The evolutionary maintenance of Lévy flight foraging.

Lévy flight is a type of random walk that characterizes the behaviour of many natural phenomena studied across a multiplicity of academic disciplines; within biology specifically, the behaviour of fish, birds, insects, mollusks, bacteria, plants, slime molds, t-cells, and human populations. The Lévy flight foraging hypothesis states that because Lévy flights can maximize an organism's search efficiency, natural selection should result in Lévy-like behaviour. Empirical and theoretical research has provided ample evidence of Lévy walks in both extinct and extant species, and its efficiency across models with a diversity of resource distributions. However, no model has addressed the maintenance of Lévy flight foraging through evolutionary processes, and existing models lack ecological breadth. We use numerical simulations, including lineage-based models of evolution with a distribution of move lengths as a variable and heritable trait, to test the Lévy flight foraging hypothesis. We include biological and ecological contexts such as population size, searching costs, lifespan, resource distribution, speed, and consider both energy accumulated at the end of a lifespan and averaged over a lifespan. We demonstrate that selection often results in Lévy-like behaviour, although conditional; smaller populations, longer searches, and low searching costs increase the fitness of Lévy-like behaviour relative to Brownian behaviour. Interestingly, our results also evidence a bet-hedging strategy; Lévy-like behaviour reduces fitness variance, thus maximizing geometric mean fitness over multiple generations.

The evolution of moral rules in a model of indirect reciprocity with private assessment.

Moral rules allow humans to cooperate by indirect reciprocity. Yet, it is not clear which moral rules best implement indirect reciprocity and are favoured by natural selection. Previous studies either considered only public assessment, where individuals are deemed good or bad by all others, or compared a subset of possible strategies. Here we fill this gap by identifying which rules are evolutionary stable strategies (ESS) among all possible moral rules while considering private assessment. We develop an analytical model describing the frequency of long-term cooperation, determining when a strategy can be invaded by another. We show that there are numerous ESSs in absence of errors, which however cease to exist when errors are present. We identify the underlying properties of cooperative ESSs. Overall, this paper provides a first exhaustive evolutionary invasion analysis of moral rules considering private assessment. Moreover, this model is extendable to incorporate higher-order rules and other processes.

Prediction of Genetic Resistance for Scrapie in Ungenotyped Sheep Using a Linear Animal Model.

Selection based on scrapie genotypes could improve the genetic resistance for scrapie in sheep. However, in practice, few animals are genotyped. The objectives were to define numerical values of scrapie resistance genotypes and adjust for their non-additive genetic effect; evaluate prediction accuracy of ungenotyped animals using linear animal model; and predict and assess selection response based on estimated breeding values (EBV) of ungenotyped animals. The scrapie resistance (SR) was defined by ranking scrapie genotypes from low (0) to high (4) resistance based on genotype risk groups and was also adjusted for non-additive genetic effect of the haplotypes. Genotypes were simulated for 1,671,890 animals from pedigree. The simulated alleles were assigned to scrapie haplotypes in two scenarios of high (SRh) and low (SRl) resistance populations. A sample of 20,000 genotyped animals were used to predict ungenotyped using animal model. Prediction accuracies for ungenotyped animals for SRh and SRl were 0.60 and 0.54, and for allele content were from 0.41 to 0.71, respectively. Response to selection on SRh and SRl increased SR by 0.52 and 0.28, and on allele content from 0.13 to 0.50, respectively. In addition, the selected animals had large proportion of homozygous for the favorable haplotypes. Thus, pre-selection prior to genotyping could reduce genotyping costs for breeding programs. Using a linear animal model to predict SR makes better use of available information for the breeding programs.

Two theories of action - Edelman's Neuronal group Selection and the Poetics of Paul Valéry.

