Search

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]

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]

In nature, most microbial populations have complex spatial structures that can affect their evolution. Evolutionary graph theory predicts that some spatial structures modelled by placing individuals on the nodes of a graph affect the probability that a mutant will fix. Evolution experiments are beginning to explicitly address the impact of graph structures on mutant fixation. However, the assumptions of evolutionary graph theory differ from the conditions of modern evolution experiments, making the comparison between theory and experiment challenging. Here, we aim to bridge this gap by using our new model of spatially structured populations. This model considers connected subpopulations that lie on the nodes of a graph, and allows asymmetric migrations. It can handle large populations, and explicitly models serial passage events with migrations, thus closely mimicking experimental conditions. We analyze recent experiments in light of this model. We suggest useful parameter regimes for future experiments, and we make quantitative predictions for these experiments. In particular, we propose experiments to directly test our recent prediction that the star graph with asymmetric migrations suppresses natural selection and can accelerate mutant fixation or extinction, compared to a well-mixed population. Author summary: Predicting how mutations spread through a population and eventually take over is important for understanding evolution. Complex spatial structures are ubiquitous in natural microbial populations, and can impact the fate of mutants. Theoretical models have been developed to describe this effect. They predict that some spatial structures have mutant fixation probabilities that differ from those of well-mixed populations. Experiments are beginning to probe these effects in the laboratory. However, there is a disconnect between models and experiments, because they consider different conditions. In this work, we connect them through a new model that closely matches experimental conditions. We analyze recent experiments and propose new ones that should allow testing the effects of complex population spatial structures on mutant fate. [ABSTRACT FROM AUTHOR]

Introduction: Among cultivated tea plants (Camellia sinensis), only four mitogenomes for C. sinensis var. assamica (CSA) have been reported so far but none for C. sinensis var. sinensis (CSS). Here, two mitogenomes of CSS (CSSDHP and CSSRG) have been sequenced and assembled. Methods: Using a combination of Illumina and Nanopore data for the first time. Comparison between CSS and CSA mitogenomes revealed a huge heterogeneity. Results: The number of the repetitive sequences was proportional to the mitogenome size and the repetitive sequences dominated the intracellular gene transfer segments (accounting for 88.7%- 92.8% of the total length). Predictive RNA editing analysis revealed that there might be significant editing in NADH dehydrogenase subunit transcripts. Codon preference analysis showed a tendency to favor A/T bases and T was used more frequently at the third base of the codon. ENc plots analysis showed that the natural selection play an important role in shaping the codon usage bias, and Ka/Ks ratios analysis indicated Nad1 and Sdh3 genes may have undergone positive selection. Further, phylogenetic analysis shows that six C. sinensis clustered together, with the CSA and CSS forming two distinct branches, suggesting two different evolutionary pathway. Discussion: Altogether, this investigation provided an insight into evolution and phylogeny relationship of C. sinensis mitogenome, thereby enhancing comprehension of the evolutionary patterns within C. sinensis species. [ABSTRACT FROM AUTHOR]

High-density genomic data analyzed by accurate statistical methods are of potential to enlighten past breeding practices such as selection by unraveling fixed regions. In this study, four native Turkish sheep breeds (80 samples) were genotyped via 296.097 single nucleotide polymorphisms (SNPs) detected by double-digest restriction site-associated DNA (ddRADseq) library preparation combined with the Illumina HiSeq X Ten instrument in order to identify genes under selection pressure. A total of 32, 136, 133, and 119 protein-coding genes were detected under selection pressure by runs of homozygosity (ROH), integrated haplotype score (iHS), the ratio of extended haplotype homozygosity (Rsb), and fixation index (FST) approaches, respectively. Of these, a total of 129 genes were identified by at least two statistical models which overlapped with a total of 52 quantitative trait loci (QTL)-associated SNPs, known to be related to fiber diameter, milk content, body weight, carcass traits, some blood parameters, and entropion. A total of six genes under selection pressure were validated by three statistical approaches five of which are of potential to be integrated into animal breeding since they were associated with wool fiber diameter (ZNF208B), behaviors related to neurocognitive development (CBX1 and NFE2L1), adaptation to high-altitude (SDK1), and anxiety causing internal stress (GSG1L). The sixth gene (COPZ1) turned out to play an important role in coping with different types of cancer in mammals. In particular, ROH analysis uncovered significant findings that the Güney Karaman (GKR) had experienced different selection practices than the Akkaraman (AKR) breed. Moreover, some genes specifically under selection in the GKR breed turned out to be associated with olfaction (OR6K6, OR6N1, OR6N2, and OR4C16), survival during the gestation period (PRR15L), and heat stress (CDK5RAP9). The results of this study imply that GKR may become genetically different from the AKR breed at the genome level due to most probably experiencing different adaptation processes occurring in raised climatic conditions. These differences should be conserved to face future challenges, while other native Turkish sheep breeds could be monitored via genome-wide high-density SNP data to obtain deeper knowledge about the effects of natural selection. [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]

Without heritable variation natural selection cannot effect evolutionary change. In the case of group selection, there must be variation in the population of groups. Where does this variation come from? One source of variation is from the stochastic birth–death processes that occur within groups. This is where variation between groups comes from in most mathematical models of group selection. Here, we argue that another important source of variation between groups is fission, the (generally random) group-level reproduction where parent groups split into two or more offspring groups. We construct a simple model of the fissioning process with a parameter that controls how much variation is produced among the offspring groups. We then illustrate the effect of that parameter with some examples. In most models of group selection in the literature, no variation is produced during group reproduction events; that is, groups "clone" themselves when they reproduce. Fission is often a more biologically realistic method of group reproduction, and it can significantly increase the efficacy of group selection. [ABSTRACT FROM AUTHOR]

Hybrid zones are dynamic systems where natural selection, sexual selection, and other evolutionary forces can act on reshuffled combinations of distinct genomes. The movement of hybrid zones, individual traits, or both are of particular interest for understanding the interplay between selective processes. In a hybrid zone involving two lek-breeding birds, secondary sexual plumage traits of Manacus vitellinus , including bright yellow collar and olive belly color, have introgressed ~50 km asymmetrically across the genomic center of the zone into populations more genetically similar to Manacus candei. Males with yellow collars are preferred by females and are more aggressive than parental M. candei , suggesting that sexual selection was responsible for the introgression of male traits. We assessed the spatial and temporal dynamics of this hybrid zone using historical (1989–1994) and contemporary (2017–2020) transect samples to survey both morphological and genetic variation. Genome-wide single nucleotide polymorphism data and several male phenotypic traits show that the genomic center of the zone has remained spatially stable, whereas the olive belly color of male M. vitellinus has continued to introgress over this time period. Our data suggest that sexual selection can continue to shape phenotypes dynamically, independent of a stable genomic transition between species. [ABSTRACT FROM AUTHOR]

Understanding the drivers of community assembly is critical for predicting the future of biodiversity and ecosystem services. Ecological selection ubiquitously shapes communities by selecting for individuals with the most suitable trait combinations. Detecting selection types on key traits across environmental gradients and over time has the potential to reveal the underlying abiotic and biotic drivers of community dynamics. Here, we present a model‐based predictive framework to quantify the multidimensional trait distributions of communities (community trait spaces), which we use to identify ecological selection types shaping communities along environmental gradients. We apply the framework to over 3600 boreal forest understory plant communities with results indicating that directional, stabilizing, and divergent selection all modify community trait distributions and that the selection type acting on individual traits may change over time. Our results provide novel and rare empirical evidence for divergent selection within a natural system. Our approach provides a framework for identifying key traits under selection and facilitates the detection of processes underlying community dynamics. [ABSTRACT FROM AUTHOR]

