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The paper models evolution in pecunia--in the realm of finance. Financial markets are explored as evolving biological systems. Diverse investment strategies compete for the market capital invested in long-lived dividend-paying assets. Some strategies survive and some become extinct. The basis of our paper is that dividends are not exogenous but increase with the wealth invested in an asset, as is the case in a production economy. This might create a positive feedback loop in which more investment in some asset leads to higher dividends which in turn lead to higher investments. Nevertheless, we are able to identify a unique evolutionary stable investment strategy. The problem is studied in a framework combining stochastic dynamics and evolutionary game theory. The model proposed employs only objectively observable market data, in contrast with traditional settings relying upon unobservable investors' characteristics (utilities and beliefs). Our method is analytical and based on mathematical reasoning. A numerical illustration of the main result is provided. [ABSTRACT FROM AUTHOR]

This article reviews some key strands of demographic research on past trends in human longevity and explores possible future trends in life expectancy at birth. Demographic data on age-specific mortality are used to estimate life expectancy, and validated data on exceptional life spans are used to study the maximum length of life. In the countries doing best each year, life expectancy started to increase around 1840 at a pace of almost 2.5 y per decade. This trend has continued until the present. Contrary to classical evolutionary theories of senescence and contrary to the predictions of many experts, the frontier of survival is advancing to higher ages. Furthermore, individual life spans are becoming more equal, reducing inequalities, with octogenarians and nonagenarians accounting for most deaths in countries with the highest life expectancy. If the current pace of progress in life expectancy continues, most children born this millennium will celebrate their 100th birthday. Considerable uncertainty, however, clouds forecasts: Life expectancy and maximum life span might increase very little if at all, or longevity might rise much faster than in the past. Substantial progress has been made over the past three decades in deepening understanding of how long humans have lived and how long they might live. The social, economic, health, cultural, and political consequences of further increases in longevity are so significant that the development of more powerful methods of forecasting is a priority. [ABSTRACT FROM AUTHOR]

Autocatalysis is essential for the origin of life and chemical evolution. However, the lack of a unified framework so far prevents a systematic study of autocatalysis. Here, we derive, from basic principles, general stoichiometric conditions for catalysis and autocatalysis in chemical reaction networks. This allows for a classification of minimal autocatalytic motifs called cores. While all known autocatalytic systems indeed contain minimal motifs, the classification also reveals hitherto unidentified motifs. We further examine conditions for kinetic viability of such networks, which depends on the autocatalytic motifs they contain and is notably increased by internal catalytic cycles. Finally, we show how this framework extends the range of conceivable autocatalytic systems, by applying our stoichiometric and kinetic analysis to autocatalysis emerging from coupled compartments. The unified approach to autocatalysis presented in this work lays a foundation toward the building of a systems-level theory of chemical evolution. [ABSTRACT FROM AUTHOR]

What explains variation in levels of prosocial behavior across communities? And are members of the ingroup and outgroup treated differently? According to evolutionary theories of generalized altruism, market integration should lead to greater levels of prosociality: Market exchange forces people to interact with unknown others, thus creating the conditions for the extension of prosocial behavior beyond close-knit circles to include outgroup members and strangers. Moving away from the evolutionary focus on cross-cultural variation, this article uses the marketintegration hypothesis to explain intracultural variation in levels of prosociality in an advanced society. Taking advantage of an ideal setting, this study reports results from a large-scale, nationwide lost-letter experiment in which 5,980 letters were dispersed in a sample of 188 Italian communities. The study confirms the relevance of market integration in accounting for differences in levels of prosociality: In areas where market exchange is dominant, return rates are high. It also casts a light on the relationship between ingroup and outgroup prosociality: Return rates for both Italian and foreign recipients are the same; they vary together; and ingroup returns are highly predictive of outgroup returns at the community level. [ABSTRACT FROM AUTHOR]

Sperm competition favors large, costly ejaculates, and theory predicts the evolution of allocation strategies that enable males to plastically tailor ejaculate expenditure to sperm competition threat. While greater sperm transfer in response to a perceived increase in the risk of sperm competition is well-supported, we have a poor understanding ofwhether males (i) respond to changes in perceived intensity of sperm competition, (ii) use the same allocation rules for sperm and seminal fluid, and (iii) experience changes in current and future reproductive performance as a result of ejaculate compositional changes. Combining quantitative proteomics with fluorescent sperm labeling, we show that Drosophila melanogaster males exercise independent control over the transfer of sperm and seminal fluid proteins (SFPs) under different levels of male-male competition. While sperm transfer peaks at low competition, consistent with some theoretical predictions based on sperm competition intensity, the abundance of transferred SFPs generally increases at high competition levels. However, we find that clusters of SFPs vary in the directionality and sensitivity of their response to competition, promoting compositional change in seminal fluid. By tracking the degree of decline inmale mating probability and offspring production across successive matings, we provide evidence that ejaculate compositional change represents an adaptive response to current spermcompetition, but one that comes at a cost to future mating performance. Our work reveals a previously unknown divergence in ejaculate component allocation rules, exposes downstream costs of elevated ejaculate investment, and ultimately suggests a central role for ejaculate compositional plasticity in sexual selection. [ABSTRACT FROM AUTHOR]

Cooperation can be sustained by institutions that punish free-riders. Such institutions, however, tend to be subverted by corruption if they are not closely watched. Monitoring can uphold the enforcement of binding agreements ensuring cooperation, but this usually comes at a price. The temptation to skip monitoring and take the institution's integrity for granted leads to outbreaks of corruption and the breakdown of cooperation. We model the corresponding mechanism by means of evolutionary game theory, using analytical methods and numerical simulations, and find that it leads to sustained or damped oscillations. The results confirm the view that corruption is endemic and transparency a major factor in reducing it. [ABSTRACT FROM AUTHOR]

The potential impact of structural variants includes not only the duplication or deletion of coding sequences, but also the perturbation of noncoding DNA regulatory elements and structural chromatin features, including topological domains (TADs). Structural variants disrupting TAD boundaries have been implicated both in cancer and developmental disease; this likely occurs via "enhancer hijacking," whereby removal of the TAD boundary exposes enhancers to new target transcription start sites (TSSs). With this functional role, we hypothesized that boundaries would display evidence for negative selection. Here we demonstrate that the chromatin landscape constrains structural variation both within healthy humans and across primate evolution. In contrast, in patients with developmental delay, variants occur remarkably uniformly across genomic features, suggesting a potentially broad role for enhancer hijacking in human disease. [ABSTRACT FROM AUTHOR]

