long periods of isolation. The pronounced divergence of Palana River population may be the result of both genetic drift and natural selection, driven by the challenging smoltification and specific conditions of freshwater period in this watershed. At the same time in the Okhota River population, demographic factors such as genetic drift and bottlenecks played a key role. [ABSTRACT FROM AUTHOR]

The origin of life and its evolution are generally taught as occurring by abiogenesis and gene-centric neo-Darwinism. Significant biological evolutionary changes are preserved and given direction (descent with modification) by Darwin's (Spencer's) natural selection by survival of the fittest. Only survival of the fittest (adapted/broadened) is available to provide a 'naturalistic' direction to prefer one outcome/reaction over another for abiogenesis. Thus, assembly of first life must reach some threshold (the first minimal cell) before 'survival of the fittest' (the only naturalistic explanation available) can function as Darwin proposed for biological change. We propose the novel concept that the requirement for co-origination of vitamins with enzymes is a fundamental, but overlooked, problem that survival of the fittest (even broadly redefined beyond Darwin) cannot reasonably overcome. We support this conclusion with probability calculations. We focus on the stage of evolution involving the transition from non-life to the first, minimal living cell. We show that co-origination of required biochemical processes makes the origin of life probabilistically absurdly improbable even when all assumptions are chosen to unreasonably favor evolutionary theories. [ABSTRACT FROM AUTHOR]

Introduction: Whereas (GCC)-repeats are overrepresented in genic regions, and mutation hotspots, they are largely unexplored with regard to their link with natural selection. Across numerous primate species and tissues, SMAD9 (SMAD Family Member 9) reaches highest level of expression in the human brain. This gene contains a (GCC)-repeat in the interval between + 1 and + 60 of the transcription start site, which is in the high-ranking (GCC)-repeats with respect to length. Methods: Here we sequenced this (GCC)-repeat in 396 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 181) and controls (N = 215). Results: We detected two predominantly abundant alleles of 7 and 9 repeats, forming 96.2% of the allele pool. The (GCC)7/(GCC)9 ratio was in the reverse order in the NCD group versus controls (p = 0.005), resulting from excess of (GCC)7 in the NCD group (p = 0.003) and (GCC)9 in the controls (p = 0.01). Five genotypes, predominantly consisting of (GCC)7 and lacking (GCC)9 were detected in the NCD group only (p = 0.008). The patients harboring those genotypes received the diagnoses of Alzheimer's disease (AD) and vascular dementia (VD). Five genotypes consisting of (GCC)9 and lacking (GCC)7 were detected in the control group only (p = 0.002). The group-specific genotypes formed approximately 4% of the genotype pool in the human samples studied. Conclusion: We propose natural selection and a novel locus for late-onset AD and VD at the SMAD9 (GCC)-repeat in humans. [ABSTRACT FROM AUTHOR]

Recent observational and numerical studies have revealed the dependence of the intensification rate on the inner-core size of tropical cyclones (TCs). In this study, with the initial inner-core size (i.e., the radius of maximum wind—RMW) varied from 20–180 km in idealized simulations using two different numerical models, we found a nonmonotonic dependence of the lifetime maximum intensification rate (LMIR) on the inner-core size. Namely, there is an optimal inner-core size for the LMIR of a TC. Tangential wind budget analysis shows that, compared to large TCs, small TCs have large inward flux of absolute vorticity due to large absolute vorticity inside the RMW. However, small TCs also suffer from strong lateral diffusion across the eyewall, which partly offsets the positive contribution from large inward flux of absolute vorticity. These two competing processes ultimately lead to the TC with an intermediate initial inner-core size having the largest LMIR. Results from sensitivity experiments show that the optimal size varies in the range of 40–120 km and increases with higher sea surface temperature, lower latitude, larger horizontal mixing length, and weaker initial TC intensity. The 40–120 km RMW corresponds to the inner-core size most commonly found for intensifying TCs in observations, suggesting the natural selection of initial TC size for intensification. This study highlights the importance of accurate representation of TC inner-core size to TC intensity forecasts by numerical weather prediction models. [ABSTRACT FROM AUTHOR]