We investigate natural selection on polygenic scores in the contemporary US, using the Health and Retirement Study. Across three generations, scores which correlate negatively (positively) with education are selected for (against). However, results only partially support the economic theory of fertility as an explanation for natural selection. The theory predicts that selection coefficients should be stronger among low-income, less educated, unmarried and younger parents, but these predictions are only half borne out: coefficients are larger only among low-income parents and unmarried parents. We also estimate effect sizes corrected for noise in the polygenic scores. Selection for some health traits is similar in magnitude to that for cognitive traits. [ABSTRACT FROM AUTHOR]

Life history studies support the fast–slow continuum as the dominant but not unique axis structuring life history variation. Other important axes of life history variation associated with development and reproductive tactics exist, and exploration of further axes, clusters, and boundaries of life history variation is needed. Existing life history analyses are venturing far from theory and could benefit from a stronger focus on hypothesis testing rather than exploration. We make recommendations to identify the structuring axes of life history variation through data choices and analytical methods of dimensionality reduction with recourse to a comprehensive model of life history. Life history strategies, which combine schedules of survival, development, and reproduction, shape how natural selection acts on species' heritable traits and organismal fitness. Comparative analyses have historically ranked life histories along a fast–slow continuum, describing a negative association between time allocation to reproduction and development versus survival. However, higher-quality, more representative data and analyses have revealed that life history variation cannot be fully accounted for by this single continuum. Moreover, studies often do not test predictions from existing theories and instead operate as exploratory exercises. To move forward, we offer three recommendations for future investigations: standardizing life history traits, overcoming taxonomic siloes, and using theory to move from describing to understanding life history variation across the Tree of Life. [ABSTRACT FROM AUTHOR]

Adaptive differentiation of traits and underlying loci can occur at a small geographical scale if natural selection is stronger than countervailing gene flow and drift. We investigated this hypothesis using coupled quantitative genetic and genomic approaches for a wind‐pollinated tree species, Quercus rubra, along the steep, narrow gradient of the Lake Superior coast that encompasses four USDA Hardiness Zones within 100 km. For the quantitative genetic component of this study, we examined phenotypic differentiation among eight populations in a common garden, measuring seed mass, germination, height, stem diameter, leaf number, specific leaf area and survival. For the genomic component, we quantified genetic differentiation for 26 populations from the same region using RAD‐seq. Because hybridisation with Quercus ellipsoidalis occurs in other parts of the species' range, we included two populations of this congener for comparison. In the common garden study, we found a strong signal of population differentiation that was significantly associated with at least one climate factor for nine of 10 measured traits. In contrast, we found no evidence of genomic differentiation among populations based on FST or any other measures. However, both distance‐based and genotype–environment association analyses identified loci showing the signature of selection, with one locus in common across five analyses. This locus was associated with the minimum temperature of the coldest month, a factor that defines the climate zones and was also significant in the common garden analyses. In addition, we documented introgression from Q. ellipsoidalis into Q. rubra, with rates of introgression correlated with the climate gradient. In sum, this study reveals signatures of selection at the quantitative trait and genomic level consistent with climate adaptation, a pattern that is more often documented at a much broader geographical scale, especially in long‐lived wind‐pollinated species. [ABSTRACT FROM AUTHOR]

Superabundant microbes (SAMs), such as marine phytoplankton, are extremely important in Earth's ecosystems. Evolutionary processes have been mainly studied in much smaller populations, and it is poorly understood how evolution works in the huge populations of SAMs. The standard tools of evolutionary genetics were developed for populations of smaller sizes, and many of these tools may not be suitable to study evolution in astronomically large SAM populations. Nucleotide sequence polymorphism is surprisingly low in SAMs, corresponding to a population of a few million individuals, but the reasons for this lack of diversity are unclear. Marine phytoplankton play crucial roles in the Earth's ecological, chemical, and geological processes. They are responsible for about half of global primary production and drive the ocean biological carbon pump. Understanding how plankton species may adapt to the Earth's rapidly changing environments is evidently an urgent priority. This problem requires evolutionary genetic approaches as evolution occurs at the level of allele frequency change within populations driven by genetic drift and natural selection (microevolution). Plankters such as the coccolithophore Gephyrocapsa huxleyi and the cyanobacterium Prochlorococcus 'marinus' are among Earth's most abundant organisms. In this opinion paper we discuss how evolution in astronomically large populations of superabundant microbes (SAMs) may act fundamentally differently than it does in the populations of more modest size found in well-studied organisms. This offers exciting opportunities to study evolution in the conditions that have yet to be explored and also leads to unique challenges. Exploring these opportunities and challenges is the goal of this article. [ABSTRACT FROM AUTHOR]

Maintaining genetic diversity and variation in livestock populations is critical for natural and artificial selection promoting genetic improvement while avoiding problems due to inbreeding. In Laos, there are concerns that there has been a decline in genetic diversity and a rise in inbreeding among native goats in their village‐based smallholder system. In this study, we investigated the genetic diversity of Lao native goats in Phin, Songkhone and Sepon districts in Central Laos for the first time using Illumina's Goat SNP50 BeadChip. We also explored the genetic relationships between Lao goats with 163 global goat populations from 36 countries. Our results revealled a close genetic relationship between Lao native goats and Chinese, Mongolian and Pakistani goats, sharing ancestries with Guangfen, Jining Grey and Luoping Yellow breeds (China) and Teddi goats (Pakistan). The observed (Ho) and expected (He) heterozygosity were 0.292 and 0.303 (Laos), 0.288 and 0.288 (Sepon), 0.299 and 0.308 (Phin) and 0.289 and 0.305 (Songkhone), respectively. There was low to moderate genetic differentiation (FST: 0.011–0.043) and negligible inbreeding coefficients (FIS: −0.001 to 0.052) between goat districts. The runs of homozygosity (ROH) had an average length of 5.92–6.85 Mb, with short ROH segments (1–5 Mb length) being the most prevalent (66.34%). Longer ROH segments (20–40 and >40 Mb length categories) were less common, comprising only 4.81% and 1.01%, respectively. Lao goats exhibit moderate genetic diversity, low‐inbreeding levels and adequate effective population size. Some genetic distinctions between Lao goats may be explained by geographic and cultural features. [ABSTRACT FROM AUTHOR]

Hepatitis E virus is a primary cause of acute hepatitis worldwide. The present study attempts to assess the genetic variability and evolutionary divergence among HEV genotypes. A vaccine promising capsid‐protein coding ORF‐2 gene sequences of HEV was evaluated using phylogenetics, model‐based population genetic methods and principal component analysis. The analyses unveiled nine distinct clusters as subpopulations for six HEV genotypes. HEV‐3 genotype samples stratified into four different subgroups, while HEV‐4 stratified into three additional subclusters. Rabbit‐infectious HEV‐3ra samples constitute a distinct cluster. Pairwise analysis identified marked genetic distinction of HEV‐4c and HEV‐4i subgenotypes compared to other genotypes. Numerous admixed, inter and intragenotype recombinant strains were detected. The MEME method identified several ORF‐2 codon sites under positive selection. Some selection signatures lead to amino acid substitutions within ORF‐2, resulting in altered physicochemical features. Moreover, a pattern of host‐specific adaptive signatures was identified among HEV genotypes. The analyses conclusively depict that recombination and episodic positive selection events have shaped the observed genetic diversity among different HEV genotypes. The significant genetic diversity and stratification of HEV‐3 and HEV‐4 genotypes into subgroups, as identified in the current study, are noteworthy and may have implications for the efficacy of anti‐HEV vaccines. [ABSTRACT FROM AUTHOR]

