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Music is a deeply entrenched human phenomenon. In this article, I argue that its evolutionary origins are intrinsically intertwined with the incremental anatomical, cognitive, social, and technological evolution of the hominin lineage. I propose an account of the evolution of Plio-Pleistocene hominins, focusing on traits that would be later implicated in music making. Such traits can be conceived as comprising the musicality mosaic or the multifaceted foundations of musicality. I then articulate and defend an account of protomusical behaviour, drawing theoretical licence from the social brain framework of Robin Dunbar and colleagues, as well as the evolutionary framework for human culture and cooperation developed by Kim Sterelny. The role of gene-culture co-evolution and niche construction is brought to the fore in articulating the evolutionary account. Finally, I defend the view that music subsequently developed via processes of social learning and cumulative culture. [ABSTRACT FROM AUTHOR]

As interfaces between human beings and the digital world, mobile phones have evolved from relatively simple devices (e.g. feature phones) to complex products (e.g. smartphones). Many firms in emerging countries such as China have successfully entered the mobile phone sector. A research question that emerges from the evidence on China is whether the entry strategies of these catching up firms have been affected by the introduction of smartphones. In order to investigate this question, the article follows the methodology of evolutionary theory and history-friendly models. It first examines historically the various strategies of the Chinese entrants in the mobile phone sector. On the basis of this empirical analysis, it then develops appreciative theorizing on the factors that have affected the catch-up entry strategies. Our results show that the successful catch-up entry strategies differ depending on the sectoral environment. A technology-driven strategy is more appropriate when there is a market sheltered from competition, so that technological capabilities can be accumulated; on the contrary a marketing-driven strategy is more appropriate when standardized technological solutions become widely available. The article contributes to the catch-up literature by identifying a new entry strategy and by pointing at the role of the sectoral environment, and to the sectoral innovation system literature by addressing the catch-up strategies of latecomer firms under different technological, industrial structure, and market conditions. [ABSTRACT FROM AUTHOR]

Firm growth is an essential feature of market economies, shaping together macroeconomic performance and the evolution of industry structures. As a potential indicator of organizational "fitness" within a competitive environment, firm growth is also a central concern to both the practice and theory of business strategy. Despite both its theoretical and practical importance, though, growth remains a poorly understood property of firms. While previous studies have documented the fat-tailed nature of firm growth rates, we know far less about the patterns of growth rates over long periods of time. For instance, do "fast growers" tend to maintain their relative growth rates advantages over long periods or is superior growth a transitory phenomenon? Is, as predicted by evolutionary and capability-based theories of the firm, the process of firm growth path-dependent or is it more akin to a random walk? The answers to these questions are central to building a robust theory of firm growth. This article attempts to address this gap in our empirical knowledge of firm growth using a dataset that spans 50 years, which allows the abandonment of the assumption, common to all incumbent studies, that the stochastic paths of all firms stem from the same generating process. These exploratory results indicate that growth rate persistence is there and may be even substantial for some firms, but it is rare. We also study the links between the micro-properties of firm growth within sectors and the patterns of aggregate growth of these same sectors. Indeed, we find circumstantial but widespread evidence that heterogeneity across firms correlates with industry dynamism. [ABSTRACT FROM AUTHOR]

I argue that our general disposition to make moral judgments and our core moral intuitions are likely the product of social selection—a kind of gene–culture coevolution driven by the enforcement of collectively agreed-upon rules. Social selection could potentially track mind-independent moral truth by a process that I term realist social selection: our ancestors could have acquired moral knowledge via reason and enforced rules based on that knowledge, thereby creating selection pressures that drove the evolution of our moral psychology. Given anthropological evidence that early humans designed rules with the conscious aim of preserving individual autonomy and advancing their collective interests, the theory of realist social selection appears to be attractive for moral realists. The goal of evolutionary debunking arguments should be to show not that our moral beliefs are the product of natural selection, but that realist social selection did not occur. [ABSTRACT FROM AUTHOR]

The determining roles played by communication in the ongoing evolution of our species remain largely unexplored in communications-related disciplines. An unhelpful controversy that raged over E. O. Wilson's sociobiology last century contributed to the problem and is reconsidered here in terms of the fault lines that run between natural science, social science, and politics. The article describes paths for future theoretical development by focusing first on the link between human communications behavior and evolutionary psychology. With an emphasis on understanding the crisis of community facing the world today, evolutionary communication is proposed as a theoretical alternative to limited proximate perspectives afforded by cultural analysis alone. The inherent interdisciplinary nature of communication makes the field a prime candidate for conducting research grounded in the deep-time explanatory framework of evolutionary theory and the epistemological assumptions of scientific humanism. [ABSTRACT FROM AUTHOR]

In the book "Religion Evolving: Cultural, Cognitive, and Ecological Dynamics" by Benjamin Grant Purzycki and Richard Sosis, the authors present a comprehensive and holistic approach to understanding the evolution of religion. They argue that religious systems are complex adaptive systems, meaning that they are irreducible and linked to fitness challenges in their environment. The authors address concerns about the relevance of evolution in understanding human culture and provide empirical evidence to support the integration of evolutionary theory into the study of religious beliefs and behaviors. They also explore the relationship between supernatural beliefs and rituals, highlighting the ways in which they are interconnected and influenced by socioecological contexts. The book concludes with a theoretical framework for understanding religions as complex adaptive systems, emphasizing the need for further collaborative research in this field. Overall, this book provides a solid foundation for future studies on the evolution of religion. [Extracted from the article]

Evolutionary theories of economic change identify the processes of idiosyncratic learning by individual firms and of market selection as the two main drivers of the dynamics of industries. Are such processes able to account for the statistical regularities which industrial structures and dynamics display? In this work we address this question by means of a simple multi-firm model formalizing the mechanisms of learning and selection. As such, despite its simplicity, the model is able to robustly reproduce an ensemble of empirical stylized facts, including ample heterogeneity in productivity distributions, persistent market turbulence, and fat-tailed distribution of growth rates. [ABSTRACT FROM AUTHOR]

In evolutionary genomics, it is fundamentally important to understand how characteristics of genomic sequences, such as gene expression level, determine the rate of adaptive evolution. While numerous statistical methods, such as the McDonald–Kreitman (MK) test, are available to examine the association between genomic features and the rate of adaptation, we currently lack a statistical approach to disentangle the independent effect of a genomic feature from the effects of other correlated genomic features. To address this problem, I present a novel statistical model, the MK regression, which augments the MK test with a generalized linear model. Analogous to the classical multiple regression model, the MK regression can analyze multiple genomic features simultaneously to infer the independent effect of a genomic feature, holding constant all other genomic features. Using the MK regression, I identify numerous genomic features driving positive selection in chimpanzees. These features include well-known ones, such as local mutation rate, residue exposure level, tissue specificity, and immune genes, as well as new features not previously reported, such as gene expression level and metabolic genes. In particular, I show that highly expressed genes may have a higher adaptation rate than their weakly expressed counterparts, even though a higher expression level may impose stronger negative selection. Also, I show that metabolic genes may have a higher adaptation rate than their nonmetabolic counterparts, possibly due to recent changes in diet in primate evolution. Overall, the MK regression is a powerful approach to elucidate the genomic basis of adaptation. [ABSTRACT FROM AUTHOR]