What kind of genetic variation contributes the most to adaptation is a fundamental question in evolutionary biology. By resequencing genomes of 80 individuals, we inferred the origin of genomic variants associated with a complex adaptive syndrome involving multiple quantitative traits, namely, adaptation between high and low altitudes, in the vinous-throated parrotbill (Sinosuthora webbiana) in Taiwan. By comparing these variants with those in the Asian mainland population, we revealed standing variation in 24 noncoding genomic regions to be the predominant genetic source of adaptation. Parrotbills at both high and low altitudes exhibited signatures of recent selection, suggesting that not only the front but also the trailing edges of postglacial expanding populations could be subjected to environmental stresses. This study verifies and quantifies the importance of standing variation in adaptation in a cohort of genes, illustrating that the evolutionary potential of a population depends significantly on its preexisting genetic diversity. These findings provide important context for understanding adaptation and conservation of species in the Anthropocene. [ABSTRACT FROM AUTHOR]

Increasing evidence for rapid evolution suggests that the maintenance of species diversity in ecological communities may be influenced by more than purely ecological processes. Classic theory shows that interspecific competition may select for traits that increase niche differentiation, weakening competition and thus promoting species coexistence. While empirical work has demonstrated trait evolution in response to competition, if and how evolution affects the dynamics of the competing species--the key step for completing the required eco-evolutionary feedback--has been difficult to resolve. Here, we show that evolution in response to interspecific competition feeds back to change the course of competitive population dynamics of aquatic plant species over 10-15 generations in the field. By manipulating selection imposed by heterospecific competitors in experimental ponds, we demonstrate that (i) interspecific competition drives rapid genotypic change, and (ii) this evolutionary change in one competitor, while not changing the coexistence outcome, causes the population trajectories of the two competing species to converge. In contrast to the common expectation that interspecific competition should drive the evolution of niche differentiation, our results suggest that genotypic evolution resulted in phenotypic changes that altered population dynamics by affecting the competitive hierarchy. This result is consistent with theory suggesting that competition for essential resources can limit opportunities for the evolution of niche differentiation. Our finding that rapid evolution regulates the dynamics of competing species suggests that ecosystems may rely on continuous feedbacks between ecology and evolution to maintain species diversity. [ABSTRACT FROM AUTHOR]

Phylogenetic evidence suggests that the invasion and proliferation of retroelements, selfish mobile genetic elements that copy and paste themselves within a host genome, was one of the early evolutionary events in the emergence of eukaryotes. Here we test the effects of this event by determining the pressures retroelements exert on simple genomes. We transferred two retroelements, human LINE-1 and the bacterial group II intron Ll.LtrB, into bacteria, and find that both are functional and detrimental to growth. We find, surprisingly, that retroelement lethality and proliferation are enhanced by the ability to perform eukaryotic-like nonhomologous end-joining (NHEJ) DNA repair. We show that the only stable evolutionary consequence in simple cells is maintenance of retroelements in low numbers, suggesting how retro-transposition rates and costs in early eukaryotes could have been constrained to allow proliferation. Our results suggest that the interplay between NHEJ and retroelements may have played a fundamental and previously unappreciated role in facilitating the proliferation of retroelements, elements of which became the ancestors of the spliceosome components in eukaryotes. [ABSTRACT FROM AUTHOR]

The primate foot functions as a grasping organ. As such, its bones, soft tissues, and joints evolved to maximize power and stability in a variety of grasping configurations. Humans are the obvious exception to this primate pattern, with feet that evolved to support the unique biomechanical demands of bipedal locomotion. Of key functional importance to bipedalism is the morphology of the joints at the forefoot, known as the metatarsophalangeal joints (MTPJs), but a comprehensive analysis of homininMTPJ morphology is currently lacking. Here we present the results of a multivariate shape and Bayesian phylogenetic comparative analyses of metatarsals (MTs) from a broad selection of anthropoid primates (including fossil apes and stem catarrhines) and most of the early hominin pedal fossil record, including the oldest hominin for which good pedal remains exist, Ardipithecus ramidus. Results corroborate the importance of specific bony morphologies such as dorsal MT head expansion and "doming" to the evolution of terrestrial bipedalism in hominins. Further, our evolutionary models reveal that the MT1 of Ar. ramidus shifts away from the reconstructed optimum of our last common ancestor with apes, but not necessarily in the direction of modern humans. However, the lateral rays of Ar. ramidus are transformed in a more human-like direction, suggesting that they were the digits first recruited by hominins into the primary role of terrestrial propulsion. This pattern of evolutionary change is seen consistently throughout the evolution of the foot, highlighting the mosaic nature of pedal evolution and the emergence of a derived, modern hallux relatively late in human evolution. [ABSTRACT FROM AUTHOR]

Acid-sensing ion channels (ASICs) are proton-gated ion channels broadly expressed in the vertebrate nervous system, converting decreased extracellular pH into excitatory sodium current. ASICs were previously thought to be a vertebrate-specific branch of the DEG/ENaC family, a broadly conserved but functionally diverse family of channels. Here, we provide phylogenetic and experimental evidence that ASICs are conserved throughout deuterostome animals, showing that ASICs evolved over 600 million years ago. We also provide evidence of ASIC expression in the central nervous system of the tunicate, Oikopleura dioica. Furthermore, by comparing broadly related ASICs, we identify key molecular determinants of proton sensitivity and establish that proton sensitivity of the ASIC4 isoform was lost in the mammalian lineage. Taken together, these results suggest that contributions of ASICs to neuronal function may also be conserved broadly in numerous animal phyla. [ABSTRACT FROM AUTHOR]