Heterochely denotes the presence of dissimilarly sized chelipeds on opposite sides of the body, a prevalent occurrence in diverse crustaceans. Conversely, heterometry pertains to the quantifiable disparities in size between these chelipeds. Both chelipeds hold pivotal roles in activities such as foraging, mating, and defense. Consequently, individuals of both genders in heterochelic species exhibit this morphological pattern. Previous studies have identified sexual dimorphism in cheliped size, with males displaying larger major chelipeds compared to females, albeit solely relying on propodus length as a size proxy and focusing solely on the major cheliped. In our study, we meticulously examined 190 specimens of the common European hermit crab Pagurus bernhardus from two collections. We sought to elucidate allometric relationships and assess whether heterometry exhibited sex‐based differences when adjusting for body size by using ratios. Our findings revealed that male chelipeds displayed hyperallometric growth relative to females, and all three calculated heterometry indices exhibited significant disparities between the sexes. Consequently, male specimens exhibited larger major and minor chelipeds, even when theoretically matched for body size with females. This phenomenon may be attributed, among other factors, to male–male contests. Should indirect mate selection favor males with larger chelipeds in proportion to their body size, this dynamic could potentiate sexual selection in their favor. [ABSTRACT FROM AUTHOR]

Predation is a powerful driving force leading to the evolution of antipredator defences in prey. The effectiveness of the antipredator defences can depend on various ecological contexts such as predator density and the development stages of the prey species. Males and females often exhibit remarkably different morphologies, behaviours and life histories, and the sexual differences are expected to generate different ecological contexts for males and females, potentially driving the evolution of sex-specific antipredator defences. In the horned beetle Gnatocerus cornutus , males have enlarged mandibles, but females lack this exaggeration. As potential defences against predators, these beetles either become immobile or run away. In this study, we established populations subjected to sex-specific predation. We found that male locomotion was increased in populations subjected to male-specific predation and that female immobility was increased in populations subjected to female-specific predation. We also found that males appeared on the surface of food resources more frequently than females. Given such differences in microhabitat preferences, the males are more likely to be detected by predators than the females. The sexual differences in morphology and microhabitat preferences may generate different predatory environments for males and females, resulting in males using locomotion to escape from predators and females using immobility to hide from them. In this laboratory selection experiment, we did not observe the evolution of the opposite sex's antipredator traits in response to sex-specific predation. We detected no intersexual genetic correlation of immobility and locomotion. The genetic decoupling and different predatory contexts for the two sexes may promote sexually different antipredator defences in G. cornutus. • Males and females are predicted to evolve different defences against natural enemies. • Male Gnatocerus cornutus evolved to flee when confronted by natural enemies. • Females evolved to hide when confronted by natural enemies. [ABSTRACT FROM AUTHOR]

Background and Scope Plant functional traits are the result of natural selection to optimize carbon gain, leading to a broad spectrum of traits across environmental gradients. Among plant traits, leaf water storage capacity is paramount for plant drought resistance. We explored whether leaf-succulent taxa follow trait correlations similar to those of non-leaf-succulent taxa to evaluate whether both are similarly constrained by relationships between leaf water storage and climate. Methods We tested the relationships among three leaf traits related to water storage capacity and resource use strategies in 132 species comprising three primary leaf types: succulent, sclerophyllous, and leaves with rapid returns on water investment, referred to as fast return. Correlation coefficients among specific leaf area (SLA), water mass per unit of area (WMA), and saturated water content (SWC) were tested, along with relationships between leaf trait spectra and aridity determined from species occurrence records. Results Both SWC and WMA at a given SLA were ~10-fold higher in succulent leaves than in non-succulent leaves. While SWC actually increased with SLA in non-succulent leaves, no relationship was detected between SWC and SLA in succulent leaves, although WMA decreased with SLA in all leaf types. A principal component analysis (PCA) revealed that succulent taxa occupied a widely different mean trait space than either fast-return (P  < 0.0001) or sclerophyllous (P  < 0.0001) taxa along the first PCA axis, which explained 63 % of mean trait expression among species. However, aridity only explained 12 % of the variation in PCA1 values. This study is among the first to establish a structural leaf trait spectrum in succulent leaf taxa and quantify contrasts in leaf water storage among leaf types relative to specific leaf area. Conclusions Trait coordination in succulent leaf taxa may not follow patterns similar to those of widely studied non-succulent taxa. [ABSTRACT FROM AUTHOR]

Philosophers of biology have recently been debating about whether random genetic drift is a distinct process from that of natural selection. One camp argues that drift is a process of “indiscriminate sampling” that is logically and ontologically distinct from the “discriminate sampling” process that is natural selection. The other camp argues that, rather than being two autonomous processes, natural selection and drift are just two aspects or facets of a single process. I argue that the two positions involved in this dispute are not mutually exclusive. Indeed, by explicitly taking into account its sources, I argue that two kinds of drift are theoretically possible. The first kind – that I call circumstantial-drift – involves a process of its own, separate from the process of natural selection, or, more specifically, it requires that differences in a circumstantial trait cause differences in reproductive output of biological entities. The second kind – that I label probabilistic-drift – requires no other process than a probabilistic causal relation between a heritable physical trait and reproductive output, i.e. requires only the causal relation on which the work of natural selection could also depend. If both of these kinds of drift are theoretically possible, then neither defining, nor empirically identifying drift need to be zero-sum games. [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]