Morphospaces—representations of phenotypic characteristics—are often populated unevenly, leaving large parts unoccupied. Such patterns are typically ascribed to contingency, or else to natural selection disfavoring certain parts of the morphospace. The extent to which developmental bias, the tendency of certain phenotypes to preferentially appear as potential variation, also explains these patterns is hotly debated. Here we demonstrate quantitatively that developmental bias is the primary explanation for the occupation of the morphospace of RNA secondary structure (SS) shapes. Upon random mutations, some RNA SS shapes (the frequent ones) are much more likely to appear than others. By using the RNAshapes method to define coarse-grained SS classes, we can directly compare the frequencies that noncoding RNA SS shapes appear in the RNAcentral database to frequencies obtained upon a random sampling of sequences. We show that: 1) only the most frequent structures appear in nature; the vast majority of possible structures in the morphospace have not yet been explored; 2) remarkably small numbers of random sequences are needed to produce all the RNA SS shapes found in nature so far; and 3) perhaps most surprisingly, the natural frequencies are accurately predicted, over several orders of magnitude in variation, by the likelihood that structures appear upon a uniform random sampling of sequences. The ultimate cause of these patterns is not natural selection, but rather a strong phenotype bias in the RNA genotype–phenotype map, a type of developmental bias or "findability constraint," which limits evolutionary dynamics to a hugely reduced subset of structures that are easy to "find." [ABSTRACT FROM AUTHOR]

Influenza A viruses (IAVs) are constantly evolving. Crucial steps in the infection cycle, such as sialic acid (SA) receptor binding on the host cell surface, can either promote or hamper the emergence of new variants. We previously assessed the relative fitness in Japanese quail of H9N2 variant viruses differing at a single amino acid position, residue 216 in the hemagglutinin (HA) viral surface protein. This site is known to modulate SA recognition. Our prior study generated a valuable set of longitudinal samples from quail transmission groups where the inoculum comprised different mixed populations of HA 216 variant viruses. Here, we leveraged these samples to examine the evolutionary dynamics of viral populations within and between inoculated and naïve contact quails. We found that positive selection dominated HA gene evolution, but fixation of the fittest variant depended on the competition mixture. Analysis of the whole genome revealed further evidence of positive selection acting both within and between hosts. Positive selection drove fixation of variants in non-HA segments within inoculated and contact quails. Importantly, transmission bottlenecks were modulated by the molecular signature at HA 216, revealing viral receptor usage as a determinant of transmitted diversity. Overall, we show that selection strongly shaped the evolutionary dynamics within and between quails. These findings support the notion that selective processes act effectively on IAV populations in poultry hosts, facilitating rapid viral evolution in this ecological niche. [ABSTRACT FROM AUTHOR]

Viroids are tiny, circular, and noncoding RNAs that are able to replicate and systemically infect plants. The smallest known pathogens, viroids have been proposed to represent survivors from the RNA world that likely preceded the cellular world currently dominating life on the earth. Although the small, circular, and compact nature of viroid genomes, some of which are also endowed with catalytic activity mediated by hammerhead ribozymes, support this proposal, the lack of feasible evolutionary routes and the identification of hammerhead ribozymes in a large number of DNA genomes of organisms along the tree of life have led some to question such a proposal. Here, we reassess the origin and subsequent evolution of viroids by complementing phylogenetic reconstructions with molecular data, including the primary and higher-order structure of the genomic RNAs, their replication, and recombination mechanisms and selected biological information. Features of some viroid-like RNAs found in plants, animals, and possibly fungi are also considered. The resulting evolutionary scenario supports the emergence of protoviroids in the RNA world, mainly as replicative modules, followed by a further increase in genome complexity based on module/domain shuffling and combination and mutation. Such a modular evolutionary scenario would have facilitated the inclusion in the protoviroid genomes of complex RNA structures (or coding sequences, as in the case of hepatitis delta virus and delta-like agents), likely needed for their adaptation from the RNA world to a life based on cells, thus generating the ancestors of current infectious viroids and viroid-like RNAs. Other noninfectious viroid-like RNAs, such as retroviroid-like RNA elements and retrozymes, could also be derived from protoviroids if their reverse transcription and integration into viral or eukaryotic DNA, respectively, are considered as a possible key step in their evolution. Comparison of evidence supporting a general and modular evolutionary model for viroids and viroid-like RNAs with that favoring alternative scenarios provides reasonable reasons to keep alive the hypothesis that these small RNA pathogens may be relics of a precellular world. [ABSTRACT FROM AUTHOR]

Gravitational coupling between protoplanetary discs and planets embedded in them leads to the emergence of spiral density waves, which evolve into shocks as they propagate through the disc. We explore the performance of a semi-analytical framework for describing the non-linear evolution of the global planet-driven density waves, focusing on the low planet mass regime (below the so-called thermal mass). We show that this framework accurately captures the (quasi-)self-similar evolution of the wave properties expressed in terms of properly rescaled variables, provided that certain theoretical inputs are calibrated using numerical simulations (an approximate, first principles calculation of the wave evolution based on the inviscid Burgers equation is in qualitative agreement with simulations but overpredicts wave damping at the quantitative level). We provide fitting formulae for such inputs, in particular, the strength and global shape of the planet-driven shock accounting for non-linear effects. We use this non-linear framework to theoretically compute vortensity production in the disc by the global spiral shock and numerically verify the accuracy of this calculation. Our results can be used for interpreting observations of spiral features in discs, kinematic signatures of embedded planets in CO line emission ('kinks'), and for understanding the emergence of planet-driven vortices in protoplanetary discs. [ABSTRACT FROM AUTHOR]

China's approach to International Development Cooperation (IDC) has been one of continuous evolution. The 2000s version of Chinese IDC applied a request-/project-centrism methodology, focused on the infrastructure sector, and mixed aid with business. Since the launch of the Belt and Road Initiative (BRI), the methodological dimension of the existing IDC model has changed by virtue of a growing emphasis on top-level design, sectoral programmes, and high standards for project implementation. How to explain these changes? Different from the conventional material-functionalist approaches, this article attributes the development of China's IDC to cognitive evolution—an intra-community collective learning mechanism that drives changes in norms and practices. Cognitive evolution consists of the following three interconnected processes: uncertainty build-up; experimentation; and selection. Three factors that may shape the trajectories of cognitive evolution are as follows: the legacy of orthodox norms; the availability of transferable local ideas; and the communal interpretation of candidate ideas' performance. The IDC model of the 2000s was constructed based on critical reflections on the internationalist foreign aid model of the Mao era and on the IDC policy community's interpretation and transplantation of China's development experience. The methodology of this IDC model—request-/project-centrism—has come under new pressure for change due to the BRI's ambition to engender more substantial and sustainable developmental impact. [ABSTRACT FROM AUTHOR]