Summary: Local adaptation to contrasting environmental conditions along environmental gradients is a widespread phenomenon in plant populations, yet we lack a mechanistic understanding of how individual agents of selection contribute to this evolutionary process.Here, we developed a novel evolutionary functional–structural plant (E‐FSP) model that recreates local adaptation of virtual plants along an environmental gradient. First, we validate the model by testing if it can reproduce two elevational ecotypes of Dianthus carthusianorum occurring in the Swiss Alps. Second, we use the E‐FSP model to disentangle the relative contribution of abiotic (temperature) and biotic (competition and pollination) selection pressures to elevational adaptation in D. carthusianorum.Our results suggest that elevational adaptation in D. carthusianorum is predominantly driven by the abiotic environment. The model reproduced the qualitative differences between the elevational ecotypes in two phenological (germination and flowering time) and one morphological trait (stalk height), as well as qualitative differences in four performance variables that emerge from G × E interactions (flowering time, number of stalks, rosette area and seed production).Our approach shows how E‐FSP models incorporating physiological, ecological and evolutionary mechanisms can be used in combination with experiments to examine hypotheses about patterns of adaptation observed in the field. [ABSTRACT FROM AUTHOR]

Leveraging past allele frequencies has proven to be key for identifying the impact of natural selection across time. However, this approach suffers from imprecise estimations of the intensity (s) and timing (T) of selection, particularly when ancient samples are scarce in specific epochs. Here, we aimed to bypass the computation of allele frequencies across arbitrarily defined past epochs and refine the estimations of selection parameters by implementing convolutional neural networks (CNNs) algorithms that directly use ancient genotypes sampled across time. Using computer simulations, we first show that genotype‐based CNNs consistently outperform an approximate Bayesian computation (ABC) approach based on past allele frequency trajectories, regardless of the selection model assumed and the number of available ancient genotypes. When applying this method to empirical data from modern and ancient Europeans, we replicated the reported increased number of selection events in post‐Neolithic Europe, independently of the continental subregion studied. Furthermore, we substantially refined the ABC‐based estimations of s and T for a set of positively and negatively selected variants, including iconic cases of positive selection and experimentally validated disease‐risk variants. Our CNN predictions support a history of recent positive and negative selection targeting variants associated with host defence against pathogens, aligning with previous work that highlights the significant impact of infectious diseases, such as tuberculosis, in Europe. These findings collectively demonstrate that detecting the footprints of natural selection on ancient genomes is crucial for unravelling the history of severe human diseases. [ABSTRACT FROM AUTHOR]

Proponents of the Extended Evolutionary Synthesis (EES) emphasize the critical role that organisms and their development play in the process of evolution. This framework explicitly rejects the genocentric focus that once dominated interpretations of the Modern Synthesis in evolutionary theory. In place of genocentrism, EES highlights processes like niche construction, developmental constraint, and extragenetic inheritance as central to any understanding of the evolutionary process. However, much more is at stake in adopting the EES than simply moving beyond the gene-dominant viewpoint of the Modern Synthesis. The EES, in fact, represents a fundamental challenge to the core of classic Darwinism itself by actively repudiating Darwin's key idea that natural selection acts as a creative force in the construction of phenotypes and phenotypic change. In this paper, we more fully explore the assumptive base of Darwinism's population-oriented, selectional focus. We demonstrate how taking development seriously in evolutionary theory mandates a systematic overhaul of Darwinism's assumptive base in favor of grounding all understanding of phenotypic construction in the developmental processes of self-organization endemic to organisms' active engagement with their worlds. [ABSTRACT FROM AUTHOR]

Plasmopara viticola (Berk. & M. A. Curtis) Berl. & De Toni, the causal agent of downy mildew, affects both cultivated and wild grapevine. Wild species of the genus Vitis L. are reliable sources of resistance to many of the diseases that affect cultivated grapevines. For this reason, it is important to study wildly growing (typical wild and feral) accessions belonging to V. vinifera L. The aim of this research was to study the levels of resistance to P. viticola of 57 Georgian wildly growing grapevine accessions by leaf disc method. The data were collected over eight years, from 2014 to 2021. Different degrees of resistance have been detected, ranging from susceptible (8.8% of accessions), low resistance (8.8% of accessions) moderate resistance (22.8%), and resistance (12.3% of accessions). Resistance of the 33,3% of the tested accessions was unstable and varied from susceptible to resistance across the years. Among resistant wildly growing grapevine genotypes, there are several accessions with a high density of the trichomes, although the data showed that the density of prostrate and erect hairs of the leaves is not correlated with the resistance trait. A large number of resistant genotypes among wildly growing grapevines suggests that in its natural habitat more resistant forms to downy mildew survives in the process of natural selection. Further studies are needed to characterize the plant-pathogen interaction and the mechanism of resistance of the wild accessions, although the resistant accessions, such as Tedotsminda 07, Tedotsminda 09, Tedotsimda 10 can be interesting for the breeding purposes in the future. [ABSTRACT FROM AUTHOR]