Signals of natural selection can be quickly eroded in high gene flow systems, curtailing efforts to understand how and when genetic adaptation occurs in the ocean. This long‐standing, unresolved topic in ecology and evolution has renewed importance because changing environmental conditions are driving range expansions that may necessitate rapid evolutionary responses. One example occurs in Kellet's whelk (Kelletia kelletii), a common subtidal gastropod with an ~40‐ to 60‐day pelagic larval duration that expanded their biogeographic range northwards in the 1970s by over 300 km. To test for genetic adaptation, we performed a series of experimental crosses with Kellet's whelk adults collected from their historical (HxH) and recently expanded range (ExE), and conducted RNA‐Seq on offspring that we reared in a common garden environment. We identified 2770 differentially expressed genes (DEGs) between 54 offspring samples with either only historical range (HxH offspring) or expanded range (ExE offspring) ancestry. Using SNPs called directly from the DEGs, we assigned samples of known origin back to their range of origin with unprecedented accuracy for a marine species (92.6% and 94.5% for HxH and ExE offspring, respectively). The SNP with the highest predictive importance occurred on triosephosphate isomerase (TPI), an essential metabolic enzyme involved in cold stress response. TPI was significantly upregulated and contained a non‐synonymous mutation in the expanded range. Our findings pave the way for accurately identifying patterns of dispersal, gene flow and population connectivity in the ocean by demonstrating that experimental transcriptomics can reveal mechanisms for how marine organisms respond to changing environmental conditions. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Maternal investment theory is the study of how breeding females allocate resources between offspring size and brood size to achieve reproductive success. In classical trade-off models, r/K-selection and bet-hedging selection, the primary predictors of maternal investments in offspring are population density and resource stability. In crowded, stable environments, K-selected females invest in large offspring at an equivalent cost in brood size. In uncrowded, unstable environments, r-selected females invest in large broods at an equivalent cost in offspring size. In unpredictable resource environments, bet-hedging females invest moderately in brood size and offspring size. The maternal risk-management model represents a profound departure from classical trade-off models. Maternal investments in offspring size, brood size, and brood number are shaped independently by autonomous risk factors: the duration of gaps in resources during seasonal cycles, rates of predation, and unpredictable catastrophic events. To date, no single model has risen to a position of preeminence. Here in sharks, we show that maternal investments within and across species do not agree with the predictions of trade-off models and instead agree with the predictions of the maternal risk-management model. Within and across shark species, offspring size and brood size were independent maternal investment strategies. The risk of starvation favored investments in larger offspring. The risk of predation favored investments in larger broods. If empirical studies continue to confirm its predictions, maternal-risk management may yet emerge as a unifying model of diverse reproductive adaptations by means of natural selection. [ABSTRACT FROM AUTHOR]

ABSTRACT Two views claim to account for the origins of great ape gestural forms. On the Leipzig view, gestural forms are ontogenetically ritualised from action sequences between pairs of individuals. On the St Andrews view, gestures are the product of natural selection for shared gestural forms. The Leipzig view predicts within‐ and between‐group differences between gestural forms that arise as a product of learning in ontogeny. The St Andrews view predicts universal gestural forms comprehensible within and between species that arise because gestural forms were a target of natural selection. We reject both accounts and propose an alternative “recruitment view” of the origins of great ape gestures. According to the recruitment view, great ape gestures recruit features of their existing behavioural repertoire for communicative purposes. Their gestures inherit their communicative functions from visual (and sometimes tactile) presentations of familiar and easily recognisable action schemas and states and parts of the body. To the extent that great ape species possess similar bodies, this predicts mutual comprehensibility within and between species – but without supposing that gestural forms were themselves targets of natural selection. Additionally, we locate great ape gestural communication within a pragmatic framework that is continuous with human communication, and make testable predications for adjudicating between the three alternative views. We propose that the recruitment view best explains existing data, and does so within a mechanistic framework that emphasises continuity between human and non‐human great ape communication. [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]

Background: The invasive pest Spotted-Wing Drosophila, Drosophila suzukii (Matsumura), causes extensive damage and production losses of soft-skinned fruits. Native to Asia, the species has now spread worldwide, with first reports in Portugal in 2012. In this study, we focus on the genomic signatures of the recent Portuguese invasion, in the context of worldwide patterns established in previous works. We analyzed whole genome pool sequencing data from three Portuguese populations (N = 240) sampled in 2019 and 2021. Results: The correlation of allele frequencies suggested that Portuguese populations are related to South European ones, indicating a Mediterranean invasion route. While two populations exhibited levels of genetic variation comparable to others in the invasive range, a third showed low levels of genetic diversity, which may result from a recent colonization of the region. Genome-wide analyses of natural selection identified ten genes previously associated with D. suzukii's invasive capacity, which may have contributed to the species' success in Portugal. Additionally, we pinpointed six genes evolving under positive selection across Portuguese populations but not in European ones, which is indicative of local adaptation. One of these genes, nAChRalpha7, encodes a nicotinic acetylcholine receptor, which are known targets for insecticides widely used for D. suzukii control, such as neonicotinoids and spinosyns. Although spinosyn resistance has been associated with mutations in the nAChRalpha6 in other Drosophila species, the putative role of nAChRalpha7 in insecticide resistance and local adaptation in Portuguese D. suzukii populations encourages future investigation. Conclusions: Our results highlight the complex nature of rapid species invasions and the role of rapid local adaptation in determining the invasive capacity of these species. [ABSTRACT FROM AUTHOR]

Over the past 2 decades, biologists have come to appreciate that hybridization, or genetic exchange between distinct lineages, is remarkably common—not just in particular lineages but in taxonomic groups across the tree of life. As a result, the genomes of many modern species harbor regions inherited from related species. This observation has raised fundamental questions about the degree to which the genomic outcomes of hybridization are repeatable and the degree to which natural selection drives such repeatability. However, a lack of appropriate systems to answer these questions has limited empirical progress in this area. Here, we leverage independently formed hybrid populations between the swordtail fish Xiphophorus birchmanni and X. cortezi to address this fundamental question. We find that local ancestry in one hybrid population is remarkably predictive of local ancestry in another, demographically independent hybrid population. Applying newly developed methods, we can attribute much of this repeatability to strong selection in the earliest generations after initial hybridization. We complement these analyses with time-series data that demonstrates that ancestry at regions under selection has remained stable over the past approximately 40 generations of evolution. Finally, we compare our results to the well-studied X. birchmanni × X. malinche hybrid populations and conclude that deeper evolutionary divergence has resulted in stronger selection and higher repeatability in patterns of local ancestry in hybrids between X. birchmanni and X. cortezi. How repeatable are the genomic outcomes of hybridization, and how much does natural selection drive such repeatability? This study of hybrid populations of swordtail fish reveals high repeatability due to strong selection in the earliest generations after initial hybridization; deeper evolutionary divergence results in stronger selection and higher repeatability. [ABSTRACT FROM AUTHOR]

Secondary contact between closely related taxa represents a "moment of truth" for speciation—an opportunity to test the efficacy of reproductive isolation that evolved in allopatry and to identify the genetic, behavioral, and/or ecological barriers that separate species in sympatry. Sex chromosomes are known to rapidly accumulate differences between species, an effect that may be exacerbated for neo-sex chromosomes that are transitioning from autosomal to sex-specific inheritance. Here we report that, in the Solomon Islands, two closely related bird species in the honeyeater family—Myzomela cardinalis and Myzomela tristrami—carry neo-sex chromosomes and have come into recent secondary contact after ~1.1 my of geographic isolation. Hybrids of the two species were first observed in sympatry ~100 years ago. To determine the genetic consequences of hybridization, we use population genomic analyses of individuals sampled in allopatry and in sympatry to characterize gene flow in the contact zone. Using genome-wide estimates of diversity, differentiation, and divergence, we find that the degree and direction of introgression varies dramatically across the genome. For sympatric birds, autosomal introgression is bidirectional, with phenotypic hybrids and phenotypic parentals of both species showing admixed ancestry. In other regions of the genome, however, the story is different. While introgression on the Z/neo-Z-linked sequence is limited, introgression of W/neo-W regions and mitochondrial sequence (mtDNA) is highly asymmetric, moving only from the invading M. cardinalis to the resident M. tristrami. The recent hybridization between these species has thus enabled gene flow in some genomic regions but the interaction of admixture, asymmetric mate choice, and/or natural selection has led to the variation in the amount and direction of gene flow at sex-linked regions of the genome. Author summary: When an invasive species colonizes an island and interacts with a closely related resident species, we are provided with a rare opportunity to study the consequences of interbreeding and the factors that keep species distinct. Regions of the genome that evolve rapidly and/or influence mate choice may be especially likely to act as incidental barriers to gene flow. The red Myzomela cardinalis, birds in the honeyeater family, have invaded Makira in the Solomon Islands, coming into contact with the endemic, all black Myzomela tristrami. We used population genomic analyses of individuals in geographic isolation, and those in geographic contact, to understand the history of these two species and the consequences of their recent range overlap. We found that sex-specific regions of the genome (i.e., sex chromosomes) were either limited in their ability to move between species, or only moved in one direction, from the invading M. cardinalis to the resident M. tristrami. This work highlights how certain regions of the genome may be especially important in defining species boundaries and the generation and maintenance of biodiversity. [ABSTRACT FROM AUTHOR]