Four coronaviruses (HCoV-OC43, HCoV-HKU1, HCoV-NL63, and HCoV-229E) are endemic in human populations. All these viruses are seasonal and generate short-term immunity. Like the highly pathogenic coronaviruses, the endemic coronaviruses have zoonotic origins. Thus, understanding the evolutionary dynamics of these human viruses might provide insight into the future trajectories of SARS-CoV-2 evolution. Because the zoonotic sources of HCoV-OC43 and HCoV-229E are known, we applied a population genetics–phylogenetic approach to investigate which selective events accompanied the divergence of these viruses from the animal ones. Results indicated that positive selection drove the evolution of some accessory proteins, as well as of the membrane proteins. However, the spike proteins of both viruses and the hemagglutinin-esterase (HE) of HCoV-OC43 represented the major selection targets. Specifically, for both viruses, most positively selected sites map to the receptor-binding domains (RBDs) and are polymorphic. Molecular dating for the HCoV-229E spike protein indicated that RBD Classes I, II, III, and IV emerged 3–9 years apart. However, since the appearance of Class V (with much higher binding affinity), around 25 years ago, limited genetic diversity accumulated in the RBD. These different time intervals are not fully consistent with the hypothesis that HCoV-229E spike evolution was driven by antigenic drift. An alternative, not mutually exclusive possibility is that strains with higher affinity for the cellular receptor have out-competed strains with lower affinity. The evolution of the HCoV-OC43 spike protein was also suggested to undergo antigenic drift. However, we also found abundant signals of positive selection in HE. Whereas such signals might result from antigenic drift, as well, previous data showing co-evolution of the spike protein with HE suggest that optimization for human cell infection also drove the evolution of this virus. These data provide insight into the possible trajectories of SARS-CoV-2 evolution, especially in case the virus should become endemic. [ABSTRACT FROM AUTHOR]

Emergence of resistant bacteria during antimicrobial treatment is one of the most critical and universal health threats. It is known that several stress-induced mutagenesis and heteroresistance mechanisms can enhance microbial adaptation to antibiotics. Here, we demonstrate that the pathogen Bartonella can undergo stress-induced mutagenesis despite the fact it lacks error-prone polymerases, the rpoS gene and functional UV-induced mutagenesis. We demonstrate that Bartonella acquire de novo single mutations during rifampicin exposure at suprainhibitory concentrations at a much higher rate than expected from spontaneous fluctuations. This is while exhibiting a minimal heteroresistance capacity. The emerged resistant mutants acquired a single rpoB mutation, whereas no other mutations were found in their whole genome. Interestingly, the emergence of resistance in Bartonella occurred only during gradual exposure to the antibiotic, indicating that Bartonella sense and react to the changing environment. Using a mathematical model, we demonstrated that, to reproduce the experimental results, mutation rates should be transiently increased over 1,000-folds, and a larger population size or greater heteroresistance capacity is required. RNA expression analysis suggests that the increased mutation rate is due to downregulation of key DNA repair genes (mutS , mutY , and recA), associated with DNA breaks caused by massive prophage inductions. These results provide new evidence of the hazard of antibiotic overuse in medicine and agriculture. [ABSTRACT FROM AUTHOR]

The date palm, Phoenix dactylifera , has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti , currently restricted to Crete and Turkey, and P. sylvestris , widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti , and P. sylvestris , indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera / P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera , and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding. [ABSTRACT FROM AUTHOR]

Previous evolutionary reconstructions have concluded that early eukaryotic ancestors including both the last common ancestor of eukaryotes and of all fungi had intron-rich genomes. By contrast, some extant eukaryotes have few introns, underscoring the complex histories of intron–exon structures, and raising the question as to why these few introns are retained. Here, we have used recently available fungal genomes to address a variety of questions related to intron evolution. Evolutionary reconstruction of intron presence and absence using 263 diverse fungal species supports the idea that massive intron reduction through intron loss has occurred in multiple clades. The intron densities estimated in various fungal ancestors differ from zero to 7.6 introns per 1 kb of protein-coding sequence. Massive intron loss has occurred not only in microsporidian parasites and saccharomycetous yeasts, but also in diverse smuts and allies. To investigate the roles of the remaining introns in highly-reduced species, we have searched for their special characteristics in eight intron-poor fungi. Notably, the introns of ribosome-associated genes RPL7 and NOG2 have conserved positions; both intron-containing genes encoding snoRNAs. Furthermore, both the proteins and snoRNAs are involved in ribosome biogenesis, suggesting that the expression of the protein-coding genes and noncoding snoRNAs may be functionally coordinated. Indeed, these introns are also conserved in three-quarters of fungi species. Our study shows that fungal introns have a complex evolutionary history and underappreciated roles in gene expression. [ABSTRACT FROM AUTHOR]

The number of olfactory receptor genes (ORs), which are responsible for detecting diverse odor molecules varies extensively among mammals as a result of frequent gene gains and losses that contribute to olfactory specialization. However, how OR expansions/contractions in fish are influenced by habitat and feeding habit and which OR subfamilies are important in each ecological niche is unknown. Here, we report a major OR expansion in a freshwater herbivorous fish, Megalobrama amblycephala , using a highly contiguous, chromosome-level assembly. We evaluate the possible contribution of OR expansion to habitat and feeding specialization by comparing the OR repertoire in 28 phylogenetically and ecologically diverse teleosts. In total, we analyzed > 4,000 ORs including 3,253 intact, 122 truncated, and 913 pseudogenes. The number of intact ORs is highly variable ranging from 20 to 279. We estimate that the most recent common ancestor of Osteichthyes had 62 intact ORs , which declined in most lineages except the freshwater Otophysa clade that has a substantial expansion in subfamily β and ε ORs. Across teleosts, we found a strong association between duplications of β and ε ORs and freshwater habitat. Nearly, all ORs were expressed in the olfactory epithelium (OE) in three tested fish species. Specifically, all the expanded β and ε ORs were highly expressed in OE of M. amblycephala. Together, we provide molecular and functional evidence for how OR repertoires in fish have undergone gain and loss with respect to ecological factors and highlight the role of β and ε OR in freshwater adaptation. [ABSTRACT FROM AUTHOR]

Horizontal gene transfer (HGT) is a major driving force for bacterial evolution. To avoid the deleterious effects due to the unregulated expression of newly acquired foreign genes, bacteria have evolved specific proteins named xenogeneic silencers to recognize foreign DNA sequences and suppress their transcription. As there is considerable diversity in genomic base compositions among bacteria, how xenogeneic silencers distinguish self- from nonself DNA in different bacteria remains poorly understood. This review summarizes the progress in studying the DNA binding preferences and the underlying molecular mechanisms of known xenogeneic silencer families, represented by H-NS of Escherichia coli , Lsr2 of Mycobacterium , MvaT of Pseudomonas , and Rok of Bacillus. Comparative analyses of the published data indicate that the differences in DNA recognition mechanisms enable these xenogeneic silencers to have clear characteristics in DNA sequence preferences, which are further correlated with different host genomic features. These correlations provide insights into the mechanisms of how these xenogeneic silencers selectively target foreign DNA in different genomic backgrounds. Furthermore, it is revealed that the genomic AT contents of bacterial species with the same xenogeneic silencer family proteins are distributed in a limited range and are generally lower than those species without any known xenogeneic silencers in the same phylum/class/genus, indicating that xenogeneic silencers have multifaceted roles on bacterial genome evolution. In addition to regulating horizontal gene transfer, xenogeneic silencers also act as a selective force against the GC to AT mutational bias found in bacterial genomes and help the host genomic AT contents maintained at relatively low levels. [ABSTRACT FROM AUTHOR]