(CCG) short tandem repeats (STRs) are predominantly enriched in genic regions, mutation hotspots for C to T truncating substitutions, and involved in various neurological and neurodevelopmental disorders. However, intact blocks of this class of STRs are widely overlooked with respect to their link with natural selection. The human neuron-specific gene, DISP2 (dispatched RND transporter family member 2), contains a (CCG) repeat in its 5′ untranslated region. Here, we sequenced this STR in a sample of 448 Iranian individuals, consisting of late-onset neurocognitive disorder (NCD) (N = 203) and controls (N = 245). We found that the region spanning the (CCG) repeat was highly mutated, resulting in several flanking (CCG) residues. However, an 8-repeat of the (CCG) repeat was predominantly abundant (frequency = 0.92) across the two groups. While the overall distribution of genotypes was not different between the two groups (p > 0.05), we detected four genotypes in the NCD group only (2% of the NCD genotypes, Mid-p = 0.02), consisting of extreme short alleles, 5- and 6-repeats, that were not detected in the control group. The patients harboring those genotypes received the diagnoses of probable Alzheimer's disease and vascular dementia. We also found six genotypes in the control group only (2.5% of the control genotypes, Mid-p = 0.01) that consisted of the 8-repeat and extreme long alleles, 9- and 10-repeats, of which the 10-repeat was not detected in the NCD group. The (CCG) repeat specifically expanded in primates. In conclusion, we report an indication of natural selection at a novel hypermutable region in the human genome and divergent alleles and genotypes in late-onset NhCDs and controls. These findings reinforce the hypothesis that a collection of rare alleles and genotypes in a number of genes may unambiguously contribute to the cognition impairment component of late-onset NCDs. [ABSTRACT FROM AUTHOR]

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Developmental plasticity is the capacity of a single genotype to express multiple phenotypes in response to different early‐life environments. Such responses are defined by reaction norms, which may vary among individuals or populations. Variation in developmental reaction norms allows natural selection to operate on plasticity and is rarely examined in vertebrates. We quantified variation in embryonic developmental plasticity within and between populations using the brown anole lizard. We captured lizards from two islands in the Matanzas River (Florida, USA) and incubated their eggs under one of two multivariate treatments that mimicked the temperature, moisture and substrates of nest sites in either a shaded or open habitat. We measured hatchling morphology, performance, and physiology to quantify variation in family‐level reaction norms. We observed evidence of family‐level variation in reaction norms for morphology but not for performance or physiology, indicating an opportunity for natural selection to shape plasticity in hatchling body size. Overall, the results indicate that multiple abiotic conditions in natural nests combine to increase or reduce phenotypic variation, and that family‐level variation in reaction norms provides a potential for natural selection to shape plasticity. [ABSTRACT FROM AUTHOR]

Plants synthesize a broad array of specialized chemical compounds that mediate their interactions with the surrounding environment. Some of this chemical diversity is functional and subject to natural selection, but the factors underlying chemical evolution at the intraspecific level remain largely unknown. Here, we combined chemical, environmental and genetic data to investigate the effect of aridity on the expression of chemotypes in the invasive shrub Senecio pterophorus. We studied the variation in pyrrolizidine alkaloids (PAs), a group of specialized metabolites widespread across the families Boraginaceae, Asteraceae and Fabaceae, from native populations spanning a cline of aridity and from three cross‐continental introductions, under natural and common garden conditions. We examined whether the relationship between chemistry and aridity was compatible with a process of adaptive differentiation using a method that partitions the variance and covariance by controlling for the population neutral genetic structure. We found a consistent shift from retrorsine‐like to seneciphylline‐like compounds under increasing aridity in both natural and controlled conditions in coherence with the biosynthetic pathways. This pattern was independent of the neutral genetic structure and occurred along the environmental gradient in the native range and in a convergent manner in all nonnative regions, which suggests adaptive differentiation in response to aridity. Our findings show that the diversity of PAs in S. pterophorus has been partially shaped by aridity. Investigating how abiotic factors influence chemical evolution is key to elucidating the plant responses in future climate scenarios and the cascading effects on other trophic levels. [ABSTRACT FROM AUTHOR]