Background: The recombination landscape and subsequent natural selection have vast consequences forevolution and speciation. However, most of the crossover and recombination hotspots are yet to be discovered. We previously reported the relevance of C and G trinucleotide two-repeat units (CG-TTUs) in crossovers and recombination. Methods: On a genome-wide scale, here we mapped all combinations of A and T trinucleotide two-repeat units (AT-TTUs) in human, consisting of AATAAT, ATAATA, ATTATT, TTATTA, TATTAT, and TAATAA. We also compared a number of the colonies formed by the AT-TTUs (distance between consecutive AT-TTUs < 500 bp) in several other primates and mouse. Results: We found that the majority of the AT-TTUs (> 96%) resided in approximately 1.4 million colonies, spread throughout the human genome. In comparison to the CG-TTU colonies, the AT-TTU colonies were significantly more abundant and larger in size. Pure units and overlapping units of the pure units were readily detectable in the same colonies, signifying that the units were the sites of unequal crossover. We discovered dynamic sharedness of several of the colonies across the primate species studied, which mainly reached maximum complexity and size in human. Conclusions: We report novel crossover and recombination hotspots of the finest molecular resolution, massively spread and shared across the genomes of human and several other primates. With respect to crossovers and recombination, these genomes are far more dynamic than previously envisioned. [ABSTRACT FROM AUTHOR]

Background: Adaptation to cold was essential for human migration across Eurasia. Non-shivering thermogenesis through brown adipose tissue (BAT) participates in cold adaptation because some genes involved in the differentiation and function of BAT exhibit signatures of positive natural selection in populations at high latitudes. Whether these genes are associated with the inter-individual variability in BAT thermogenesis remains unclear. In this study, we evaluated the potential associations between BAT activity and single nucleotide polymorphisms (SNPs) in candidate gene regions in East Asian populations. Methods: BAT activity induced by mild cold exposure was measured in 399 healthy Japanese men and women using fluorodeoxyglucose-positron emission tomography and computed tomography (FDG-PET/CT). The capacity for cold-induced thermogenesis and fat oxidation was measured in 56 men. Association analyses with physiological traits were performed for 11 SNPs at six loci (LEPR, ANGPTL8, PLA2G2A, PLIN1, TBX15-WARS2, and FADS1) reported to be under positive natural selection. Associations found in the FDG-PET/CT population were further validated in 84 healthy East Asian men and women, in whom BAT activity was measured using infrared thermography. Associations between the SNP genotypes and BAT activity or other related traits were tested using multiple logistic and linear regression models. Results: Of the 11 putative adaptive alleles of the six genes, two intronic SNPs in LEPR (rs1022981 and rs12405556) tended to be associated with higher BAT activity. However, these did not survive multiple test comparisons. Associations with lower body fat percentage, plasma triglyceride, insulin, and HOMA-IR levels were observed in the FDG-PET/CT population (P < 0.05). Other loci, including TBX15-WARS2, which is speculated to mediate cold adaptation in Greenland Inuits, did not show significant differences in BAT thermogenesis. Conclusions: Our results suggest a marginal but significant association between LEPR SNPs. However, robust supporting evidence was not established for the involvement of other loci under positive natural selection in cold adaptation through BAT thermogenesis in East Asian adults. Given the pleiotropic function of these genes, factors other than cold adaptation through BAT thermogenesis, such as diet adaptation, may contribute to positive natural selection at these loci. [ABSTRACT FROM AUTHOR]

Background: Understanding evolution is an important part of undergraduate biology education. Despite its importance, however, students often struggle to understand evolution, often holding preconceived notions of what evolution is. Here, we investigate how students in both majors and non-majors introductory biology define and conceive of evolution at the start of the semester for a two-year college and a four-year university near each other. We analyze open-ended responses to an in-class activity on the first day of the semester that asked students to define evolution, generating insight into how students are thinking of evolution prior to any formal instruction on evolution in college. Results: Our analysis of over 300 student responses reveals that students hold diverse conceptions about evolution, with some students perceiving evolution in the context of evolutionary processes while other students define evolution by referring to perceived evolutionary consequences. In addition, we identify multiple non-normative conceptions about evolution, including students viewing evolution and natural selection as synonymous and not recognizing other evolutionary forces, and find that very few students likely have developed mental models linking evolution and genetics. In addition, we find few differences between how students at the two- and four-year institutions perceive evolution, and similarly few differences between students in a majors and non-majors introductory biology, suggesting that these conceptions of evolution are widespread at the beginning of introductory biology, regardless of major or institution. Conclusions: We situate our results in the existing literature examining student conceptions of evolution, with our results extending past work that has primarily relied on more closed-ended questions or focused on specific evolutionary concepts (e.g., natural selection). Our results largely align with past work on student thinking of evolution but provide a broader, more holistic perspective at the ideas and framework that students are drawing upon when introductory biology instructors first introduce the term 'evolution'. We conclude our paper by discussing implications for the biology education research community as well as instructors. [ABSTRACT FROM AUTHOR]

The study of evolutionary rates and patterns is the key to understand how natural selection shaped the current and past diversity of phenotypes. Phylogenetic comparative methods offer an array of solutions to undertake this challenging task, and help understanding phenotypic variation in full in most circumstances. However, complex, three-dimensional structures such as the skull and the brain serve disparate goals, and different portions of these phenotypes often fulfil different functions, making it hard to understand which parts truly were recruited by natural selection. In the recent past, we developed tools apt to chart evolutionary rate and patterns directly on three-dimensional shapes, according to their magnitude and direction. Here, we present further developments of these tools, which now allow to restitute the mapping of rates and patterns with full biological realism. The tools are condensed in a new R software package. Evolutionary rates embody the velocity of evolution. Parcellating different velocities across the phenotype is difficult. RRmorph resolves this conundrum by charting evolutionary patterns on 3D shapes, according to their magnitude and direction. [ABSTRACT FROM AUTHOR]

Summary: Increased temperature can induce plastic changes in many plant traits. However, little is known about how these changes affect plant interactions with insect pollinators and herbivores, and what the consequences for plant fitness and selection are.We grew fast‐cycling Brassica rapa plants at two temperatures (ambient and increased temperature) and phenotyped them (floral traits, scent, colour and glucosinolates). We then exposed plants to both pollinators (Bombus terrestris) and pollinating herbivores (Pieris rapae). We measured flower visitation, oviposition of P. rapae, herbivore development and seed output.Plants in the hot environment produced more but smaller flowers, with lower UV reflectance and emitted a different volatile blend with overall lower volatile emission. Moreover, these plants received fewer first‐choice visits by bumblebees and butterflies, and fewer flower visits by butterflies. Seed production was lower in hot environment plants, both because of a reduction in flower fertility due to temperature and because of the reduced visitation of pollinators. The selection on plant traits changed in strength and direction between temperatures.Our study highlights an important mechanism by which global warming can change plant–pollinator interactions and negatively impact plant fitness, as well as potentially alter plant evolution through changes in phenotypic selection. [ABSTRACT FROM AUTHOR]