Aims 3′ untranslated region (3′ UTR) of mRNA is more conserved than other non-coding sequences in vertebrate genomes, and its sequence space has substantially expanded during the evolution of higher organisms, which substantiates their significance in biological regulation. However, the independent role of 3′ UTR in cardiovascular disease was largely unknown. Methods and results Using bioinformatics, RNA fluorescent in situ hybridization and quantitative real-time polymerase chain reaction, we found that 3′ UTR and coding sequence regions of Ckip-1 mRNA exhibited diverse expression and localization in cardiomyocytes. We generated cardiac-specific Ckip-1 3′ UTR overexpression mice under wild type and casein kinase 2 interacting protein-1 (CKIP-1) knockout background. Cardiac remodelling was assessed by histological, echocardiography, and molecular analyses at 4 weeks after transverse aortic constriction (TAC) surgery. The results showed that cardiac Ckip-1 3′ UTR significantly inhibited TAC-induced cardiac hypertrophy independent of CKIP-1 protein. To determine the mechanism of Ckip-1 3′ UTR in cardiac hypertrophy, we performed transcriptome and metabolomics analyses, RNA immunoprecipitation, biotin-based RNA pull-down, and reporter gene assays. We found that Ckip-1 3′ UTR promoted fatty acid metabolism through AMPK–PPARα–CPT1b axis, leading to its protection against pathological cardiac hypertrophy. Moreover, Ckip-1 3′ UTR RNA therapy using adeno-associated virus obviously alleviates cardiac hypertrophy and improves heart function. Conclusions These findings disclose that Ckip-1 3′ UTR inhibits cardiac hypertrophy independently of its cognate protein. Ckip-1 3′ UTR is an effective RNA-based therapy tool for treating cardiac hypertrophy and heart failure. [ABSTRACT FROM AUTHOR]

OCBIL theory provides a basis for understanding of the evolution and ecology of biota on old, climatically buffered, infertile landscapes (OCBILs) worldwide. Here, we test a genetic hypothesis presented in OCBIL theory that predicts highly differentiated intraspecific population systems on OCBILs vs. more limited differentiation on young, often disturbed, fertile landscapes (YODFELs). We examined patterns of genomic and morphological divergence in Banksia seminuda across OCBILs and YODFELs in south-western Australia. We also used these data to determine whether these OCBIL and YODFEL populations represent distinct subspecific lineages, a point of previous contention among taxonomists. As hypothesized, genomic analyses based on 3466 SNP loci revealed strong structuring within B. seminuda , with high differentiation across narrow geographic scales among OCBIL populations vs. lower differentiation across much larger geographic scales among YODFEL populations. In addition, genomic and morphological divergence was found between OCBIL and YODFEL populations, providing comprehensive quantitative evidence for two subspecies. These findings have taxonomic implications for the species and provide support for OCBIL theory and its insights into the evolution, ecology and conservation of biota on ancient landscapes. [ABSTRACT FROM AUTHOR]

Evolutionary theories of ageing predict a reduction in selection efficiency with age, a so-called "selection shadow," due to extrinsic mortality decreasing effective population size with age. Classic symptoms of ageing include a deterioration in transcriptional regulation and protein homeostasis. Understanding how ant queens defy the trade-off between fecundity and lifespan remains a major challenge for the evolutionary theory of ageing. It has often been discussed that the low extrinsic mortality of ant queens, that are generally well protected within the nest by workers and soldiers, should reduce the selection shadow acting on old queens. We tested this by comparing strength of selection acting on genes upregulated in young and old queens of the ant, Cardiocondyla obscurior. In support of a reduced selection shadow, we find old-biased genes to be under strong purifying selection. We also analyzed a gene coexpression network (GCN) with the aim to detect signs of ageing in the form of deteriorating regulation and proteostasis. We find no evidence for ageing. In fact, we detect higher connectivity in old queens indicating increased transcriptional regulation with age. Within the GCN, we discover five highly correlated modules that are upregulated with age. These old-biased modules regulate several antiageing mechanisms such as maintenance of proteostasis, transcriptional regulation, and stress response. We observe stronger purifying selection on central hub genes of these old-biased modules compared with young-biased modules. These results indicate a lack of transcriptional ageing in old C. obscurior queens, possibly facilitated by strong selection at old age and well-regulated antiageing mechanisms. [ABSTRACT FROM AUTHOR]

The Modern Synthesis (or "Neo‐Darwinism"), which arose out of the reconciliation of Darwin's theory of natural selection and Mendel's research on genetics, remains the foundation of evolutionary theory. However, since its inception, it has been a lightning rod for criticism, which has ranged from minor quibbles to complete dismissal. Among the most famous of the critics was Stephen Jay Gould, who, in 1980, proclaimed that the Modern Synthesis was "effectively dead." Gould and others claimed that the action of natural selection on random mutations was insufficient on its own to explain patterns of macroevolutionary diversity and divergence, and that new processes were required to explain findings from the fossil record. In 1982, Charlesworth, Lande, and Slatkin published a response to this critique in Evolution, in which they argued that Neo‐Darwinism was indeed sufficient to explain macroevolutionary patterns. In this Perspective for the 75th Anniversary of the Society for the Study of Evolution, we review Charlesworth et al. in its historical context and provide modern support for their arguments. We emphasize the importance of microevolutionary processes in the study of macroevolutionary patterns. Ultimately, we conclude that punctuated equilibrium did not represent a major revolution in evolutionary biology – although debate on this point stimulated significant research and furthered the field – and that Neo‐Darwinism is alive and well. [ABSTRACT FROM AUTHOR]

We consider the possibility that LIGO events GW190521, GW190425, and GW190814 may have emerged from the mirror world binaries. Theories of star evolution predict so-called upper and lower mass gaps and masses of these merger components lie in that gaps. In order to explain these challenging events very specific assumptions are required and we argue that such scenarios are order of magnitude more probable in mirror world, where star formation begins earlier and matter density can exceed five times the ordinary matter density. [ABSTRACT FROM AUTHOR]

The alignment between halo spins and the cosmic web is still poorly understood despite being a widely studied topic. Here, we study this alignment within the context of tidal torque theory (TTT) and deviations from it. To this end, we analyse the evolution of the shape and spin direction of proto-haloes, i.e. of all the volume elements associated to a z  = 0 halo, with respect to the present-day filaments. We find that the major axis of proto-haloes undergoes a major change, from being strongly perpendicular to the filament spine in the initial conditions, to being preferentially aligned at the present time. In comparison, the spin orientation shows only a mild evolution: it starts slightly parallel to the filament spine, but the subsequent evolution, up to z ∼ 1, gradually changes its orientation to preferentially perpendicular. In order to analyse these signals in the TTT framework, we split the haloes according to their net spin growth with respect to the median TTT expectation, finding a clear correlation with the spin–filament alignment. At the present time, haloes whose spin grew the most are the ones most perpendicular to the filament spine, while haloes whose spin grew below the median TTT expectation are typically more aligned. The dependence of spin directions on net spin growth is already present in the initial conditions, and gets further modified by late-time, z < 2, evolution. Also, spin directions mildly deviate from the TTT predictions even at high redshift, indicating the need for extensions to the model. [ABSTRACT FROM AUTHOR]