Polypentagonal water networks were recently observed in a protein capable of binding to ice crystals, or ice-binding protein (IBP). To examine such water networks and clarify their role in icebinding, we determined X-ray crystal structures of a 65-residue defective isoform of a Zoarcidae-derived IBP (wild type, WT) and its five single mutants (A20L, A20G, A20T, A20V, and A20I). Polypentagonal water networks composed of ~50 semiclathrate waters were observed solely on the strongest A20I mutant, which appeared to include a tetrahedral water cluster exhibiting a perfect position match to the (10110) first prism plane of a single ice crystal. Inclusion of another symmetrical water cluster in the polypentagonal network showed a perfect complementarity to the waters constructing the (20221) pyramidal ice plane. The order of ice-binding strength was A20L < A20G < WT < A20T < A20V < A20I, where the top three mutants capable of binding to the first prism and the pyramidal ice planes commonly contained a bifurcated γ-CH3 group. These results suggest that a fine-tuning of the surface of Zoarcidae-derived IBP assisted by a side-chain group regulates the holding property of its polypentagonal water network, the function of which is to freeze the host protein to specific ice planes. [ABSTRACT FROM AUTHOR]

Viruses are remarkable nanomachines that efficiently hijack cellular functions to replicate and self-assemble their components within a complex biological environment. As all steps of the viral life cycle depend on formation of a protective proteinaceous shell that packages the DNA or RNA genome, bottom-up construction of virus-like nucleocapsids from nonviral materials could provide valuable insights into virion assembly and evolution. Such constructs could also serve as safe alternatives to natural viruses for diverse nano- and biotechnological applications. Here we show that artificial virus-like nucleocapsids can be generated-rapidly and surprisingly easily-by engineering and laboratory evolution of a nonviral protein cage formed by Aquifex aeolicus lumazine synthase (AaLS) and its encoding mRNA. Cationic peptides were appended to the engineered capsid proteins to enable specific recognition of packaging signals on cognate mRNAs, and subsequent evolutionary optimization afforded nucleocapsids with expanded spherical structures that encapsulate their own full-length RNA genome in vivo and protect the cargo molecules from nucleases. These findings provide strong experimental support for the hypothesis that subcellular protein-bounded compartments may have facilitated the emergence of ancient viruses. [ABSTRACT FROM AUTHOR]

The evolutionary emergence of humans' remarkably economical walking gait remains a focus of research and debate, but experimentally validated approaches linking locomotor capability to postcranial anatomy are limited. In this study, we integrated 3D morphometrics of hominoid pelvic shape with experimental measurements of hip kinematics and kinetics during walking and climbing, hamstring activity, and passive range of hip extension in humans, apes, and other primates to assess arboreal-terrestrial trade-offs in ischium morphology among living taxa. We show that hamstring-powered hip extension during habitual walking and climbing in living apes and humans is strongly predicted, and likely constrained, by the relative length and orientation of the ischium. Ape pelves permit greater extensor moments at the hip, enhancing climbing capability, but limit their range of hip extension, resulting in a crouched gait. Human pelves reduce hip extensor moments but permit a greater degree of hip extension, which greatly improves walking economy (i.e., distance traveled/energy consumed). Applying these results to fossil pelves suggests that early hominins differed from both humans and extant apes in having an economical walking gait without sacrificing climbing capability. Ardipithecus was capable of nearly human-like hip extension during bipedal walking, but retained the capacity for powerful, ape-like hip extension during vertical climbing. Hip extension capability was essentially human-like in Australopithecus afarensis and Australopithecus africanus, suggesting an economical walking gait but reduced mechanical advantage for powered hip extension during climbing. [ABSTRACT FROM AUTHOR]

The Bayesian method is noted to produce spuriously high posterior probabilities for phylogenetic trees in analysis of large datasets, but the precise reasons for this overconfidence are unknown. In general, the performance of Bayesian selection of misspecified models is poorly understood, even though this is of great scientific interest since models are never true in real data analysis. Here we characterize the asymptotic behavior of Bayesian model selection and show that when the competing models are equally wrong, Bayesian model selection exhibits surprising and polarized behaviors in large datasets, supporting one model with full force while rejecting the others. If one model is slightly less wrong than the other, the less wrong model will eventually win when the amount of data increases, but the method may become overconfident before it becomes reliable. We suggest that this extreme behavior may be a major factor for the spuriously high posterior probabilities for evolutionary trees. The philosophical implications of our results to the application of Bayesian model selection to evaluate opposing scientific hypotheses are yet to be explored, as are the behaviors of non-Bayesian methods in similar situations. [ABSTRACT FROM AUTHOR]

Slowing the evolution of antimicrobial resistance is essential if we are to continue to successfully treat infectious diseases. Whether a drug-resistant mutant grows to high densities, and so sickens the patient and spreads to new hosts, is determined by the competitive interactions it has with drug-susceptible pathogens within the host. Competitive interactions thus represent a good target for resistance management strategies. Using an in vivo model of malaria infection, we show that limiting a resource that is disproportionately required by resistant parasites retards the evolution of drug resistance by intensifying competitive interactions between susceptible and resistant parasites. Resource limitation prevented resistance emergence regardless of whether resistant mutants arose de novo or were experimentally added before drug treatment. Our work provides proof of principle that chemotherapy paired with an "ecological" intervention can slow the evolution of resistance to antimicrobial drugs, even when resistant pathogens are present at high frequencies. It also suggests that a broad range of previously untapped compounds could be used for treating infectious diseases. [ABSTRACT FROM AUTHOR]

Nonideal, nonsingle-domain magnetic grains are ubiquitous in rocks; however, they can have a detrimental impact on the fidelity of paleomagnetic records--in particular the determination of ancient magnetic field strength (paleointensity), a key means of understanding the evolution of the earliest geodynamo and the formation of the solar system. As a consequence, great effort has been expended to link rock magnetic behavior to paleointensity results, but with little quantitative success. Using the most comprehensive rock magnetic and paleointensity data compilations, we quantify a stability trend in hysteresis data that characterizes the bulk domain stability (BDS) of the magnetic carriers in a paleomagnetic specimen. This trend is evident in both geological and archeological materials that are typically used to obtain paleointensity data and is therefore pervasive throughout most paleomagnetic studies. Comparing this trend to paleointensity data from both laboratory and historical experiments reveals a quantitative relationship between BDS and paleointensity behavior. Specimens that have lower BDS values display higher curvature on the paleointensity analysis plot, which leads to more inaccurate results. In-field quantification of BDS therefore reflects low-field bulk remanence stability. Rapid hysteresis measurements can be used to provide a powerful quantitative method for preselecting paleointensity specimens and postanalyzing previous studies, further improving our ability to select high-fidelity recordings of ancient magnetic fields. BDS analyses will enhance our ability to understand the evolution of the geodynamo and can help in understanding many fundamental Earth and planetary science questions that remain shrouded in controversy. [ABSTRACT FROM AUTHOR]