Motivated by two imperatives as they are framed in Code Biology - mechanism and actualization - we have turned to other attempts of modeling life at work. Here, we present two theories devoted to minds in action - one explains neuronal function, and the other dissects poetic crafting. Neuronal networks activation and poetic composition, respectively, are seen as the selection of specific connective patterns of either neurons or words, in action. Gerald Edelman, as a scientist, has generalized the Darwinian ideas of variation and selection to the cellular level in his "Sciences of Recognition", a broader theoretical framework that includes the "Theory of Neuronal Group Selection" (TGNS) analyzed here. Paul Valéry, as a poet, has reconciled inspiration and technique in what he has called "works of the mind", the creative processes mediated by sensing and making sense, in the "Poetic Theory" we present here he advances the mechanisms of artistic composition. We have identified the main ideas conveyed in these two theories, i.e., variation and selection, integration and differentiation, ambiguity and degeneracy, binding and blending, stasis and semiosis, by pairing and comparing textual fragments from the authors. We show that TGNS and the Theory of Poetic Action reconcile Sciences and Arts by recognizing that Natural Selection is a mechanism implied by formative acts in both scenarios and discuss to which extent Natural Convention - the main contribution of Code Biology - is integrated by the two thinkers.

Growth-defense trade-offs shape population genetic composition in an iconic forest tree species.

All organisms experience fundamental conflicts between divergent metabolic processes. In plants, a pivotal conflict occurs between allocation to growth, which accelerates resource acquisition, and to defense, which protects existing tissue against herbivory. Trade-offs between growth and defense traits are not universally observed, and a central prediction of plant evolutionary ecology is that context-dependence of these trade-offs contributes to the maintenance of intraspecific variation in defense [Züst and Agrawal, Annu. Rev. Plant Biol., 68, 513-534 (2017)]. This prediction has rarely been tested, however, and the evolutionary consequences of growth-defense trade-offs in different environments are poorly understood, especially in long-lived species [Cipollini et al., Annual Plant Reviews (Wiley, 2014), pp. 263-307]. Here we show that intraspecific trait trade-offs, even when fixed across divergent environments, interact with competition to drive natural selection of tree genotypes corresponding to their growth-defense phenotypes. Our results show that a functional trait trade-off, when coupled with environmental variation, causes real-time divergence in the genetic architecture of tree populations in an experimental setting. Specifically, competitive selection for faster growth resulted in dominance by fast-growing tree genotypes that were poorly defended against natural enemies. This outcome is a signature example of eco-evolutionary dynamics: Competitive interactions affected microevolutionary trajectories on a timescale relevant to subsequent ecological interactions [Brunner et al., Funct. Ecol. 33, 7-12 (2019)]. Eco-evolutionary drivers of tree growth and defense are thus critical to stand-level trait variation, which structures communities and ecosystems over expansive spatiotemporal scales.

Analysis of correlated responses in key ejaculatory traits to artificial selection on a diversifying secondary sexual trait.

Positive genetic covariance between male sexual display traits and fertilizing capacity can arise through different mechanisms and has important implications for sexual trait evolution. Evidence for such genetic covariance is rare, and when it has been found, specific physiological traits underlying variation in fertilization success linked to trait expression have not been identified. A previous study of correlated responses to bidirectional artificial selection on the male sex comb, a secondary sexual trait, in Drosophila bipectinata Duda documented a positive genetic correlation between sexual trait size and competitive fertilization success, and found that transcript levels of multiple seminal fluid proteins (SFPs) were significantly increased in the large sex comb (high) genetic lines. These results suggest that changes in SFP activity may be a causal factor underlying the increased fertilizing capacity of high line males. Here, we tested for correlated responses to this selection in a suite of additional reproductive traits, measured in the context of variation in male age and exposure to rivals. Whereas several traits including sperm length, number and viability, and accessory gland size, increased with age, only sperm viability was influenced by selection treatment, but in complex fashion. Sperm viability of high line males surpassed that of their smaller-combed counterparts when they had been housed with rivals and were 5-6 days old or older. Interestingly, this interaction effect was evident for sperm sampled from the female seminal receptacle, but not from the male seminal vesicles (where sperm have yet to be combined with accessory gland products), consistent with the differential SFP activity between the lines previously found. Our results suggest that differences in sperm quality (as viability) may be a contributing factor to the positive genetic correlation between sexual trait size and competitive fertilization capacity in D. bipectinata.

The dinucleotide composition of the Zika virus genome is shaped by conflicting evolutionary pressures in mammalian hosts and mosquito vectors.