Background: Evolution continues to be one of the most difficult biological topics to teach, warranting innovative pedagogical tools and assessment strategies for enhancing evolutionary instruction. A major advance in measuring the evolution knowledge of undergraduate students came with the development of the Conceptual Assessment of Natural Selections (CANS). In this study, we use the CANS to measure knowledge and learning of natural selection in a large (N > 6000) sample of undergraduate students to expand upon prior validity testing of this instrument and advance knowledge of student evolutionary reasoning. We apply the Rasch measurement framework to examine if the CANS productively measures the intended construct and investigate the patterns of knowledge and learning about evolution among students with different backgrounds and demographic characteristics. Results: While a unidimensional Rasch model demonstrated acceptable reliabilities and fit for most of the CANS items, some items showed problematic fit statistics and were resistant to instruction. The instrument items also did not span the full range of student abilities, which suggests relatively low measurement precision. Our large sample also allowed rigorous tests of multidimensionality, revealing the presence of multiple dimensions or constructs, some of which may not be intentional. These results generated specific item-level recommendations for improving this instrument. Using Rasch measures to examine learning patterns, we found that pre-test evolution knowledge was low but that there were high learning gains by the end of the course. However, some concept categories were found to be more difficult than others, suggesting the need for more attention to these areas by instructors. We also identified pre-test disparities in evolutionary knowledge by socially defined race and biological sex, yet students from all groups achieved comparable learning gains at the end of the course. Conclusion: The CANS holds great potential to generate critical insights about student evolutionary reasoning and provide information about which instructional approaches most effectively mitigate the notable knowledge disparities among students. We leverage the findings of this study to propose tangible ways in which this instrument may be improved in order to better achieve both of these goals. [ABSTRACT FROM AUTHOR]

ABSTRACT Plants adapt to their local environment through complex interactions between genes, gene networks and hormones. Although the impact of gene expression on trait regulation and evolution has been recognised for many decades, its role in the evolution of adaptation is still a subject of intense exploration. We used a Multi‐parent Advanced Generation Inter‐Cross (MAGIC) population, which we derived from crossing multiple parents from two distinct coastal ecotypes of an Australia wildflower, Senecio lautus. We focused on studying the contrasting gravitropic behaviours of these ecotypes, which have evolved independently multiple times and show strong responses to natural selection in field experiments, emphasising the role of natural selection in their evolution. Here, we investigated how gene expression differences have contributed to the adaptive evolution of gravitropism. We studied gene expression in 60 pools at five time points (30, 60, 120, 240 and 480 min) after rotating half of the pools 90°. We found 428 genes with differential expression in response to the 90° rotation treatment. Of these, 81 genes (~19%) have predicted functions related to the plant hormones auxin and ethylene, which are crucial for the gravitropic response. By combining insights from Arabidopsis mutant studies and analysing our gene networks, we propose a preliminary model to explain the differences in gravitropism between ecotypes. This model suggests that the differences arise from changes in the transport and availability of the two hormones auxin and ethylene. Our findings indicate that the genetic basis of adaptation involves interconnected signalling pathways that work together to give rise to new ecotypes. [ABSTRACT FROM AUTHOR]

Inbreeding depression is predicted to increase with age, because natural selection is less efficient at purging deleterious alleles that are only expressed later in life. However, empirical results are scarce, and equivocal between studies. Here we performed controlled matings between related and unrelated individuals of domesticated Japanese quail (Coturnix japonica), and monitored the performance of their offspring for all fitness components over their complete life course. We found rapid senescence in adult survival and egg laying performance, and inbreeding depression at all life stages (reduced embryo viability, increased age at maturity, as well as reduced adult survival and reproduction). Inbreeding depression did not increase at later ages for survival, but did so for egg laying, thereby accelerating reproductive senescence. Moreover, the effect of inbreeding on egg laying persisted after correcting for lifespan, indicating that both survival and reproduction were independently affected by inbreeding. We suggest that in heterogeneous populations intra‐generational purging may at earlier ages already select out the individuals that are homozygous for the specific alleles responsible for depressed survival, preventing the appearance of increased inbreeding depression in survival with age. Given that inbreeding affects reproduction independent of survival this should not apply to reproductive senescence or homogeneous populations, which may explain equivocal results between traits and studies. [ABSTRACT FROM AUTHOR]