Biology is marked by a hierarchical organization: all life consists of cells; in some cases, these cells assemble into groups, such as endosymbionts or multicellular organisms; in turn, multicellular organisms sometimes assemble into yet other groups, such as primate societies or ant colonies. The construction of new organizational layers results from hierarchical evolutionary transitions, in which biological units (e.g., cells) form groups that evolve into new units of biological organization (e.g., multicellular organisms). Despite considerable advances, there is no bottom-up, dynamical account of how, starting from the solitary ancestor, the first groups originate and subsequently evolve the organizing principles that qualify them as new units. Guided by six central questions, we propose an integrative bottom-up approach for studying the dynamics underlying hierarchical evolutionary transitions, which builds on and synthesizes existing knowledge. This approach highlights the crucial role of the ecology and development of the solitary ancestor in the emergence and subsequent evolution of groups, and it stresses the paramount importance of the life cycle: only by evaluating groups in the context of their life cycle can we unravel the evolutionary trajectory of hierarchical transitions. These insights also provide a starting point for understanding the types of subsequent organizational complexity. The central research questions outlined here naturally link existing research programs on biological construction (e.g., on cooperation, multilevel selection, self-organization, and development) and thereby help integrate knowledge stemming from diverse fields of biology. [ABSTRACT FROM AUTHOR]

Fungi belong to one of the largest and most diverse kingdoms of living organisms. The evolutionary kinship within a fungal population has so far been inferred mostly from the gene-information-based trees ("gene trees"), constructed commonly based on the degree of differences of proteins or DNA sequences of a small number of highly conserved genes common among the population by a multiple sequence alignment (MSA) method. Since each gene evolves under different evolutionary pressure and time scale, it has been known that one gene tree for a population may differ from other gene trees for the same population depending on the subjective selection of the genes. Within the last decade, a large number of whole-genome sequences of fungi have become publicly available, which represent, at present, the most fundamental and complete information about each fungal organism. This presents an opportunity to infer kinship among fungi using a whole-genome information-based tree ("genome tree"). The method we used allows comparison of whole-genome information without MSA, and is a variation of a computational algorithm developed to find semantic similarities or plagiarism in two books, where we represent whole-genomic information of an organism as a book of words without spaces. The genome tree reveals several significant and notable differences from the gene trees, and these differences invoke new discussions about alternative narratives for the evolution of some of the currently accepted fungal groups. [ABSTRACT FROM AUTHOR]

When humans and other animals make cultural innovations, they also change their environment, thereby imposing new selective pressures that can modify their biological traits. For example, there is evidence that dairy farming by humans favored alleles for adult lactose tolerance. Similarly, the invention of cooking possibly affected the evolution of jaw and tooth morphology. However, when it comes to cognitive traits and learning mechanisms, it is much more difficult to determine whether and how their evolution was affected by culture or by their use in cultural transmission. Here we argue that, excluding very recent cultural innovations, the assumption that culture shaped the evolution of cognition is both more parsimonious and more productive than assuming the opposite. In considering how culture shapes cognition, we suggest that a process-level model of cognitive evolution is necessary and offer such a model. The model employs relatively simple coevolving mechanisms of learning and data acquisition that jointly construct a complex network of a type previously shown to be capable of supporting a range of cognitive abilities. The evolution of cognition, and thus the effect of culture on cognitive evolution, is captured through small modifications of these coevolving learning and data-acquisition mechanisms, whose coordinated action is critical for building an effective network. We use the model to show how these mechanisms are likely to evolve in response to cultural phenomena, such as language and tool-making, which are associated with major changes in data patterns and with new computational and statistical challenges. [ABSTRACT FROM AUTHOR]

The article focuses on role of animal culture to drive evolution. It offers information on Killer whales that have a geographic range stretching from the Antarctic to the Arctic; and mentions two streams of information of animal populations such as genetic and cultural. It also reflects on cultural hitchhiking at work in a population of bottlenose dolphins in western Shark Bay, Western Australia.

Phenological responses of vegetation to climate, in particular to the ongoing warming trend, have received much attention. However, divergent results from the analyses of remote sensing data have been obtained for the Tibetan Plateau (TP), the world's largest highelevation region. This study provides a perspective on vegetation phenology shifts during 1960-2014, gained using an innovative approach based on a well-validated, process-based, tree-ring growth model that is independent of temporal changes in technical properties and image quality of remote sensing products. Twenty composite site chronologies were analyzed, comprising about 3,000 trees from forested areas across the TP. We found that the start of the growing season (SOS) has advanced, on average, by 0.28 d/y over the period 1960-2014. The end of the growing season (EOS) has been delayed, by an estimated 0.33 d/y during 1982-2014. No significant changes in SOS or EOS were observed during 1960-1981. April-June and August-September minimum temperatures are the main climatic drivers for SOS and EOS, respectively. An increase of 1 °C in April-June minimum temperature shifted the dates of xylem phenology by 6 to 7 d, lengthening the period of tree-ring formation. This study extends the chronology of TP phenology farther back in time and reconciles the disparate views on SOS derived from remote sensing data. Scaling up this analysis may improve understanding of climate change effects and related phenological and plant productivity on a global scale. [ABSTRACT FROM AUTHOR]