In Geological Evidences of the Antiquity of Man (1863), Charles Lyell appraised the distinct contribution made by his protégé, Charles Darwin (On the Origin of Species (1859)), to evolutionary theory: 'Progression ... is not a necessary accompaniment of variation and natural selection [... Darwin's theory accounts] equally well for what is called degradation, or a retrogressive movement towards a simple structure'. In Rhoda Broughton's first novel, Not Wisely, but Too Well (1867), written contemporaneously with Lyell's book, the Crystal Palace at Sydenham prompts precisely this sort of Darwinian ambivalence to progress; but whether British civilization 'advance[s] or retreat[s]', her narrator adds that this prophesized state 'will not be in our days' – its realization exceeds the single lifespan. This article argues that Not Wisely, but Too Well is attentive to the irreconcilability of Darwinism to the Victorian 'idea of progress': Broughton's novel, distinctly from its peers, raises the retrogressive and nihilistic potentials of Darwin's theory and purposes them to reflect on the status of the individual in mid-century Britain. [ABSTRACT FROM AUTHOR]

Viruses exhibit a diverse array of strategies for infecting host cells and for virion release after replication. Cell exit strategies generally involve either budding from the cell membrane or killing the host cell. The conditions under which either is at a selective advantage is a key question in the evolutionary theory of viruses, with the outcome having potentially important impacts on the course of infection and pathogenicity. Although a plethora of external factors will influence the fitness of either strategy; here, we focus just on the effects of the physical properties of the system. We develop theoretical approaches to assess the effects of the time delays between initial infection and virion release. We show that the length of the delay before apoptosis is an important trait in virus evolutionary dynamics. Our results show that for a fixed time to apoptosis, intermediate delays lead to virus fitness that is lower than short times to apoptosis — leading to an apoptotic strategy — and long times to apoptosis — leading to a budding strategy at the between-cell level. At fitness minima, selection is expected to be disruptive and the potential for adaptive radiation in virus strategies is feasible. Hence, the physical properties of the system are sufficient to explain the existence of both budding and virus-induced apoptosis. The fitness functions presented here provide a formal basis for further work focusing on the evolutionary implications of trade-offs between time delays, intracellular replication and resulting mutation rates. [ABSTRACT FROM AUTHOR]

Flaviviruses display diverse epidemiological and ecological features. Tick-borne and mosquito-borne flaviviruses (TBFV and MBFV, respectively) are important human pathogens that alternate replication in invertebrate vectors and vertebrate hosts. The Flavivirus genus also includes insect-specific viruses (ISFVs) and viruses with unknown invertebrate hosts. It is generally accepted that viruses that alternate between taxonomically different hosts evolve slowly and that the evolution of MBFVs and TBFVs is dominated by strong constraints, with limited episodes of positive selection. We exploited the availability of flavivirus genomes to test these hypotheses and to compare their rates and patterns of evolution. We estimated the substitution rates of CFAV and CxFV (two ISFVs) and, by taking into account the time-frame of measurement, compared them with those of other flaviviruses. Results indicated that CFAV and CxFV display relatively different substitution rates. However, these data, together with estimates for single-host members of the Flaviviridae family, indicated that MBFVs do not display relatively slower evolution. Conversely, TBFVs displayed some of lowest substitution rates among flaviviruses. Analysis of selective patterns over longer evolutionary time-frames confirmed that MBFVs evolve under strong purifying selection. Interestingly, TBFVs and ISFVs did not show extremely different levels of constraint, although TBFVs alternate among hosts, whereas ISFVs do not. Additional results showed that episodic positive selection drove the evolution of MBFVs, despite their high constraint. Positive selection was also detected on two branches of the TBFVs phylogeny that define the seabird clade. Thus, positive selection was much more common during the evolution of arthropod-borne flaviviruses than previously thought. Overall, our data indicate that flavivirus evolutionary patterns are complex and most likely determined by multiple factors, not limited to the alternation between taxonomically divergent hosts. The frequency of both positive and purifying selection, especially in MBFVs, suggests that a minority of sites in the viral polyprotein experience weak constraint and can evolve to generate new viral phenotypes and possibly promote adaptation to new hosts. [ABSTRACT FROM AUTHOR]

Recombination has been shown to contribute to human immunodeficiency virus-1 (HIV-1) evolution in vivo , but the underlying dynamics are extremely complex, depending on the nature of the fitness landscapes and of epistatic interactions. A less well-studied determinant of recombinant evolution is the mode of virus transmission in the cell population. HIV-1 can spread by free virus transmission, resulting largely in singly infected cells, and also by direct cell-to-cell transmission, resulting in the simultaneous infection of cells with multiple viruses. We investigate the contribution of these two transmission pathways to recombinant evolution, by applying mathematical models to in vitro experimental data on the growth of fluorescent reporter viruses under static conditions (where both transmission pathways operate), and under gentle shaking conditions, where cell-to-cell transmission is largely inhibited. The parameterized mathematical models are then used to extrapolate the viral evolutionary dynamics beyond the experimental settings. Assuming a fixed basic reproductive ratio of the virus (independent of transmission pathway), we find that recombinant evolution is fastest if virus spread is driven only by cell-to-cell transmission and slows down if both transmission pathways operate. Recombinant evolution is slowest if all virus spread occurs through free virus transmission. This is due to cell-to-cell transmission 1, increasing infection multiplicity; 2, promoting the co-transmission of different virus strains from cell to cell; and 3, increasing the rate at which point mutations are generated as a result of more reverse transcription events. This study further resulted in the estimation of various parameters that characterize these evolutionary processes. For example, we estimate that during cell-to-cell transmission, an average of three viruses successfully integrated into the target cell, which can significantly raise the infection multiplicity compared to free virus transmission. In general, our study points towards the importance of infection multiplicity and cell-to-cell transmission for HIV evolution. [ABSTRACT FROM AUTHOR]

HIV set point viral load (SPVL), the viral load established shortly after initial infection, is a proxy for HIV virulence: higher SPVLs lead to higher risk of transmission and faster disease progression. Three models of test-and-treat scenarios, mainly in heterosexual populations, found that increasing treatment coverage selected for more virulent viruses. We modeled virulence evolution in a population of men who have sex with men (MSM) with increasing test-and-treat coverage. We extended a stochastic, dynamic network model (EvoNetHIV). We varied relationship patterns (MSM vs. heterosexual), HIV transmission models (increasing vs. plateauing probability of transmission at very high viral loads), and treatment roll-out (with explicit testing or fixed intervals between infection and treatment). In scenarios most similar to previous models (longer relational durations and the plateauing transmission function), we replicated trends previously found: increasing treatment coverage led to increased virulence (0.12 log10 increase in mean population SPVL between 20% and 100% treatment coverage). In scenarios reflecting MSM behavioral data using the increasing transmission function, increasing treatment coverage selected for viruses with lower virulence (0.16 log10 decrease in mean population SPVL between 20% and 100% treatment coverage). These findings emphasize the impact of sexual network conditions and transmission function details on predicted epidemiological and evolutionary outcomes. Varying these features creates very different evolutionary environments, which in turn lead to opposite effects in mean population SPVL evolution. Our results suggest that, under some realistic conditions, effective test-and-treat strategies may not face the previously reported tradeoff in which increasing coverage leads to evolution of greater virulence. This suggests instead that a virtuous cycle of increasing treatment coverage and diminishing virulence is possible. [ABSTRACT FROM AUTHOR]