Most vertebrate RNA viruses show pervasive suppression of CpG and UpA dinucleotides, closely resembling the dinucleotide composition of host cell transcriptomes. In contrast, CpG suppression is absent in both invertebrate mRNA and RNA viruses that exclusively infect arthropods. Arthropod-borne (arbo) viruses are transmitted between vertebrate hosts by invertebrate vectors and thus encounter potentially conflicting evolutionary pressures in the different cytoplasmic environments. Using a newly developed Zika virus (ZIKV) model, we have investigated how demands for CpG suppression in vertebrate cells can be reconciled with potentially quite different compositional requirements in invertebrates and how this affects ZIKV replication and transmission. Mutant viruses with synonymously elevated CpG or UpA dinucleotide frequencies showed attenuated replication in vertebrate cell lines, which was rescued by knockout of the zinc-finger antiviral protein (ZAP). Conversely, in mosquito cells, ZIKV mutants with elevated CpG dinucleotide frequencies showed substantially enhanced replication compared to wild type. Host-driven effects on virus replication attenuation and enhancement were even more apparent in mouse and mosquito models. Infections with CpG- or UpA-high ZIKV mutants in mice did not cause typical ZIKV-induced tissue damage and completely protected mice during subsequent challenge with wild-type virus, which demonstrates their potential as live-attenuated vaccines. In contrast, the CpG-high mutants displayed enhanced replication in Aedes aegypti mosquitoes and a larger proportion of mosquitoes carried infectious virus in their saliva. These findings show that mosquito cells are also capable of discriminating RNA based on dinucleotide composition. However, the evolutionary pressure on the CpG dinucleotides of viral genomes in arthropod vectors directly opposes the pressure present in vertebrate host cells, which provides evidence that an adaptive compromise is required for arbovirus transmission. This suggests that the genome composition of arbo flaviviruses is crucial to maintain the balance between high-level replication in the vertebrate host and persistent replication in the mosquito vector.

Genetic Variants in Transcription Factor Binding Sites in Humans: Triggered by Natural Selection and Triggers of Diseases.

Variants of transcription factor binding sites (TFBSs) constitute an important part of the human genome. Current evidence demonstrates close links between nucleotides within TFBSs and gene expression. There are multiple pathways through which genomic sequences located in TFBSs regulate gene expression, and recent genome-wide association studies have shown the biological significance of TFBS variation in human phenotypes. However, numerous challenges remain in the study of TFBS polymorphisms. This article aims to cover the current state of understanding as regards the genomic features of TFBSs and TFBS variants; the mechanisms through which TFBS variants regulate gene expression; the approaches to studying the effects of nucleotide changes that create or disrupt TFBSs; the challenges faced in studies of TFBS sequence variations; the effects of natural selection on collections of TFBSs; in addition to the insights gained from the study of TFBS alleles related to gout, its associated comorbidities (increased body mass index, chronic kidney disease, diabetes, dyslipidemia, coronary artery disease, ischemic heart disease, hypertension, hyperuricemia, osteoporosis, and prostate cancer), and the treatment responses of patients.

Responses of intended and unintended receivers to a novel sexual signal suggest clandestine communication.

Inadvertent cues can be refined into signals through coevolution between signalers and receivers, yet the earliest steps in this process remain elusive. In Hawaiian populations of the Pacific field cricket, a new morph producing a novel and incredibly variable song (purring) has spread across islands. Here we characterize the current sexual and natural selection landscape acting on the novel signal by (1) determining fitness advantages of purring through attraction to mates and protection from a prominent deadly natural enemy, and (2) testing alternative hypotheses about the strength and form of selection acting on the novel signal. In field studies, female crickets respond positively to purrs, but eavesdropping parasitoid flies do not, suggesting purring may allow private communication among crickets. Contrary to the sensory bias and preference for novelty hypotheses, preference functions (selective pressure) are nearly flat, driven by extreme inter-individual variation in function shape. Our study offers a rare empirical test of the roles of natural and sexual selection in the earliest stages of signal evolution.

Widespread signatures of natural selection across human complex traits and functional genomic categories.