Animals have evolved an array of pattern-recognition receptor families essential for recognizing conserved molecular motifs characteristic of pathogenic microbes. One such family is the Tolllike receptors (TLRs). On pathogen binding, TLRs initiate specialized cytokine signaling catered to the class of invading pathogen. This signaling is pivotal for activating adaptive immunity in vertebrates, suggesting a close evolutionary relationship between innate and adaptive immune systems. Despite significant advances toward understanding TLR-facilitated immunity in vertebrates, knowledge of TLR pathway evolution in other deuterostomes is limited. By analyzing genomes and transcriptomes across 37 deuterostome taxa, we shed light on the evolution and diversity of TLR pathway signaling elements. Here, we show that the deuterostome ancestor possessed a molecular toolkit homologous to that which drives canonical MYD88- dependent TLR signaling in contemporary mammalian lineages. We also provide evidence that TLR3-facilitated antiviral signaling predates the origin of its TCAM1 dependence recognized in the vertebrates. SARM1, a negative regulator of TCAM1-dependent pathways in vertebrates, was also found to be present across all major deuterostome lineages despite the apparent absence of TCAM1 in invertebrate deuterostomes. Whether the presence of SARM1 is the result of its role in immunity regulation, neuron physiology, or a function of both is unclear. Additionally, Bayesian phylogenetic analyses corroborate several lineage-specific TLR gene expansions in urchins and cephalochordates. Importantly, our results underscore the need to sample across taxonomic groups to understand evolutionary patterns of the innate immunity foundation on which complex immunological novelties arose. [ABSTRACT FROM AUTHOR]

Recently, a rigorous mathematical theory has been developed for spatial games with weak selection, i.e., when the payoff differences between strategies are small. The key to the analysis is that when space and time are suitably rescaled, the spatial model converges to the solution of a partial differential equation (PDE). This approach can be used to analyze all 2 x 2 games, but there are a number of 3 x 3 games for which the behavior of the limiting PDE is not known. In this paper, we give rules for determining the behavior of a large class of 3 x 3 games and check their validity using simulation. In words, the effect of space is equivalent to making changes in the payoff matrix, and once this is done, the behavior of the spatial game can be predicted from the behavior of the replicator equation for the modified game. We say predicted here because in some cases the behavior of the spatial game is different from that of the replicator equation for the modified game. For example, if a rock-paper-scissors game has a replicator equation that spirals out to the boundary, space stabilizes the system and produces an equilibrium. [ABSTRACT FROM AUTHOR]

New genes can arise by duplication and divergence, but there is a fundamental gap in our understanding of the relationship between these genes, the evolving proteins they encode, and the fitness of the organism. Here we used crystallography, NMR dynamics, kinetics, and mass spectrometry to explain the molecular innovations that arose during a previous real-time evolution experiment. In that experiment, the (βα)8 barrel enzyme HisA was under selection for two functions (HisA and TrpF), resulting in duplication and divergence of the hisA gene to encode TrpF specialists, HisA specialists, and bifunctional generalists. We found that selection affects enzyme structure and dynamics, and thus substrate preference, simultaneously and sequentially. Bifunctionality is associated with two distinct sets of loop conformations, each essential for one function. We observed two mechanisms for functional specialization: structural stabilization of each loop conformation and substrate-specific adaptation of the active site. Intracellular enzyme performance, calculated as the product of catalytic efficiency and relative expression level, was not linearly related to fitness. Instead, we observed thresholds for each activity above which further improvements in catalytic efficiency had little if any effect on growth rate. Overall, we have shown how beneficial substitutions selected during real-time evolution can lead to manifold changes in enzyme function and bacterial fitness. This work emphasizes the speed at which adaptive evolution can yield enzymes with sufficiently high activities such that they no longer limit the growth of their host organism, and confirms the (βα)8 barrel as an inherently evolvable protein scaffold. [ABSTRACT FROM AUTHOR]

During adolescence, the human cortex undergoes substantial remodeling to support a rapid expansion of behavioral repertoire. Accurately quantifying these changes is a prerequisite for understanding normal brain development, as well as the neuropsychiatric disorders that emerge in this vulnerable period. Past accounts have demonstrated substantial regional heterogeneity in patterns of brain development, but frequently have been limited by small samples and analytics that do not evaluate complex multivariate imaging patterns. Capitalizing on recent advances in multivariate analysis methods, we used nonnegative matrix factorization (NMF) to uncover coordinated patterns of cortical development in a sample of 934 youths ages 8–20, who completed structural neuroimaging as part of the Philadelphia Neurodevelopmental Cohort. Patterns of structural covariance (PSCs) derived by NMF were highly reproducible over a range of resolutions, and differed markedly from common gyral-based structural atlases. Moreover, PSCs were largely symmetric and showed correspondence to specific large-scale functional networks. The level of correspondence was ordered according to their functional role and position in the evolutionary hierarchy, being high in lower-order visual and somatomotor networks and diminishing in higher-order association cortex. Furthermore, PSCs showed divergent developmental associations, with PSCs in higher-order association cortex networks showing greater changes with age than primary somatomotor and visual networks. Critically, such developmental changes within PSCs were significantly associated with the degree of evolutionary cortical expansion. Together, our findings delineate a set of structural brain networks that undergo coordinated cortical thinning during adolescence, which is in part governed by evolutionary novelty and functional specialization. [ABSTRACT FROM AUTHOR]

Intrinsically disordered regions (IDRs) are characterized by their lack of stable secondary or tertiary structure and comprise a large part of the eukaryotic proteome. Although these regions play a variety of signaling and regulatory roles, they appear to be rapidly evolving at the primary sequence level. To understand the functional implications of this rapid evolution, we focused on a highly diverged IDR in Saccharomyces cerevisiae that is involved in regulating multiple conserved MAPK pathways. We hypothesized that under stabilizing selection, the functional output of orthologous IDRs could be maintained, such that diverse genotypes could lead to similar function and fitness. Consistent with the stabilizing selection hypothesis, we find that diverged, orthologous IDRs can mostly recapitulate wildtype function and fitness in S. cerevisiae. We also find that the electrostatic charge of the IDR is correlated with signaling output and, using phylogenetic comparative methods, find evidence for selection maintaining this quantitative molecular trait despite underlying genotypic divergence. [ABSTRACT FROM AUTHOR]