The difficulty of designing simple autocatalysts that grow exponentially in the absence of enzymes, external drives or ingenious internal mechanisms severely constrains scenarios for the emergence of evolution by natural selection in chemical and physical systems. Here, we systematically analyze these difficulties in the simplest and most generic autocatalyst: a dimeric molecule that duplicates by templated ligation. We show that despite its simplicity, such an autocatalyst can achieve exponential growth autonomously. We also show, however, that it is possible to design as simple sub-exponential autocatalysts that have an advantage over exponential autocatalysts when competing for a common resource. We reach these conclusions by developing a theoretical framework based on kinetic barrier diagrams. Besides challenging commonly accepted assumptions in the field of the origin of life, our results provide a blueprint for the experimental realization of elementary autocatalysts exhibiting a form of natural selection, whether on a molecular or colloidal scale. Autocatalysis plays an important role in the origin of life and molecular evolution, however, designing simple autocatalysts that grow exponentially remains challenging. Here, the authors computationally design simple autocatalysts-- dimeric molecules that duplicate by templated ligation, --and show that these autocatalysts can achieve exponential growth autonomously. [ABSTRACT FROM AUTHOR]

Physics describes reality through the understanding and elucidation of physical laws. From these laws, the universe is predictable. It has indeed been suggested that explanation of observable phenomena comes from our ability to predict these events, through our understanding of physical laws and causal processes. Biological entities operate, of course, through physical and chemical laws. But there exist biological processes that have emergent properties, notably the evolution of adaptation through natural selection, which add an extra dimension to the concept of the understanding of biological phenotypes. The population genetic theory of evolution is mathematically formulated, and contains elements of determinism, typified by the action of natural selection, and elements of randomness, typified by the action of genetic drift and by the randomness of mutation. But is the goal-directed property of natural selection sufficient to conclude that the deterministic elements of the evolutionary process make evolutionary change predictable? And to what extent can we expect 'adaptation' to function as an explanation of biological phenotypes? In this Essay, John Brookfield considers parallels between the operation of physical laws and the processes of population genetic change and suggests that the operation of selection will be too complex and unpredictable for the process to have a predictability that matches those seen in the physical sciences. [ABSTRACT FROM AUTHOR]

ABSTRACT Aim Location Taxon Methods Results Main Conclusions Warm deserts are characterised by water shortages and high temperature extremes. A commonly reported adaptive strategy in such environments is maximisation of photosynthetic capacity, which allows plants to achieve positive carbon budgets by taking advantage of short periods of water availability and non‐inhibitory temperatures. Considering the well‐supported interspecific covariation between photosynthetic capacity and leaf N concentration, we tested the hypothesis that environmental aridity is related to an elevated leaf nitrogen content.53 locations in the transitional zone spanning the Mediterranean and the Sahara Desert in Morocco. The mean maximal temperature (Tmax) within the area varied between 35.7°C and 43.5°C, and the mean annual precipitation (MAP) was between 12 and 246 mm.225 vascular species representative of local vegetation.Leaf samples were collected along a regional aridity gradient and preserved in herbarium presses. The leaf mass per area (LMA) and N concentrations expressed on leaf mass (Nmass) and area (Narea) basis were determined. We also obtained LMA and Nmass values for 6711 species from a worldwide database for comparative analysis.Significant increases in mean LMA, Nmass and Narea accompanied the increase in Tmax and the decrease in MAP in woody species and in non‐graminoid herbs, but not in graminoids. Considering the overall aridity of our sampling area, we compared the Nmass values of Moroccan plants with those from a worldwide database. We found that at a common LMA, the Moroccan plants showed on average elevated Nmass relative to global values.These two lines of evidence: regional gradient and global comparison confirm that hot deserts select for high leaf N content. This result suggests the direction of natural selection that will accompany future climate warming and habitat aridification. [ABSTRACT FROM AUTHOR]