Understanding how natural selection has shaped genetic architecture of complex traits is of importance in medical and evolutionary genetics. Bayesian methods have been developed using individual-level GWAS data to estimate multiple genetic architecture parameters including selection signature. Here, we present a method (SBayesS) that only requires GWAS summary statistics. We analyse data for 155 complex traits (n = 27k-547k) and project the estimates onto those obtained from evolutionary simulations. We estimate that, on average across traits, about 1% of human genome sequence are mutational targets with a mean selection coefficient of ~0.001. Common diseases, on average, show a smaller number of mutational targets and have been under stronger selection, compared to other traits. SBayesS analyses incorporating functional annotations reveal that selection signatures vary across genomic regions, among which coding regions have the strongest selection signature and are enriched for both the number of associated variants and the magnitude of effect sizes.

Continuous versus discrete quantity discrimination in dune snail (Mollusca: Gastropoda) seeking thermal refuges.

The ability of invertebrates to discriminate quantities is poorly studied, and it is unknown whether other phyla possess the same richness and sophistication of quantification mechanisms observed in vertebrates. The dune snail, Theba pisana, occupies a harsh habitat characterised by sparse vegetation and diurnal soil temperatures well above the thermal tolerance of this species. To survive, a snail must locate and climb one of the rare tall herbs each dawn and spend the daytime hours in an elevated refuge position. Based on their ecology, we predicted that dune snails would prefer larger to smaller groups of refuges. We simulated shelter choice under controlled laboratory conditions. Snails' acuity in discriminating quantity of shelters was comparable to that of mammals and birds, reaching the 4 versus 5 item discrimination, suggesting that natural selection could drive the evolution of advanced cognitive abilities even in small-brained animals if these functions have a high survival value. In a subsequent series of experiments, we investigated whether snails used numerical information or based their decisions upon continuous quantities, such as cumulative surface, density or convex hull, which co-varies with number. Though our results tend to underplay the role of these continuous cues, behavioural data alone are insufficient to determine if dune snails were using numerical information, leaving open the question of whether gastropod molluscans possess elementary abilities for numerical processing.

What are the origins of growing microbial resistance? Both Lamarck and Darwin were right.

INTRODUCTION: Microorganisms of clinical importance frequently develop resistance to drug therapy, now a growing problem. The experience with Mycobacterium tuberculosis is a representative example of increasing multi-drug resistance. To avoid reaching a crisis in which patients could be left without adequate treatment, a new strategy is needed. Anti-microbial therapy has historically targeted the mechanisms rather than origin of drug resistance, thus allowing microorganisms to adapt and survive. AREAS COVERED: This contribution analyses the historical development (1943-2020) of the evolution of multi-drug resistance by M. tuberculosis strains in light of Darwin's and Lamarck's theories of evolution. EXPERT OPINION: Regarding the molecular origin of microbial drug resistance, genetic mutations and epigenetic modifications are known to participate. The analysis of the history of drug resistance by M. tuberculosis evidences a gradual development of resistance to some antibiotics, undoubtedly due to random mutations together with natural selection based on environmental pressures (e.g., antibiotics), representing Darwin's idea. More rapid adaptation of M. tuberculosis to new antibiotic treatments has also occurred, probably because of heritable acquired characteristics, evidencing Lamarck's proposal. Therefore, microbial infections should be treated with an antibiotic producing null or low mutagenic activity along with a resistance inhibitor, preferably in a single medication.

Fluctuating optimum and temporally variable selection on breeding date in birds and mammals.

Temporal variation in natural selection is predicted to strongly impact the evolution and demography of natural populations, with consequences for the rate of adaptation, evolution of plasticity, and extinction risk. Most of the theory underlying these predictions assumes a moving optimum phenotype, with predictions expressed in terms of the temporal variance and autocorrelation of this optimum. However, empirical studies seldom estimate patterns of fluctuations of an optimum phenotype, precluding further progress in connecting theory with observations. To bridge this gap, we assess the evidence for temporal variation in selection on breeding date by modeling a fitness function with a fluctuating optimum, across 39 populations of 21 wild animals, one of the largest compilations of long-term datasets with individual measurements of trait and fitness components. We find compelling evidence for fluctuations in the fitness function, causing temporal variation in the magnitude, but not the direction of selection. However, fluctuations of the optimum phenotype need not directly translate into variation in selection gradients, because their impact can be buffered by partial tracking of the optimum by the mean phenotype. Analyzing individuals that reproduce in consecutive years, we find that plastic changes track movements of the optimum phenotype across years, especially in bird species, reducing temporal variation in directional selection. This suggests that phenological plasticity has evolved to cope with fluctuations in the optimum, despite their currently modest contribution to variation in selection.