There are intriguing parallels between plants and animals, with respect to the structures of their innate immune receptors, that suggest universal principles of innate immunity. The cytosolic nucleotide binding site-leucine rich repeat (NBS-LRR) resistance proteins of plants (R-proteins) and the so-called NOD-like receptors of animals (NLRs) share a domain architecture that includes a STAND (signal transduction ATPases with numerous domains) family NTPase followed by a series of LRRs, suggesting inheritance from a common ancestor with that architecture. Focusing on the STAND NTPases of plant R-proteins, animal NLRs, and their homologs that represent the NB-ARC (nucleotide- binding adaptor shared by APAF-1, certain R gene products and CED-4) and NACHT (named for NAIP, CIIA, HET-E, and TEP1) subfamilies of the STAND NTPases, we analyzed the phylogenetic distribution of the NBS-LRR domain architecture, used maximum-likelihood methods to infer a phylogeny of the NTPase domains of R-proteins, and reconstructed the domain structure of the protein containing the common ancestor of the STAND NTPase domain of R-proteins and NLRs. Our analyses reject monophyly of plant R-proteins and NLRs and suggest that the protein containing the last common ancestor of the STAND NTPases of plant R-proteins and animal NLRs (and, by extension, all NB-ARC and NACHT domains) possessed a domain structure that included a STAND NTPase paired with a series of tetratricopeptide repeats. These analyses reject the hypothesis that the domain architecture of R-proteins and NLRs was inherited from a common ancestor and instead suggest the domain architecture evolved at least twice. It remains unclear whether the NBS-LRR architectures were innovations of plants and animals themselves or were acquired by one or both lineages through horizontal gene transfer. [ABSTRACT FROM AUTHOR]

Vibrio cholerae has caused seven cholera pandemics since 1817, imposing terror on much of the world, but bacterial strains are currently only available for the sixth and seventh pandemics. The El Tor biotype seventh pandemic began in 1961 in Indonesia, but did not originate directly from the classical biotype sixth-pandemic strain. Previous studies focused mainly on the spread of the seventh pandemic after 1970. Here, we analyze in unprecedented detail the origin, evolution, and transition to pandemicity of the seventh-pandemic strain. We used high-resolution comparative genomic analysis of strains collected from 1930 to 1964, covering the evolution from the first available El Tor biotype strain to the start of the seventh pandemic. We define six stages leading to the pandemic strain and reveal all key events. The seventh pandemic originated from a nonpathogenic strain in the Middle East, first observed in 1897. It subsequently underwent explosive diversification, including the spawning of the pandemic lineage. This rapid diversification suggests that, when first observed, the strain had only recently arrived in theMiddle East, possibly from the Asian homeland of cholera. The lineage migrated toMakassar, Indonesia, where it gained the important virulence-associated elements Vibrio seventh pandemic island I (VSP-I), VSP-II, and El Tor type cholera toxin prophage by 1954, and it then became pandemic in 1961 after only 12 additional mutations. Our data indicate that specific niches in the Middle East and Makassar were important in generating the pandemic strain by providing gene sources and the driving forces for genetic events. [ABSTRACT FROM AUTHOR]

The naming of colors has long been a topic of interest in the study of human culture and cognition. Color term research has asked diverse questions about thought and communication, but no previous research has used an evolutionary framework. We show that there is broad support for the most influential theory of color term development (most strongly represented by Berlin and Kay [Berlin B, Kay P (1969) (Univ of California Press, Berkeley, CA)]); however, we find extensive evidence for the loss (as well as gain) of color terms. We find alternative trajectories of color term evolution beyond those considered in the standard theories. These results not only refine our knowledge of how humans lexicalize the color space and how the systems change over time; they illustrate the promise of phylogenetic methods within the domain of cognitive science, and they show how language change interacts with human perception. [ABSTRACT FROM AUTHOR]

Proper folding of proteins is critical to producing the biological machinery essential for cellular function. The rates and energetics of a protein's folding process, which is described by its energy landscape, are encoded in the amino acid sequence. Over the course of evolution, this landscape must be maintained such that the protein folds and remains folded over a biologically relevant time scale. How exactly a protein's energy landscape is maintained or altered throughout evolution is unclear. To study how a protein's energy landscape changed over time, we characterized the folding trajectories of ancestral proteins of the ribonuclease H (RNase H) family using ancestral sequence reconstruction to access the evolutionary history between RNases H from mesophilic and thermophilic bacteria. We found that despite large sequence divergence, the overall folding pathway is conserved over billions of years of evolution. There are robust trends in the rates of protein folding and unfolding; both modern RNases H evolved to be more kinetically stable than their most recent common ancestor. Finally, our study demonstrates how a partially folded intermediate provides a readily adaptable folding landscape by allowing the independent tuning of kinetics and thermodynamics. [ABSTRACT FROM AUTHOR]

Organisms can adapt to a randomly varying environment by creating phenotypic diversity in their population, a phenomenon often referred to as "bet hedging." The favorable level of phenotypic diversity depends on the statistics of environmental variations over timescales of many generations. Could organisms gather such long-term environmental information to adjust their phenotypic diversity? We show that this process can be achieved through a simple and general learning mechanism based on a transgenerational feedback: The phenotype of the parent is progressively reinforced in the distribution of phenotypes among the offspring. The molecular basis of this learning mechanism could be searched for in model organisms showing epigenetic inheritance. [ABSTRACT FROM AUTHOR]

The ATP synthase (F-ATPase) is a highly complex rotary machine that synthesizes ATP, powered by a proton electrochemical gradient. Why did evolution select such an elaborate mechanism over arguably simpler alternating-access processes that can be reversed to perform ATP synthesis? We studied a systematic enumeration of alternative mechanisms, using numerical and theoretical means. When the alternative models are optimized subject to fundamental thermodynamic constraints, they fail to match the kinetic ability of the rotary mechanism over a wide range of conditions, particularly under low-energy conditions. We used a physically interpretable, closed-form solution for the steady-state rate for an arbitrary chemical cycle, which clarifies kinetic effects of complex free-energy landscapes. Our analysis also yields insights into the debated "kinetic equivalence" of ATP synthesis driven by transmembrane pH and potential difference. Overall, our study suggests that the complexity of the F-ATPase may have resulted from positive selection for its kinetic advantage. [ABSTRACT FROM AUTHOR]