Adaptive evolution can facilitate species' range expansions across environmentally heterogeneous landscapes. However, serial founder effects can limit the efficacy of selection, and the evolution of increased dispersal during range expansions may result in gene flow swamping local adaptation. Here, we study how genetic drift, gene flow and selection interact during the cane toad's (Rhinella marina) invasion across the heterogeneous landscape of Australia. Following its introduction in 1935, the cane toad colonised eastern Australia and established several stable range edges. The ongoing, more rapid range expansion in north‐central Australia has occurred concomitant with an evolved increase in dispersal capacity. Using reduced representation genomic data of Australian cane toads from the expansion front and from two areas of their established range, we test the hypothesis that high gene flow constrains local adaptation at the expansion front relative to established areas. Genetic analyses indicate the three study areas are genetically distinct but show similar levels of allelic richness, heterozygosity and inbreeding. Markedly higher gene flow or recency of colonisation at the expansion front have likely hindered local adaptation at the time of sampling, as indicated by reduced slopes of genetic‐environment associations (GEAs) estimated using a novel application of geographically weighted regression that accounts for allele surfing; GEA slopes are significantly steeper in established parts of the range. Our work bolsters evidence supporting adaptation of invasive species post‐introduction and adds novel evidence for differing strengths of evolutionary forces among geographic areas with different invasion histories. [ABSTRACT FROM AUTHOR]

Simple Summary: Positive natural selection increases the frequency of beneficial genetic variations, promoting an organism's adaptability and survival in specific environments. In this study, we conducted whole-genome resequencing and population genetic structure analysis to investigate the genetic diversity of Zaobei cattle, local yellow cattle from China. By comparing Zaobei cattle with Simmental cattle, we identified several genomic regions exhibiting positive selection. Gene annotation of these regions revealed key traits of Zaobei cattle, such as heat tolerance, fertility, and superior meat quality. These findings not only help understand the characteristics of Zaobei cattle but also provide valuable genetic information for future breeding programs, thereby improving their production efficiency and economic value. This investigation provides a comprehensive analysis of genomic diversity and selection signatures in Zaobei beef cattle, an indigenous breed known for its adaptation to hot and humid climates and superior meat quality. Whole-genome resequencing was conducted on 23 Zaobei cattle, compared with 46 Simmental cattle to highlight genetic distinctions. Population structure analysis confirmed the genetic uniqueness of Zaobei cattle. Using methods such as DASDC v1.01, XPEHH, and θπ ratio, we identified 230, 232, and 221 genes through DASDC, including hard sweeps, soft sweeps, and linkage sweeps, respectively. Coincidentally, 109 genes were identified when using XPEHH and θπ ratio methods. Together, these analyses revealed eight positive selection genes (ARHGAP15, ZNF618, USH2A, PDZRN4, SPATA6, ROR2, KCNIP3, and VWA3B), which are linked to critical traits such as heat stress adaptation, fertility, and meat quality. Moreover, functional enrichment analyses showed pathways related to autophagy, immune response, energy metabolism, and muscle development. The comprehensive genomic insights gained from this study provide valuable knowledge for breeding programs aimed at enhancing the beneficial traits in Zaobei cattle. [ABSTRACT FROM AUTHOR]

Simple Summary: Pig farming is one of the most profitable components of the livestock sector in agriculture, significantly contributing to economic development, food security, and improved livelihoods for local communities in Africa and globally. However, with the increasing concern for global environmental changes, pig production is considered one of the vulnerable livestock sectors likely to be affected the most. Africa, being a tropical continent with extraordinary geographical and biological diversity, is believed to have varieties of local pigs exhibiting valuable genetic traits that can be used to promote livestock productivity through breeding for climate-resilient breeds. Unfortunately, many of these valuable traits have not been fully identified and exploited. This study provides an overview of the current state of African pig genetic resources by highlighting their diversity and adaptability potential from both phenotypic and genetic evidence. Our results indicate that African local pigs hold potential genetic traits critical for climate change adaptation. However, these traits are threatened due to crossbreeding activities with commercial breeds that are now prevalent across the continent. Thus, to keep up with the rapid speed of climate change, efforts to realize and utilize these considerable potential traits must increase before they are permanently depleted. Africa is home to a wide diversity of locally adapted pig breeds whose genetic architecture offers important insights into livestock adaptation to climate change. However, the majority of these inherent traits have not been fully highlighted. This review presents an overview of the current state of African pig genetic resources, providing highlights on their population and production statistics, production system, population diversity indices, and genomic evidence underlying their evolutionary potential. The study results reveal an incomplete characterization of local pig genotypes across the continent. The characterized population, however, demonstrates moderate to high levels of genetic diversity, enough to support breeding and conservation programs. Owing to low genetic differentiation and limited evidence of distinct population structures, it appears that most local pig populations are strains within larger breeds. Genomic evidence has shown a higher number of selection signatures associated with various economically important traits, thus making them potential candidates for climate change adaptation. The reportedly early evidence of hybridization with wild suid groups further suggests untapped insights into disease resistance and resilience traits that need to be illuminated using higher-density markers. Nevertheless, gene introgression from commercial breeds is prevalent across Africa; thus, efforts to realize and utilize these traits must increase before they are permanently depleted. [ABSTRACT FROM AUTHOR]

Beginning with Luther's understanding of doubt using Genesis 3 as a template, the article explains how credulity differs from faith as the human mind interacts with shifting contexts and their doubts. In distinction from credulity, faith is an emergent phenomenon shaping personality and its social insertion. As faith mediates a compassionate orientation toward sufferers, it expresses the way in which the ultimate transcends into the penultimate or paramount reality dominated by the mechanisms of natural and social selection. [ABSTRACT FROM AUTHOR]

The "leafing intensity premium" hypothesis proposes that leaf size results from natural selection acting on different leafing intensities, i.e., the number of leaves per unit shoot volume or mass. The scaling relationships among various above-ground functional traits in the context of this hypothesis are important for understanding plant growth and ecology. Yet, they have not been sufficiently studied. In this study, we selected four bamboo species of the genus Indocalamus Nakai and measured the total leaf fresh mass per culm, total non-leaf above-ground fresh mass, total number of leaves per culm, and above-ground culm height of 90 culms from each species. These data were used to calculate leafing intensity (i.e., the total number of leaves per culm divided by the total non-leaf above-ground fresh mass) and mean leaf fresh mass per culm (i.e., the total leaf fresh mass per culm divided by the total number of leaves per culm). Reduced major axis regression protocols were then used to determine the scaling relationships among the various above-ground functional traits and leafing intensity. Among the four species, three exhibited an isometric (one-to-one) relationship between the total leaf fresh mass per culm and the total non-leaf above-ground fresh mass, whereas one species (Indocalamus pumilus) exhibited an allometric (not one-to-one) relationship. A negative isometric relationship was found between the mean leaf fresh mass per culm and the leafing intensity for one species (Indocalamus pedalis), whereas three negative allometric relationships between mean leaf fresh mass per culm and leafing intensity were observed for the other three species and the pooled data. An exploration of the alternative definitions of "leafing intensity" showed that the total number of leaves per culm divided by the above-ground culm height is superior because it facilitates the non-destructive calculation of leafing intensity for Indocalamus species. These results not only confirm the leafing intensity premium hypothesis for bamboo species but also highlight the interconnected scaling relationships among different functional traits, thereby contributing to our understanding of the ecological and evolutionary significance of leaf size variation and biomass investment strategies. [ABSTRACT FROM AUTHOR]