Directed evolution reveals the mechanism of HitRS signaling transduction in Bacillus anthracis.

Two component systems (TCSs) are a primary mechanism of signal sensing and response in bacteria. Systematic characterization of an entire TCS could provide a mechanistic understanding of these important signal transduction systems. Here, genetic selections were employed to dissect the molecular basis of signal transduction by the HitRS system that detects cell envelope stress in the pathogen Bacillus anthracis. Numerous point mutations were isolated within HitRS, 17 of which were in a 50-residue HAMP domain. Mutational analysis revealed the importance of hydrophobic interactions within the HAMP domain and highlighted its essentiality in TCS signaling. In addition, these data defined residues critical for activities intrinsic to HitRS, uncovered specific interactions among individual domains and between the two signaling proteins, and revealed that phosphotransfer is the rate-limiting step for signal transduction. Furthermore, this study establishes the use of unbiased genetic selections to study TCS signaling and provides a comprehensive mechanistic understanding of an entire TCS.

The rise of angiosperms pushed conifers to decline during global cooling.

Competition among species and entire clades can impact species diversification and extinction, which can shape macroevolutionary patterns. The fossil record shows successive biotic turnovers such that a dominant group is replaced by another. One striking example involves the decline of gymnosperms and the rapid diversification and ecological dominance of angiosperms in the Cretaceous. It is generally believed that angiosperms outcompeted gymnosperms, but the macroevolutionary processes and alternative drivers explaining this pattern remain elusive. Using extant time trees and vetted fossil occurrences for conifers, we tested the hypotheses that clade competition or climate change led to the decline of conifers at the expense of angiosperms. Here, we find that both fossil and molecular data show high congruence in revealing 1) low diversification rates, punctuated by speciation pulses, during warming events throughout the Phanerozoic and 2) that conifer extinction increased significantly in the Mid-Cretaceous (100 to 110 Ma) and remained high ever since. Their extinction rates are best explained by the rise of angiosperms, rejecting alternative models based on either climate change or time alone. Our results support the hypothesis of an active clade replacement, implying that direct competition with angiosperms increased the extinction of conifers by pushing their remaining species diversity and dominance out of the warm tropics. This study illustrates how entire branches on the Tree of Life may actively compete for ecological dominance under changing climates.

Transmissible cancers and the evolution of sex under the Red Queen hypothesis.

The predominance of sexual reproduction in eukaryotes remains paradoxical in evolutionary theory. Of the hypotheses proposed to resolve this paradox, the 'Red Queen hypothesis' emphasises the potential of antagonistic interactions to cause fluctuating selection, which favours the evolution and maintenance of sex. Whereas empirical and theoretical developments have focused on host-parasite interactions, the premises of the Red Queen theory apply equally well to any type of antagonistic interactions. Recently, it has been suggested that early multicellular organisms with basic anticancer defences were presumably plagued by antagonistic interactions with transmissible cancers and that this could have played a pivotal role in the evolution of sex. Here, we dissect this argument using a population genetic model. One fundamental aspect distinguishing transmissible cancers from other parasites is the continual production of cancerous cell lines from hosts' own tissues. We show that this influx dampens fluctuating selection and therefore makes the evolution of sex more difficult than in standard Red Queen models. Although coevolutionary cycling can remain sufficient to select for sex under some parameter regions of our model, we show that the size of those regions shrinks once we account for epidemiological constraints. Altogether, our results suggest that horizontal transmission of cancerous cells is unlikely to cause fluctuating selection favouring sexual reproduction. Nonetheless, we confirm that vertical transmission of cancerous cells can promote the evolution of sex through a separate mechanism, known as similarity selection, that does not depend on coevolutionary fluctuations.

The impact of global selection on local adaptation and reproductive isolation.