Evolution of complexity in eukaryotic proteomes has arisen, in part, through emergence of modular independently folded domains mediating protein interactions via binding to short linear peptides in proteins. Over 30 years, structural properties and sequence preferences of these peptides have been extensively characterized. Less successful, however, were efforts to establish relationships between physicochemical properties and functions of domain- peptide interactions. To our knowledge, we have devised the first strategy to exhaustively explore the binding specificity of protein domain-peptide interactions. We applied the strategy to SH3 domains to determine the properties of their binding peptides starting from various experimental data. The strategy identified the majority (~70%) of experimentally determined SH3 binding sites. We discovered mutual relationships among binding specificity, binding affinity, and structural properties and evolution of linear peptides. Remarkably, we found that these properties are also related to functional diversity, defined by depth of proteins within hierarchies of gene ontologies. Our results revealed that linear peptides evolved to coadapt specificity and affinity to functional diversity of domain-peptide interactions. Thus, domain-peptide interactions follow human-constructed gene ontologies, which suggest that our understanding of biological process hierarchies reflect the way chemical and thermodynamic properties of linear peptides and their interaction networks, in general, have evolved. [ABSTRACT FROM AUTHOR]

The article offers information on the research related to a mechanism for coexistence that couples niche and neutral processes together with rapid evolution. It mentions explanations for coexistence that the two species are either so dissimilar that they compete very little with each other ( niche explanation) or are so similar that they coexist for a long, but not infinite (neutral explanation) and also highlights the need for a more integrated field that spans both ecology and evolution.

The article focuses on understanding genetic changes between generations by investigating the allele frequency and the gene flow. Topics discussed include study conducted by monitoring wild population of Florida Scrub-Jays, Aphelocoma coerulescens, role of fitness measurement in evolutionary process, and unpredictability of the species due to migration.

We use a microfabricated ecology with a doxorubicin gradient and population fragmentation to produce a strong Darwinian selective pressure that drives forward the rapid emergence of doxorubicin resistance in multiple myeloma (MM) cancer cells. RNA sequencing of the resistant cells was used to examine (i) emergence of genes with high de novo substitution densities (i.e., hot genes) and (ii) genes never substituted (i.e., cold genes). The set of cold genes, which were 21% of the genes sequenced, were further winnowed down by examining excess expression levels. Both the most highly substituted genes and the most highly expressed never-substituted genes were biased in age toward the most ancient of genes. This would support the model that cancer represents a revision back to ancient forms of life adapted to high fitness under extreme stress, and suggests that these ancient genes may be targets for cancer therapy. [ABSTRACT FROM AUTHOR]

The role of symbiosis in bacterial symbiont genome evolution is well understood, yet the ways that symbiosis shapes host genomes or more particularly, host/symbiont genome coevolution in the holobiont is only now being revealed. Here, we identify three coevolutionary signatures that characterize holobiont genomes. The first signature, host/symbiont collaboration, arises when completion of essential pathways requires host/endosymbiont genome complementarity. Metabolic collaboration has evolved numerous times in the pathways of amino acid and vitamin biosynthesis. Here, we highlight collaboration in branched-chain amino acid and pantothenate (vitamin B5) biosynthesis. The second coevolutionary signature is acquisition, referring to the observation that holobiont genomes acquire novel genetic material through various means, including gene duplication, lateral gene transfer from bacteria that are not their current obligate symbionts, and full or partial endosymbiont replacement. The third signature, constraint, introduces the idea that holobiont genome evolution is constrained by the processes governing symbiont genome evolution. In addition, we propose that collaboration is constrained by the expression profile of the cell lineage from which endosymbiont-containing host cells, called bacteriocytes, are derived. In particular, we propose that such differences in bacteriocyte cell lineage may explain differences in patterns of host/endosymbiont metabolic collaboration between the sap-feeding suborders Sternorrhyncha and Auchenorrhynca. Finally, we review recent studies at the frontier of symbiosis research that are applying functional genomic approaches to characterization of the developmental and cellular mechanisms of host/endosymbiont integration, work that heralds a new era in symbiosis research. [ABSTRACT FROM AUTHOR]

The evolution of life on earth has been driven by a small number of major evolutionary transitions. These transitions have been characterized by individuals that could previously replicate independently, cooperating to form a new, more complex life form. For example, archaea and eubacteria formed eukaryotic cells, and cells formed multicellular organisms. However, not all cooperative groups are en route to major transitions. How can we explain why major evolutionary transitions have or haven't taken place on different branches of the tree of life? We break down major transitions into two steps: the formation of a cooperative group and the transformation of that group into an integrated entity. We show how these steps require cooperation, division of labor, communication, mutual dependence, and negligible within-group conflict. We find that certain ecological conditions and the ways in which groups form have played recurrent roles in driving multiple transitions. In contrast, we find that other factors have played relatively minor roles at many key points, such as within-group kin discrimination and mechanisms to actively repress competition. More generally, by identifying the small number of factors that have driven major transitions, we provide a simpler and more unified description of how life on earth has evolved. [ABSTRACT FROM AUTHOR]

Historically, conceptualizations of symbiosis and endosymbiosis have been pitted against Darwinian or neo-Darwinian evolutionary theory. In more recent times, Lynn Margulis has argued vigorously along these lines. However, there are only shallow grounds for finding Darwinian concepts or population genetic theory incompatible with endosymbiosis. But is population genetics sufficiently explanatory of endosymbiosis and its role in evolution? Population genetics "follows" genes, is replication-centric, and is concerned with vertically consistent genetic lineages. It may also have explanatory limitations with regard to macroevolution. Even so, asking whether population genetics explains endosymbiosis may have the question the wrong way around. We should instead be asking how explanatory of evolution endosymbiosis is, and exactly which features of evolution it might be explaining. This paper will discuss how metabolic innovations associated with endosymbioses can drive evolution and thus provide an explanatory account of important episodes in the history of life. Metabolic explanations are both proximate and ultimate, in the same way genetic explanations are. Endosymbioses, therefore, point evolutionary biology toward an important dimension of evolutionary explanation. [ABSTRACT FROM AUTHOR]

Setting aside high-quality large areas of habitat to protect threatened populations is becoming increasingly difficult as humans fragment and degrade the environment. Biologists and managers therefore must determine the best way to shepherd small populations through the dual challenges of reductions in both the number of individuals and genetic variability. By bringing in additional individuals, threatened populations can be increased in size (demographic rescue) or provided with variation to facilitate adaptation and reduce inbreeding (genetic rescue). The relative strengths of demographic and genetic rescue for reducing extinction and increasing growth of threatened populations are untested, and which type of rescue is effective may vary with population size. Using the flour beetle (Tribolium castaneum) in a microcosm experiment, we disentangled the genetic and demographic components of rescue, and compared them with adaptation from standing genetic variation (evolutionary rescue in the strictest sense) using 244 experimental populations founded at either a smaller (50 individuals) or larger (150 individuals) size. Both types of rescue reduced extinction, and those effects were additive. Over the course of six generations, genetic rescue increased population sizes and intrinsic fitness substantially. Both large and small populations showed evidence of being able to adapt from standing genetic variation. Our results support the practice of genetic rescue in facilitating adaptation and reducing inbreeding depression, and suggest that demographic rescue alone may suffice in larger populations even if only moderately inbred individuals are available for addition. [ABSTRACT FROM AUTHOR]