Silybum marianum (L.) Gaertn. is a multipurpose crop native to the Mediterranean and middle east regions and mainly known for the hepatoprotective properties of fruit-derived silymarin. Despite growing interest in milk thistle as a versatile crop with medicinal value, its potential in agroindustry is hindered by incomplete domestication and limited genomic knowledge, impeding the development of competitive breeding programs. The present study aimed to evaluate genetic diversity in a panel of S. marianum accessions (n = 31), previously characterized for morphological and phytochemical traits, using 5,178 polymorphic DArTseq SNP markers. The genetic structure investigated using both parametric and non-parametric approaches (e.g. PCA, AWclust, Admixture), revealed three distinctive groups reflecting geographical origins. Indeed, Pop1 grouped accessions from Central Europe and UK, Pop3 consisted mainly of accessions of Italian origin, and Pop2 included accessions from different geographical areas. Interestingly, Italian genotypes showed a divergent phenotypic distribution, particularly in fruit oleic and linoleic acid content, compared to the other two groups. Genetic differentiation among the three groups, investigated by computing pairwise fixation index (FST), confirmed a greater differentiation of Pop3 compared to other subpopulations, also based on other diversity indices (e.g. private alleles, heterozygosity). Finally, 22 markers were declared as putatively under natural selection, of which seven significantly affected some important phenotypic traits such as oleic, arachidonic, behenic and linoleic acid content. These findings suggest that these markers, and overall, the seven SNP markers identified within Pop3, could be exploited in specific breeding programs, potentially aimed at diversifying the use of milk thistle. Indeed, incorporating genetic material from Pop3 haplotypes carrying the selected loci into milk thistle breeding populations might be the basis for developing milk thistle lines with higher levels of oleic, arachidonic, and behenic acids, and lower levels of linoleic acid, paving new avenues for enhancing the nutritional and agronomic characteristics of milk thistle. [ABSTRACT FROM AUTHOR]

Phytophthora infestans is a major oomycete plant pathogen, responsible for potato late blight, which led to the Irish Potato Famine from 1845–1852. Since then, potatoes resistant to this disease have been bred and deployed worldwide. Their resistance (R) genes recognize pathogen effectors responsible for virulence and then induce a plant response stopping disease progression. However, most deployed R genes are quickly overcome by the pathogen. We use targeted sequencing of effector and R genes on herbarium specimens to examine the joint evolution in both P. infestans and potato from 1845–1954. Currently relevant effectors are historically present in P. infestans, but with alternative alleles compared to modern reference genomes. The historic FAM-1 lineage has the virulent Avr1 allele and the ability to break the R1 resistance gene before breeders deployed it in potato. The FAM-1 lineage is diploid, but later, triploid US-1 lineages appear. We show that pathogen virulence genes and host resistance genes have undergone significant changes since the Famine, from both natural and artificial selection. The joint evolution in Phytophthora infestans and potato over a one hundred period since the Famine is examined based on targeting sequencing of pathogen effector genes and host resistance genes from historic outbreak samples present in plant herbaria. [ABSTRACT FROM AUTHOR]

In many animal species, larger body size is positively correlated with male mating success and female fecundity. However, in the case of insects, in high seasonality environments, natural selection favors a faster maturation that decreases the risk of pre‐reproductive death. However, this advantageous adaptation comes at a tradeoff, resulting in a reduction in body size. Maturation time is influenced by environmental factors, such as temperature, season length, and food availability during the rains. The geographic variation in these parameters provides an opportunity to study their impact on the adaptive evolution of body size in Pyrgomorphidae grasshoppers. These grasshoppers exhibit remarkable variation in body size and wing development and can be found in diverse plant communities across Africa, Asia, Australia, and tropical America. In this study, we utilized a phylogenetic approach to examine the evolution of body size, considering climatic factors, and the influence of sexual selection on size differences between males and females. We found a positive correlation between mean annual temperature and sexual size dimorphism (SSD). Remarkably, species exhibiting a strong bias toward larger females were found to be adapted to regions with higher temperatures. In the Pyrgomorphidae family, an intermediate body size was identified as the ancestral trait. Additionally, winged male and female grasshoppers were observed to be larger than their wingless counterparts. Despite the potential conflicting pressures on body size in males and females, these grasshoppers adhere to Rench's Rule, suggesting that sexual selection on males' body size may explain the evolution of SSD. [ABSTRACT FROM AUTHOR]

Genetic drift, gene flow, and natural selection commonly influence population genetic diversity. In populations of self‐compatible hermaphrodites, the mating system (e.g., self‐fertilization) further reduces individual heterozygosity. Furthermore, selfing, as a form of inbreeding, significantly impacts genetic drift by reducing effective population size (Ne). This can potentially accelerate genetic drift, particularly in small populations where self‐fertilization is likely during founder events. To investigate the roles of genetic drift and contemporary mating system in populations of the freshwater snail Lymnaea stagnalis, we examined their effective population sizes (Ne) and Tajima's D values, which reflect genetic drift over extended time periods, as well as estimates of within‐population selfing rates and pairwise relatedness reflecting contemporary mating system. We used 4054 SNP markers obtained using restriction site associated DNA (RAD) sequencing from individuals in five snail populations originating from geographically closely located ponds. We found strong population genetic structure and differences in genetic diversity among populations. Covariation between genetic diversity and Ne estimates and Tajima's D values suggested drift being an important determinant of genetic diversity and structure in these populations. However, this effect was independent of the contemporary mating system, as indicated by the similarity of selfing rates and relatedness estimates among populations. Thus, founder events (possibly including historical inbreeding) and/or drift due to small sizes of L. stagnalis populations are likely to explain their genetic structure and limit within‐population genetic diversity. [ABSTRACT FROM AUTHOR]

The evolutionary patterns of the mitochondrial genome are influenced by both adaptive and nonadaptive forces, with their contributions varying among taxa. There appears to be a correlation linking mutagenesis and latitude, which could be due to differences in metabolic rates. These discrepancies in metabolic rates exhibit a positive connection with mutation pressure. On this basis, we hypothesise that nonadaptive forces play a role in the differences in mutation rates observed along latitudinal gradients. In this study, we selected widely distributed carnivores as representatives of mammals to test our hypothesis. We examined the correlations between the dN/dS ratio (ω), as well as the substitution rates (dS and dN), of 13 PCGs in the mtDNA of 122 carnivores, and the latitude and climatic factors. We found that taxa distributed in higher latitudes tend to have higher substitution rates, but not ω values indicating selective pressure. Notably, dN shows a strong positive correlation with dS, although dS is primarily influenced by mutation pressure, while dN is also influenced by effective population size (Ne). Phylogenetic generalised least squares (PGLS) regression analyses showed that both substitution rates were correlated with climatic factors representing the temperature, precipitation and variability of climate. Based on our findings, we propose that the mutations are primarily influenced by nonadaptive forces (mutation pressure). This forms the fundamental premise for natural selection and speciation. Moreover, the correlation between substitution rates and latitudinal distribution and climate, which are outcomes of nonadaptive factors, can aid in comprehending the global distribution of species diversity. [ABSTRACT FROM AUTHOR]