When emerging pathogens encounter new host species for which they are poorly adapted, they must evolve to escape extinction. Pathogens experience selection on traits at multiple scales, including replication rates within host individuals and transmissibility between hosts. We analyze a stochastic model linking pathogen growth and competition within individuals to transmission between individuals. Our analysis reveals a new factor, the cross-scale reproductive number of a mutant virion, that quantifies how quickly mutant strains increase in frequency when they initially appear in the infected host population. This cross-scale reproductive number combines with viral mutation rates, single-strain reproductive numbers, and transmission bottleneck width to determine the likelihood of evolutionary emergence, and whether evolution occurs swiftly or gradually within chains of transmission. We find that wider transmission bottlenecks facilitate emergence of pathogens with short-term infections, but hinder emergence of pathogens exhibiting cross-scale selective conflict and long-term infections. Our results provide a framework to advance the integration of laboratory, clinical, and field data in the context of evolutionary theory, laying the foundation for a new generation of evidence-based risk assessment of emergence threats. [ABSTRACT FROM AUTHOR]

Genomic imprinting is the differential expression alleles in diploid individuals, with the expression being dependent on the sex of the parent from which it was inherited. Haig's kinship theory hypothesizes that genomic imprinting is due to an evolutionary conflict of interest between alleles from the mother and father. In social insects, it has been suggested that genomic imprinting should be widespread. One recent study identified parent‐of‐origin expression in honey bees and found evidence supporting the kinship theory. However, little is known about genomic imprinting in insects and multiple theoretical predictions must be tested to avoid single‐study confirmation bias. We, therefore, tested for parent‐of‐origin expression in a primitively eusocial bee. We found equal numbers of maternally and paternally biased expressed genes. The most highly biased genes were maternally expressed, offering support for the kinship theory. We also found low conservation of potentially imprinted genes with the honey bee, suggesting rapid evolution of genomic imprinting in Hymenoptera. [ABSTRACT FROM AUTHOR]

MicroRNA target sites are often conserved during evolution and purifying selection to maintain such sites is expected. On the other hand, comparative analyses identified a paucity of microRNA target sites in coexpressed transcripts, and novel target sites can potentially be deleterious. We proposed that selection against novel target sites pervasive. The analysis of derived allele frequencies revealed that, when the derived allele is a target site, the proportion of nontarget sites is higher than expected, particularly for highly expressed microRNAs. Thus, new alleles generating novel microRNA target sites can be deleterious and selected against. When we analyzed ancestral target sites, the derived (nontarget) allele frequency does not show statistical support for microRNA target allele conservation. We investigated the joint effects of microRNA conservation and expression and found that selection against microRNA target sites depends mostly on the expression level of the microRNA. We identified microRNA target sites with relatively high levels of population differentiation. However, when we analyze separately target sites in which the target allele is ancestral to the population, the proportion of single-nucleotide polymorphisms with high F st significantly increases. These findings support that population differentiation is more likely in target sites that are lost than in the gain of new target sites. Our results indicate that selection against novel microRNA target sites is prevalent and, although individual sites may have a weak selective pressure, the overall effect across untranslated regions is not negligible and should be accounted when studying the evolution of genomic sequences. [ABSTRACT FROM AUTHOR]

The article describes the evolution of ‘environmentalization' of the image, especially in the context of various historical instantiations that have culminated in the contemporary virtual disposit if known as the head-mounted display (HMD). Topics include virtual reality (VR) immersive environments represent the last stage of a complex historical development; and virtual immersive environments offer themselves as actual entities to be perceived ‘in person'.

Evolutionary theories relating to aging predict that patterns of actuarial and reproductive senescence should be aligned, with a common onset of senescence set at the age of first reproduction. However, a few empirical studies reported asynchrony between actuarial and reproductive senescence. This asynchrony is expected to be particularly pronounced in organisms with indeterminate growth. Yet, this process is still poorly documented due to the lack of long-term demographic data on known-aged individuals. We investigated the asynchrony of actuarial and reproductive senescence in the European whip snake, Hierophis viridiflavus , an oviparous colubrid with indeterminate growth. Using demographic data collected over a 29-year period, we showed that females did not experience any fecundity loss late in life. In contrast, they suffered from an early, severe actuarial senescence. Our findings thus revealed a pronounced asynchrony in actuarial and reproductive senescence processes, a phenomenon that could be widespread across the tree of life. [ABSTRACT FROM AUTHOR]

A tenet of evolutionary theory is that phenotypic variation of a trait is inversely related to the intensity of stabilizing selection pressure. Among homologous bones, such as metapodials, a rudimentary, "nonfunctional" bone is expected to be more variable in length than nonrudimentary bones. This study compares variation and association in length among metapodials using 277 adult skeletons of Canis latrans. Canis latrans has a short, "functionless" first metacarpal (mc1) and "rudimentary, vestigial" first metatarsal (mt1). Results show that among the 10 metapodials, mt1 has the highest variation in length; other metapodials do not differ significantly from one another in their variation. Correlation coefficients for length of mc1 and mt1 with their ipsilateral metapodials 2‐5 are significantly lower than coefficients for all other ipsilateral pairs. The correlation coefficient between left and right mt1 is significantly the lowest among all bilateral pairs of metapodials. Results are interpreted as follows. Mt1's high variation and low association in length are the outcome of less intense stabilizing selection pressure compared with other metapodials. The nonsignificant difference for variation in length between mc1 and metapodials 2‐5 may be that mc1 is functional for development of a pollical dewclaw that helps restrain small prey. [ABSTRACT FROM AUTHOR]

The rate and spectrum of spontaneous mutations are critical parameters in basic and applied biology because they dictate the pace and character of genetic variation introduced into populations, which is a prerequisite for evolution. We use a mutation–accumulation approach to estimate mutation parameters from whole-genome sequence data from multiple genotypes from multiple populations of Daphnia magna , an ecological and evolutionary model system. We report extremely high base substitution mutation rates (⁠ µ - n , bs = 8.96 × 10−9/bp/generation [95% CI: 6.66–11.97 × 10−9/bp/generation] in the nuclear genome and µ - m , bs = 8.7 × 10−7/bp/generation [95% CI: 4.40–15.12 × 10−7/bp/generation] in the mtDNA), the highest of any eukaryote examined using this approach. Levels of intraspecific variation based on the range of estimates from the nine genotypes collected from three populations (Finland, Germany, and Israel) span 1 and 3 orders of magnitude, respectively, resulting in up to a ∼300-fold difference in rates among genomic partitions within the same lineage. In contrast, mutation spectra exhibit very consistent patterns across genotypes and populations, suggesting the mechanisms underlying the mutational process may be similar, even when the rates at which they occur differ. We discuss the implications of high levels of intraspecific variation in rates, the importance of estimating gene conversion rates using a mutation–accumulation approach, and the interacting factors influencing the evolution of mutation parameters. Our findings deepen our knowledge about mutation and provide both challenges to and support for current theories aimed at explaining the evolution of the mutation rate, as a trait, across taxa. [ABSTRACT FROM AUTHOR]