This paper develops a conceptual framework for addressing questions about reproduction, individuality, and the units of selection in symbiotic associations, with special attention to the origin of the eukaryotic cell. Three kinds of reproduction are distinguished, and a possible evolutionary sequence giving rise to a mitochondrion-containing eukaryotic cell from an endosymbiotic partnership is analyzed as a series of transitions between each of the three forms of reproduction. The sequence of changes seen in this "egalitarian" evolutionary transition is compared with those that apply in "fraternal" transitions, such as the evolution of multi-cellularity in animals. [ABSTRACT FROM AUTHOR]

This paper considers whether multispecies biofilms are evolutionary individuals. Numerous multispecies biofilms have characteristics associated with individuality, such as internal integrity, division of labor, coordination among parts, and heritable adaptive traits. However, such multispecies biofilms often fail standard reproductive criteria for individuality: they lack reproductive bottlenecks, are comprised of multiple species, do not form unified reproductive lineages, and fail to have a significant division of reproductive labor among their parts. If such biofilms are good candidates for evolutionary individuals, then evolutionary individuality is achieved through other means than frequently cited reproductive processes. The case of multispecies biofilms suggests that standard reproductive requirements placed on individuality should be reconsidered. More generally, the case of multispecies biofilms indicates that accounts of individuality that focus on single-species eukaryotes are too restrictive and that a pluralistic and open-ended account of evolutionary individuality is needed. [ABSTRACT FROM AUTHOR]

Eukaryogenesis is widely viewed as an improbable evolutionary transition uniquely affecting the evolution of life on this planet. However, scientific and popular rhetoric extolling this event as a singularity lacks rigorous evidential and statistical support. Here, we question several of the usual claims about the specialness of eukaryogenesis, focusing on both eukaryogenesis as a process and its outcome, the eukaryotic cell. We argue in favor of four ideas. First, the criteria by which we judge eukaryogenesis to have required a genuinely unlikely series of events 2 billion years in the making are being eroded by discoveries that fill in the gaps of the prokaryote:eukaryote "discontinuity." Second, eukaryogenesis confronts evolutionary theory in ways not different from other evolutionary transitions in individuality; parallel systems can be found at several hierarchical levels. Third, identifying which of several complex cellular features confer on eukaryotes a putative richer evolutionary potential remains an area of speculation: various keys to success have been proposed and rejected over the five-decade history of research in this area. Fourth, and perhaps most importantly, it is difficult and may be impossible to eliminate eukaryocentric bias from the measures by which eukaryotes as a whole are judged to have achieved greater success than prokaryotes as a whole. Overall, we question whether premises of existing theories about the uniqueness of eukaryogenesis and the greater evolutionary potential of eukaryotes have been objectively formulated and whether, despite widespread acceptance that eukaryogenesis was "special," any such notion has more than rhetorical value. [ABSTRACT FROM AUTHOR]

Frequency-dependent selection and demographic fluctuations play important roles in evolutionary and ecological processes. Under frequency-dependent selection, the average fitness of the population may increase or decrease based on interactions between individuals within the population. This should be reflected in fluctuations of the population size even in constant environments. Here, we propose a stochastic model that naturally combines these two evolutionary ingredients by assuming frequency-dependent competition between different types in an individual-based model. In contrast to previous game theoretic models, the carrying capacity of the population, and thus the population size, is determined by pairwise competition of individuals mediated by evolutionary games and demographic stochasticity. In the limit of infinite population size, the averaged stochastic dynamics is captured by deterministic competitive Lotka--Volterra equations. In small populations, demographic stochasticity may instead lead to the extinction of the entire population. Because the population size is driven by fitness in evolutionary games, a population of cooperators is less prone to go extinct than a population of defectors, whereas in the usual systems of fixed size the population would thrive regardless of its average payoff. [ABSTRACT FROM AUTHOR]

The article offers the author's insights on the study where synthetic biologists has used experimental evolution in healing scars. Topics mentioned include the in corporation of nonstandard amino acids (nsAA) to the biochemical creativity of proteins, the genome recoding of organisms that will incorporate artificial amino acids, and the production of Escherichia coli bacteria strain.

The article reflects on insights related to tiny bird fossils that are among the most diverse and widely distributed groups of vertebrate animals. It highlights controversies related to attempts correlating with the geological time scale with important events early in modern bird evolutionary history. It also highlights future efforts to refine understanding of how modern birds obtain their characteristic geographic distributions.

Whole-genome duplication (WGD) events have occurred repeatedly during flowering plant evolution, and there is growing evidence for predictable patterns of gene retention and loss following polyploidization. Despite these important insights, the rate and processes governing the earliest stages of diploidization remain poorly understood, and the relative importance of genetic drift, positive selection, and relaxed purifying selection in the process of gene degeneration and loss is unclear. Here, we conduct whole-genome resequencing in Capsella bursa-pastoris, a recently formed tetraploid with one of the most widespread species distributions of any angiosperm. Whole-genome data provide strong support for recent hybrid origins of the tetraploid species within the past 100,000-300,000 y from two diploid progenitors in the Capsella genus. Major-effect inactivating mutations are frequent, but many were inherited from the parental species and show no evidence of being fixed by positive selection. Despite a lack of large-scale gene loss, we observe a decrease in the efficacy of natural selection genome-wide due to the combined effects of demography, selfing, and genome redundancy from WGD. Our results suggest that the earliest stages of diploidization are associated with quantitative genome-wide decreases in the strength and efficacy of selection rather than rapid gene loss, and that non-functionalization can receive a "head start" through a legacy of deleterious variants and differential expression originating in parental diploid populations. [ABSTRACT FROM AUTHOR]