Adenosine-to-inosine (A-to-I) RNA editing recodes the genetic information. Apart from diversifying the proteome, another tempting advantage of RNA recoding is to correct deleterious DNA mutation and restore ancestral allele. Solid evidences for beneficial restorative editing are very rare in animals. By searching for "convergent recoding" under a phylogenetic context, we proposed this term for judging the potential restorative functions of particular editing site. For the well-known mammalian Gln>Arg (Q>R) recoding site, its ancestral state in vertebrate genomes was the pre-editing Gln, and all 470 available mammalian genomes strictly avoid other three equivalent ways to achieve Arg in protein. The absence of convergent recoding from His>Arg, or synonymous mutations on Gln codons, could be attributed to the strong maintenance on editing motif and structure, but the absence of direct A-to-G mutation is extremely unexpected. With similar ideas, we found cases of convergent recoding in Drosophila genus, reducing the possibility of their restorative function. In summary, we defined an interesting scenario of convergent recoding, the occurrence of which could be used as preliminary judgements for whether a recoding site has a sole restorative role. Our work provides novel insights to the natural selection and evolution of RNA editing. [ABSTRACT FROM AUTHOR]

Genome size variation in eukaryotes has myriad effects on organismal biology from the genomic to whole-organism level. Large genome size may be associated with lower selection efficiency because lower effective population sizes allow fixation of deleterious mutations via genetic drift, increasing genome size and decreasing selection efficiency. Because of a hypothesized negative relationship between genome size and recombination rate per base pair, increased genome size could also increase the effect of linked selection in the genome, decreasing the efficiency with which natural selection can fix or remove mutations. We used a transcriptomic dataset of 15 and a subset of six Neotropical salamander species ranging in genome size from 12 to 87 pg to study the relationship between genome size and efficiency of selection. We estimated dN/dS of salamanders with small and large genomes and tested for relaxation of selection in the larger genomes. Contrary to our expectations, we did not find a significant relationship between genome size and selection efficiency or strong evidence for higher dN/dS values in species with larger genomes for either species set. We also found little evidence for relaxation of selection in species with larger genomes. A positive correlation between genome size and range size (a proxy of population size) in this group disagrees with predictions of stronger drift in species with larger genomes. Our results highlight the complex interactions between the many forces shaping genomic variation in organisms with genomic gigantism. [ABSTRACT FROM AUTHOR]

The functions of bright bands in coral and other snakes have long been a puzzle. The most common opinion is that coral snakes display aposematic marks and that other red and black banded snakes in the Americas are mimics of coral snakes. I previously found that this prevailing opinion is weakly supported and unlikely, that red and bands had probably evolved independently or conjointly many times, and that a present selection for bands and red seems to exist in a significant fraction of the world. Here, I review the potential selective forces for red and bands in snakes. I find that snakes as predators are a priori plausible selective agents. I find that ophiophagy appears to be an exceptionally high risk in snakes that are themselves ophiophagous. Testing the working hypothesis that bands and red are protective against snake predators via their association with ophiophagy, as ophiophagous snakes are at higher risk, I find that the consumption of elongate vertebrates predicts band and red coloration with a very high level of confidence: red and bands are probably defensive against snake predators. Noting an apparent correlation of coloration with specific defensive behaviours and ontogenetic colour changes, I review both and find that ophiophagous snakes are remarkable for using stereotypical defences and not being aggressive, while ontogenetic colour changes seem to affect red and bands in snakes disproportionately. Defence against ophidian predators may be an unexpected natural selection shaping the appearance and behaviours of many snakes. [ABSTRACT FROM AUTHOR]

Summary: Understanding how widespread species adapt to variation in abiotic conditions across their ranges is fundamental to ecology. Insight may come from studying how among‐population variation (APV) in the common garden corresponds with the environmental conditions of source populations. However, there are no such studies comparing native vs non‐native populations across multiple life stages.We examined APV in the performance and functional traits of 59 Conyza canadensis populations, in response to drought, across large aridity gradients in the native (North America) and non‐native (Eurasia) ranges in three experiments. Our treatment (dry vs wet) was applied at the recruitment, juvenile, and adult life stages.We found contrasting patterns of APV in drought responses between the two ranges. In the native range, plant performance was less reduced by drought in populations from xeric than mesic habitats, but such relationship was not apparent for non‐native populations. These range‐specific patterns were consistent across the life stages.The weak adaptive responses of non‐native populations indicate that they can become highly abundant even without complete local adaptation to abiotic environments and suggest that long‐established invaders may still be evolving to the abiotic environment. These findings may explain lag times in invasions and raise concern about future expansions. [ABSTRACT FROM AUTHOR]

• We study the two-player repeated game where players can choose to be spite or not. • We investigate the case where players lack knowledge of their opponent's actions. • Evolution of spite is likely to occur when players exhibit persistence. Social behavior is divided into four types: altruism, spite, mutualism, and selfishness. The former two are costly to the actor; therefore, from the perspective of natural selection, their existence can be regarded as mysterious. One potential setup which encourages the evolution of altruism and spite is repeated interaction. Players can behave conditionally based on their opponent's previous actions in the repeated interaction. On the one hand, the retaliatory strategy (who behaves altruistically when their opponent behaved altruistically and behaves non-altruistically when the opponent player behaved non-altruistically) is likely to evolve when players choose altruistic or selfish behavior in each round. On the other hand, the anti-retaliatory strategy (who is spiteful when the opponent was not spiteful and is not spiteful when the opponent player was spiteful) is likely to evolve when players opt for spiteful or mutualistic behavior in each round. These successful conditional behaviors can be favored by natural selection. Here, we notice that information on opponent players' actions is not always available. When there is no such information, players cannot determine their behavior according to their opponent's action. By investigating the case of altruism, a previous study (Kurokawa, 2017, Mathematical Biosciences, 286, 94–103) found that persistent altruistic strategies, which choose the same action as the own previous action, are favored by natural selection. How, then, should a spiteful conditional strategy behave when the player does not know what their opponent did? By studying the repeated game, we find that persistent spiteful strategies, which choose the same action as the own previous action, are favored by natural selection. Altruism and spite differ concerning whether retaliatory or anti-retaliatory strategies are favored by natural selection; however, they are identical concerning whether persistent strategies are favored by natural selection. [ABSTRACT FROM AUTHOR]

This article focuses on responses to Darwinism among German scientists and theologians in the late nineteenth and early twentieth centuries. The Christian thinkers foregrounded in this study all commented at length on Darwinism and critically examined theories of natural selection. In doing so, they did not resort to what we now label "fundamentalist tropes," or, as I call them, "anti-modernist tropes." Rather, they were willing to accept empirical evidence and thought in broad religious and philosophical terms about evolution's mechanisms. The arguments that these scholars offered against materialists' employment of Darwin's ideas fit within the broader "revolt against positivism." [ABSTRACT FROM AUTHOR]