Introduction: There is an urgent clinical need to accurately predict the risk for disease progression in post‐treatment NSCLC patients, yet current ctDNA mutation profiling approaches are limited by low sensitivity. We represent a non‐invasive liquid biopsy assay utilizing cfDNA neomer profiling for predicting disease progression in 44 inoperable localized NSCLC patients. Methods: A total of 97 plasma samples were collected at various time points during or post‐treatments (TP1: 39, TP2: 33, TP3: 25). cfDNA neomer profiling, generated based on target sequencing data, was used to fit survival support vector machine models for each time point. Leave‐one‐out cross‐validation (LOOCV) was performed to evaluate the models' predictive performances. Results: Our cfDNA neomer profiling assay showed excellent performance in detecting patients with a high risk for disease progression. At TP1, the high‐risk patients detected by our model showed an increased risk of 3.62 times (hazard ratio [HR] = 3.62, p = 0.0026) for disease progression, compared to 3.91 times (HR = 3.91, p = 0.0022) and 4.00 times (HR = 4.00, p = 0.019) for TP2 and TP3. These neomer profiling determined HRs were higher than the ctDNA mutation‐based results (HR = 2.08, p = 0.074; HR = 1.49, p = 0.61) at TP1 and TP3. At TP1, the predictive model reached 40% sensitivity at 92.9% specificity, outperforming the mutation‐based method (40% sensitivity at 78.6% specificity), while the combination results reached a higher sensitivity (60%). Finally, the longitudinal analysis showed that the combination of neomer and ctDNA mutation‐based results could predict disease progression with an excellent sensitivity of 88.9% at 80% specificity. Conclusion: In conclusion, we developed a cfDNA neomer profiling assay for predicting disease progression in inoperable NSCLC patients. This assay showed increased predicting power during and post‐treatment compared to the ctDNA mutation‐based method, thus illustrating a great clinical potential to guide treatment decisions in inoperable NSCLC patients. Trial Registration: ClinicalTrials.gov: NCT04014465 [ABSTRACT FROM AUTHOR]

The Tibetan Plateau's distinctive high-altitude environment, marked by extreme cold and reduced oxygen levels, presents considerable survival challenges for both humans and mammals. Natural selection has led to the accumulation of adaptive mutations in Tibetan pigs, enabling them to develop distinctive adaptive phenotypes. Here, we aim to uncover the genetic mechanisms underlying the adaptation of Tibetan pigs to high-altitude hypoxia. Therefore, we conducted a systematic analysis of 140 whole-genome sequencing (WGS) data points from different representing pig populations. Our analysis identified a total of 27,614,561 mutations, including 22,386,319 single-nucleotide variants (SNVs) and 5,228,242 insertions/deletions (INDELs, size < 50 bp). A total of 11% (2,678,569) of the SNVs were newly identified in our project, significantly expanding the dataset of genetic variants in Tibetan pigs. Compared to other pig breeds, Tibetan pigs are uniquely adapted to high-altitude environments, exhibiting the highest genetic diversity and the lowest inbreeding coefficient. Employing the composite of multiple signals (CMS) method, we scanned the genome-wide Darwinian positive selection signals and identified 32,499 Tibetan pig positively selected SNVs (TBPSSs) and 129 selected genes (TBPSGs), including 213 newly discovered genes. Notably, we identified eight genes (PHACTR1, SFI1, EPM2A, SLC30A7, NKAIN2, TNNI3K, and PLIN2) with strong nature selection signals. They are likely to improve cardiorespiratory function and fat metabolism to help Tibetan pigs become adapted to the high-altitude environment. These findings provide new insights into the genetic mechanisms of high-altitude adaptation and the adaptive phenotypes of Tibetan pigs. [ABSTRACT FROM AUTHOR]

Natural or artificial selection causes animals to adapt to their environment. The adaptive changes generated by the rumen population and metabolism form the basis of ruminant evolution. In particular, the adaptive drive for environmental adaptation reflects the high-quality traits of sheep that have migrated from other places or have been distant from their origins for a long time. The Hu sheep is the most representative sheep breed in the humid and low-altitude environments (Tai Lake region) in East Asia and has been widely introduced into the arid and high-altitude environments (Tibetan Plateau and Hotan region), resulting in environmental adaptive changes in the Hu sheep. In this study, a joint analysis of the rumen microbial metagenome and metabolome was conducted on Hu sheep from different regions (area of origin and area of introduction) with the objective of investigating the quality traits of Hu sheep and identifying microorganisms that influence the adaptive drive of ruminants. The results demonstrated that the growth performance of Hu sheep was altered due to changes in rumen tissue and metabolism following their introduction to the arid area at relatively high altitude. Metagenomic and metabolomic analyses (five ramsper area) revealed that 3580 different microorganisms and 732 different metabolites were identified in the rumen fluid of arid sheep. Among these, the representative upregulated metabolites were 4,6-isocanedione, methanesulfonic acid and N2-succinyl-L-arginine, while the dominant microorganism was Prevotella ruminicola. The downregulated metabolites were identified as campesterol, teprenone and dihydroclavaminic acid, while the disadvantaged microorganisms were Dialister_succinatiphilus, Prevotella_sp._AGR2160, Prevotella_multisaccharivorax and Selenomonas_bovis. The results of the Pearson analysis indicated that the rumen microbiota and metabolite content of sheep were significantly altered and highly correlated following their relocation from a humid lowland to an arid upland. In particular, the observed changes in rumen microorganisms led to an acceleration of body metabolism, rendering sheep highly adaptable to environmental stress. Prevotella_ruminicola was identified as playing an important role in this process. These findings provide insights into the environmental adaptation mechanisms of sheep. [ABSTRACT FROM AUTHOR]