Despite the homogenizing effect of strong gene flow between two populations, adaptation under symmetric divergent selection pressures results in partial reproductive isolation: adaptive substitutions act as local barriers to gene flow, and if divergent selection continues unimpeded, this will result in complete reproductive isolation of the two populations, i.e. speciation. However, a key issue in framing the process of speciation as a tension between local adaptation and the homogenizing force of gene flow is that the mutation process is blind to changes in the environment and therefore tends to limit adaptation. Here we investigate how globally beneficial mutations (GBMs) affect divergent local adaptation and reproductive isolation. When phenotypic divergence is finite, we show that the presence of GBMs limits local adaptation, generating a persistent genetic load at the loci that contribute to the trait under divergent selection and reducing genome-wide divergence. Furthermore, we show that while GBMs cannot prohibit the process of continuous differentiation, they induce a substantial delay in the genome-wide shutdown of gene flow. This article is part of the theme issue 'Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers'.

Selection, Reversion, and Characterization of House Fly (Diptera: Muscidae) Behavioral Resistance to the Insecticide Imidacloprid.

Insecticide resistance in pest populations is an increasing problem in both urban and rural settings caused by over-application of insecticides and lack of rotation among chemical classes. The house fly (Musca domestica L.) is a cosmopolitan fly species implicated in the transmission of numerous pathogens, and which can be extremely pestiferous when present in high numbers. The evolution of insecticide resistance has long been documented in house flies, with resistance reported to all major insecticide classes. House fly resistance to imidacloprid, the most widely used neonicotinoid insecticide available for fly control, has been selected for in field populations through both physiological and behavioral resistance mechanisms. In the current study, house flies collected from a southern California dairy were selectively bred for behavioral resistance to imidacloprid, without increasing the physiological resistance profile of the selected flies. Flies were also successfully selected for behavioral susceptibility to imidacloprid. The rapid selection for either behavioral resistance or behavioral susceptibility suggests that inheritable alleles conferring behavioral resistance were already present in the wild-type fly population collected from the dairy site. The methods used for the specific selection of behavioral resistance (or susceptibility) in the fly population will be useful for further studies on the specific mechanisms conferring this resistance. House fly behavioral resistance was further investigated using behavioral observation and feeding preference assays, with resistance determined to be both contact-dependent and specific to the insecticide (imidacloprid) rather than to a non-insecticidal component of a bait matrix as previously documented.

Hurricane effects on Neotropical lizards span geographic and phylogenetic scales.

Extreme climate events such as droughts, cold snaps, and hurricanes can be powerful agents of natural selection, producing acute selective pressures very different from the everyday pressures acting on organisms. However, it remains unknown whether these infrequent but severe disruptions are quickly erased by quotidian selective forces, or whether they have the potential to durably shape biodiversity patterns across regions and clades. Here, we show that hurricanes have enduring evolutionary impacts on the morphology of anoles, a diverse Neotropical lizard clade. We first demonstrate a transgenerational effect of extreme selection on toepad area for two populations struck by hurricanes in 2017. Given this short-term effect of hurricanes, we then asked whether populations and species that more frequently experienced hurricanes have larger toepads. Using 70 y of historical hurricane data, we demonstrate that, indeed, toepad area positively correlates with hurricane activity for both 12 island populations of Anolis sagrei and 188 Anolis species throughout the Neotropics. Extreme climate events are intensifying due to climate change and may represent overlooked drivers of biogeographic and large-scale biodiversity patterns.

The evolutionary scaling of cellular traits imposed by the drift barrier.

Owing to internal homeostatic mechanisms, cellular traits may experience long periods of stable selective pressures, during which the stochastic forces of drift and mutation conspire to generate variation. However, even in the face of invariant selection, the drift barrier defined by the genetic effective population size, which is negatively associated with organism size, can have a substantial influence on the location and dispersion of the long-term steady-state distribution of mean phenotypes. In addition, for multilocus traits, the multiplicity of alternative, functionally equivalent states can draw mean phenotypes away from selective optima, even in the absence of mutation bias. Using a framework for traits with an additive genetic basis, it is shown that 1) optimal phenotypic states may be only rarely achieved; 2) gradients of mean phenotypes with respect to organism size (i.e., allometric relationships) are likely to be molded by differences in the power of random genetic drift across the tree of life; and 3) for any particular set of population-genetic conditions, significant variation in mean phenotypes may exist among lineages exposed to identical selection pressures. These results provide a potentially useful framework for understanding numerous aspects of cellular diversification and illustrate the risks of interpreting such variation in a purely adaptive framework.