Phylogenetic inference from genome-wide data (phylogenomics) has revolutionized the study of evolution because it enables accounting for discordance among evolutionary histories across the genome. To this end, summary methods have been developed to allow accurate and scalable inference of species trees from gene trees. However, most of these methods, including the widely used ASTRAL, can only handle single-copy gene trees and do not attempt to model gene duplication and gene loss. As a result, most phylogenomic studies have focused on single-copy genes and have discarded large parts of the data. Here, we first propose a measure of quartet similarity between single-copy and multicopy trees that accounts for orthology and paralogy. We then introduce a method called ASTRAL-Pro (ASTRAL for PaRalogs and Orthologs) to find the species tree that optimizes our quartet similarity measure using dynamic programing. By studying its performance on an extensive collection of simulated data sets and on real data sets, we show that ASTRAL-Pro is more accurate than alternative methods. [ABSTRACT FROM AUTHOR]

A challenging question in evolutionary theory is the origin of cell division and plausible molecular mechanisms involved. Here, we made the surprising observation that complexes formed by short alpha-helical peptides and oleic acid can create multiple membrane-enclosed spaces from a single lipid vesicle. The findings suggest that such complexes may contain the molecular information necessary to initiate and sustain this process. Based on these observations, we propose a new molecular model to understand protocell division. [ABSTRACT FROM AUTHOR]

Genomic analysis of many nonmodel species has uncovered an incredible diversity of sex chromosome systems, making it possible to empirically test the rich body of evolutionary theory that describes each stage of sex chromosome evolution. Classic theory predicts that sex chromosomes originate from a pair of homologous autosomes and recombination between them is suppressed via inversions to resolve sexual conflict. The resulting degradation of the Y chromosome gene content creates the need for dosage compensation in the heterogametic sex. Sex chromosome theory also implies a linear process, starting from sex chromosome origin and progressing to heteromorphism. Despite many convergent genomic patterns exhibited by independently evolved sex chromosome systems, and many case studies supporting these theoretical predictions, emerging data provide numerous interesting exceptions to these long-standing theories, and suggest that the remarkable diversity of sex chromosomes is matched by a similar diversity in their evolution. For example, it is clear that sex chromosome pairs are not always derived from homologous autosomes. In addition, both the cause and the mechanism of recombination suppression between sex chromosome pairs remain unclear, and it may be that the spread of recombination suppression is a more gradual process than previously thought. It is also clear that dosage compensation can be achieved in many ways, and displays a range of efficacy in different systems. Finally, the remarkable turnover of sex chromosomes in many systems, as well as variation in the rate of sex chromosome divergence, suggest that assumptions about the inevitable linearity of sex chromosome evolution are not always empirically supported, and the drivers of the birth–death cycle of sex chromosome evolution remain to be elucidated. Here, we concentrate on how the diversity in sex chromosomes across taxa highlights an equal diversity in each stage of sex chromosome evolution. [ABSTRACT FROM AUTHOR]

Theory on the evolution of niche width argues that resource heterogeneity selects for niche breadth. For parasites, this theory predicts that parasite populations will evolve, or maintain, broader host ranges when selected in genetically diverse host populations relative to homogeneous host populations. To test this prediction, we selected the bacterial parasite Serratia marcescens to kill Caenorhabditis elegans in populations that were genetically heterogeneous (50% mix of two experimental genotypes) or homogeneous (100% of either genotype). After 20 rounds of selection, we compared the host range of selected parasites by measuring parasite fitness (i.e. virulence, the selected fitness trait) on the two focal host genotypes and on a novel host genotype. As predicted, heterogeneous host populations selected for parasites with a broader host range: these parasite populations gained or maintained virulence on all host genotypes. This result contrasted with selection in homogeneous populations of one host genotype. Here, host range contracted, with parasite populations gaining virulence on the focal host genotype and losing virulence on the novel host genotype. This pattern was not, however, repeated with selection in homogeneous populations of the second host genotype: these parasite populations did not gain virulence on the focal host genotype, nor did they lose virulence on the novel host genotype. Our results indicate that host heterogeneity can maintain broader host ranges in parasite populations. Individual host genotypes, however, vary in the degree to which they select for specialization in parasite populations. [ABSTRACT FROM AUTHOR]

Although evolutionary theory predicts an association between the evolution of elaborate ornamentation and speciation, empirical evidence for links between speciation and ornament evolution has been mixed. In birds, the evolution of increasingly complex and colorful plumage may promote speciation by introducing prezygotic mating barriers. However, overall changes in color complexity, including both increases and decreases, may also promote speciation by altering the sexual signals that mediate reproductive choices. Here, we examine the relationship between complex plumage and speciation rates in the largest family of songbirds, the tanagers (Thraupidae). First, we test whether species with more complex plumage coloration are associated with higher speciation rates and find no correlation. We then test whether rates of male or female plumage color complexity evolution are correlated with speciation rates. We find that elevated rates of plumage complexity evolution are associated with higher speciation rates, regardless of sex and whether species are evolving more complex or less complex ornamentation. These results extend to whole‐plumage color complexity and regions important in signaling (crown and throat) but not nonsignaling regions (back and wingtip). Our results suggest that the extent of change in plumage traits, rather than overall values of plumage complexity, may play a role in speciation. [ABSTRACT FROM AUTHOR]

Artworks are rationally evaluable and comparable within their art form, but not from outside. Beethoven's string quartets cannot be evaluated against works of Hindustani music. This is the problem of evaluative diversity: local commensurability, global indeterminacy. This article sketches an approach to the problem based on novel conceptions of aesthetic pleasure and cultural learning, and on the Darwinian Principle of Divergence as applied to cultural evolution. [ABSTRACT FROM AUTHOR]

Dissecting the genetic regulation of gene expression is critical for understanding phenotypic variation and species evolution. However, our understanding of the transcriptional variability in sweet potato remains limited. Here, we analyzed two publicly available datasets to explore the landscape of transcriptomic variations and its genetic basis in the storage roots of sweet potato. The comprehensive analysis identified a total of 724,438 high-confidence single nucleotide polymorphisms (SNPs) and 26,026 expressed genes. Expression quantitative trait locus (eQTL) analysis revealed 4408 eQTLs regulating the expression of 3646 genes, including 2261 local eQTLs and 2147 distant eQTLs. Two distant eQTL hotspots were found with target genes significantly enriched in specific functional classifications. By combining the information from regulatory network analyses, eQTLs and association mapping, we found that IbMYB1-2 acts as a master regulator and is the major gene responsible for the activation of anthocyanin biosynthesis in the storage roots of sweet potato. Our study provides the first insight into the genetic architecture of genome-wide expression variation in sweet potato and can be used to investigate the potential effects of genetic variants on key agronomic traits in sweet potato. [ABSTRACT FROM AUTHOR]