Natural transformation is the only mechanism of genetic exchange controlled by the recipient bacteria. We quantified its rates in 786 clinical strains of the human pathogens Legionella pneumophila (Lp) and 496 clinical and environmental strains of Acinetobacter baumannii (Ab). The analysis of transformation rates in the light of phylogeny revealed they evolve by a mixture of frequent small changes and a few large quick jumps across 6 orders of magnitude. In standard conditions close to half of the strains of Lp and a more than a third in Ab are below the detection limit and thus presumably non-transformable. Ab environmental strains tend to have higher transformation rates than the clinical ones. Transitions to non-transformability were frequent and usually recent, suggesting that they are deleterious and subsequently purged by natural selection. Accordingly, we find that transformation decreases genetic linkage in both species, which might accelerate adaptation. Intragenomic conflicts with chromosomal mobile genetic elements (MGEs) and plasmids could explain these transitions and a GWAS confirmed systematic negative associations between transformation and MGEs: plasmids and other conjugative elements in Lp, prophages in Ab, and transposable elements in both. In accordance with the hypothesis of modulation of transformation rates by genetic conflicts, transformable strains have fewer MGEs in both species and some MGEs inactivate genes implicated in the transformation with heterologous DNA (in Ab). Innate defense systems against MGEs are associated with lower transformation rates, especially restriction-modification systems. In contrast, CRISPR-Cas systems are associated with higher transformation rates suggesting that adaptive defense systems may facilitate cell protection from MGEs while preserving genetic exchanges by natural transformation. Ab and Lp have different lifestyles, gene repertoires, and population structure. Nevertheless, they exhibit similar trends in terms of variation of transformation rates and its determinants, suggesting that genetic conflicts could drive the evolution of natural transformation in many bacteria. Bacterial species exhibit large variations in their transformation rates. This study of Legionella pneumophila and Acinetobacter baumannii shows that their transformation rates evolve by sudden quick changes, likely caused by intragenomic conflicts between mobile genetic elements and the host bacterium. [ABSTRACT FROM AUTHOR]

Background: Lithospermeae is the largest tribe within Boraginaceae. The tribe has been the focus of multiple phylogenetic studies over the last 15 years, with most focused on one genus or a few genera. In the present study, we newly sequenced 69 species of Lithospermeae and relatives to analyze the phylogenomic relationships among its members as well as the evolution of the plastid genome. Results: The phylogeny of Lithospermeae resolved from the plastid genome and nrDNA cistron is generally congruent with prior studies, but is better resolved and supported. Increasing character sampling across the plastid genome results in gradually more similar trees to that from the entire plastid genome. Overall, plastid genome structure was quite consistent across Lithospermeae. Codon Usage Bias (CUB) analyses demonstrate that across Lithospermeae plastid genomes were rich in AT and poor in GC. Mutation may play a greater role than selection across the plastid genome of Lithospermeae. The present study is the first to highlight the CUB characteristics of Lithospermeae species, which can help elucidate the mechanisms underlying patterns of molecular evolution and improve the expression levels of exogenous genes by codon optimization. Conclusions: This study provides a comprehensive phylogenomic analysis of Lithospermeae, significantly enhancing our understanding of the phylogenetic relationships and plastid genome evolution within this largest tribe of Boraginaceae. By utilizing an expanded genomic sampling approach, we have achieved increased resolution and support among the evolutionary relationships of the tribe, in line with but improving upon previous studies. The analyses of plastid genome structure revealed consistency across Lithospermeae, with a notable CUB. This study marks the first investigation into the CUB of Lithospermeae species and sets the stage for further research on the molecular evolution of plastid genomes across Boraginaceae. [ABSTRACT FROM AUTHOR]