A key obstacle to developing a satisfying theory of galaxy evolution is the difficulty in extending analytic descriptions of early structure formation into full non-linearity, the regime in which galaxy growth occurs. Extant techniques, though powerful, are based on approximate numerical methods whose Monte Carlo-like nature hinders intuition building. Here, we develop a new solution to this problem and its empirical validation. We first derive closed-form analytic expectations for the evolution of fixed percentiles in the real-space cosmic density distribution, averaged over representative volumes observers can track cross-sectionally. Using the Lagrangian forms of the fluid equations, we show that percentiles in δ – the density relative to the median – should grow as |$\delta (t)\propto \delta _{0}^{\alpha }\, t^{\beta }$|⁠ , where α ≡ 2 and β ≡ 2 for Newtonian gravity at epochs after the overdensities transitioned to non-linear growth. We then use 9.5 square degress of Carnegie-Spitzer-IMACS Redshift Survey data to map galaxy environmental densities over 0.2 < z < 1.5 (∼7 Gyr) and infer α = 1.98 ± 0.04 and β = 2.01 ± 0.11 – consistent with our analytic prediction. These findings – enabled by swapping the Eulerian domain of most work on density growth for a Lagrangian approach to real-space volumetric averages – provide some of the strongest evidence that a lognormal distribution of early density fluctuations indeed decoupled from cosmic expansion to grow through gravitational accretion. They also comprise the first exact, analytic description of the non-linear growth of structure extensible to (arbitrarily) low redshift. We hope these results open the door to new modelling of, and insight-building into, galaxy growth and its diversity in cosmological contexts. [ABSTRACT FROM AUTHOR]

As one goes back in time, the number of extant bowed instruments decreases gradually, and this is particularly true for loose parts such as bridges, pegs and tailpieces. The current article traces the development of bridges of instruments of the violin family, based on a study of extant instruments and around 800 iconographic sources. This study reveals the origins of the various elements of bridges found on modern instruments of the violin family, and reconstructs the different stages of their evolution. Many elements of the modern violin bridge were already present, sometimes hidden, in bowed-instrument bridges of the 16th century. The extensive appendices and many line drawings offer today's researchers, makers and restorers the possibility of providing historically informed bridges that are less fantasized than those hitherto often encountered on restorations or reconstructions of old instruments. [ABSTRACT FROM AUTHOR]

Linking the properties of galaxies to the assembly history of their dark matter haloes is a central aim of galaxy evolution theory. This paper introduces a dimensionless parameter s ∈ [0, 1], the 'tree entropy', to parametrize the geometry of a halo's entire mass assembly hierarchy, building on a generalization of Shannon's information entropy. By construction, the minimum entropy (s  = 0) corresponds to smoothly assembled haloes without any mergers. In contrast, the highest entropy (s  = 1) represents haloes grown purely by equal-mass binary mergers. Using simulated merger trees extracted from the cosmological N -body simulation SURFS, we compute the natural distribution of s , a skewed bell curve peaking near s  = 0.4. This distribution exhibits weak dependences on halo mass M and redshift z , which can be reduced to a single dependence on the relative peak height δc/σ(M, z) in the matter perturbation field. By exploring the correlations between s and global galaxy properties generated by the SHARK semi-analytic model, we find that s contains a significant amount of information on the morphology of galaxies – in fact more information than the spin, concentration, and assembly time of the halo. Therefore, the tree entropy provides an information-rich link between galaxies and their dark matter haloes. [ABSTRACT FROM AUTHOR]

This essay is an initial study of a larger project that seeks to produce a history of the term 'Darwinism'. While it is generally well-known that Darwinism could refer to a variety of different things in the Victorian period, from a general evolutionary naturalism to the particular theory of natural selection, very little has been written about the history of the term or how it was contested at given times and places. Building on James Moore's 1991 sketch of the history of Darwinism in the 1860s, this paper specifically seeks to situate Alfred Russel Wallace's 1889 book Darwinism in the context of a larger struggle over Darwin's legacy in the 1880s. It is argued that Wallace used his authority as one of the founders of evolution by natural selection to reimagine what he called 'pure Darwinism' as a teleological evolutionism, one that integrated the theory of natural selection with an interpretation of spirit phenomena thereby producing a more agreeable and holistic account of life than was previously associated with Darwinian evolution. By considering the reception of Wallace's Darwinism in the periodical press it will be argued further that Wallace's interpretation of Darwinism was generally well received, which suggests that our understanding of what Darwinism meant in the late Victorian period needs to be revisited. [ABSTRACT FROM AUTHOR]

Group‐beneficial behaviors have presented a long‐standing challenge for evolutionary theory because, although their benefits are available to all group members, their costs are borne by individuals. Consequently, an individual could benefit from "cheating" their group mates by not paying the costs while still reaping the benefits. There have been many proposed evolutionary mechanisms that could favor cooperation (and disfavor cheating) in particular circumstances. However, if cooperation is still favored in some circumstances, then we might expect evolution to favor strategic cooperation, where the level of contribution toward group‐beneficial behavior is varied in response to the social context. To uncover how and why individuals should contribute toward group‐beneficial behavior across social contexts, we model strategic cooperation as an evolutionary game where players can quantitatively adjust the amount they contribute toward group‐beneficial behavior. We find that the evolutionarily stable strategy (ESS) predicts, unsurprisingly, that players should contribute in relation to their relatedness to the group. However, we surprisingly find that players often contribute to cooperation in such a way that their fitness is inverse to their relatedness to the group such that those that contribute to cooperation end up with the same return from group‐beneficial behavior, essentially removing any potential advantage of higher relatedness. These results bring to light a paradox of group‐beneficial cooperation: groups do best when they contain highly related individuals, but those with the highest relatedness to the group will often have the lowest fitness within the group. [ABSTRACT FROM AUTHOR]

Sex chromosomes contribute substantially to key evolutionary processes such as speciation and adaptation. Several theories suggest that evolution could occur more rapidly on sex chromosomes, but currently our understanding of whether and how this occurs is limited. Here, we present an analysis of the great tit (Parus major) genome, aiming to detect signals of faster-Z evolution. We find mixed evidence of faster divergence on the Z chromosome than autosomes, with significantly higher divergence being found in ancestral repeats, but not at 4- or 0-fold degenerate sites. Interestingly, some 4-fold sites appear to be selectively constrained, which may mislead analyses that use these sites as the neutral reference (e.g., d N /d S). Consistent with other studies in birds, the mutation rate is significantly higher in males than females, and the long-term Z-to-autosome effective population size ratio is only 0.5, significantly lower than the expected value of 0.75. These are indicative of male-driven evolution and high variance in male reproductive success, respectively. We find no evidence for an increased efficacy of positive selection on the Z chromosome. In contrast, the Z chromosome in great tits appears to be affected by increased genetic drift, which has led to detectable signals of weakened intensity of purifying selection. These results provide further evidence that the Z chromosome often has a low effective population size, and that this has important consequences for its evolution. They also highlight the importance of considering multiple factors that can affect the rate of evolution and effective population sizes of sex chromosomes. [ABSTRACT FROM AUTHOR]