Convergent evolution of SARS-CoV-2 in human and animals

Recently,many SARS-CoV-2 variants including 501Y.V1,501Y.V2 and 501Y.V3 were detected in different regions(Table S1)and drew great attention from all over the world.The 501Y.V1 was firstly isolated in the United Kingdom(UK)(Davies et al.,2020)and featured with 7 substitutions including N501Y as well as 3 deletions in S protein.This variant was identified to increase the viral transmissibility by 56％in comparison with the preexisting strains.Days after this report,another SARS-CoV-2 variant(501Y.V2)featured with N501Y,K417N and E484K substitutions in S protein was supposed to rapidly outcompete the preexisting strains(Tegally et al.,2020)in South Africa.Besides,the 501Y.V3 variant was initially detected in Brazil and has caused rapidly increased infections with SNPs N501Y,K417T and E484K.Of them,N501Y,K417N/T and E484K are of particular interest because the N501Y was shared in all three variants and the K417N/T and E484K were detected simultaneous appeared with N501Y in 501Y.V2 and 501Y.V3.     

Natural selection and the evolution of neutralism

The efficiency of evolutionary search increases as the density of acceptable proteins in a protein space increases. Populations caught in regions whose density is too low to support evolution can be pulled into high density regions by hitchhiking selection. As they move into such regions, the action of natural selection becomes more effective, yet these populations will satisfy conditions which lead to predictions made by neutral, so-called non-Darwinian models.     

A test of frequency‐dependent selection in the evolution of a generalist phenotype

A solitary population of consumers frequently evolves to the middle of a resource gradient and an intermediate mean phenotype compared to a sympatric pair of competing species that diverge to either side via character displacement. The forces governing the distribution of phenotypes in these allopatric populations, however, are little investigated. Theory predicts that the intermediate mean phenotype of the generalist should be maintained by negative frequency‐dependent selection, whereby alternate extreme phenotypes are favored because they experience reduced competition for resources when rare. However, the theory makes assumptions that are not always met, and alternative explanations for an intermediate phenotype are possible. We provide a test of this prediction in a mesocosm experiment using threespine stickleback that are ecologically and phenotypically intermediate between the more specialized stickleback species that occur in pairs. We manipulated the frequency distribution of phenotypes in two treatments and then measured effects on a focal intermediate population. We found a slight frequency‐dependent effect on survival in the predicted direction but not on individual growth rates. This result suggests that frequency‐dependent selection might be a relatively weak force across the range of phenotypes within an intermediate population and we suggest several general reasons why this might be so. We propose that allopatric populations might often be maintained at an intermediate phenotype instead by stabilizing or fluctuating directional selection.     

Mechanism and evolution of human ACE2 binding by SARS-CoV-2 spike

Spike glycoprotein of SARS-CoV-2 mediates viral entry into host cells by facilitating virus attachment and membrane fusion. ACE2 is the main receptor of SARS-CoV-2 and its interaction with spike has shaped the virus’ emergence from an animal reservoir and subsequent evolution in the human host. Many structural studies on the spike:ACE2 interaction have provided insights into mechanisms driving viral evolution during the on-going pandemic. This review describes the molecular basis of spike binding to ACE2, outlines mechanisms that have optimised this interaction during viral evolution, and suggests directions for future research.     

Costs of resistance and infection by a generalist pathogen

Pathogen infection is typically costly to hosts, resulting in reduced fitness. However, pathogen exposure may also come at a cost even if the host does not become infected. These fitness reductions, referred to as “resistance costs”, are inducible physiological costs expressed as a result of a trade‐off between resistance to a pathogen and aspects of host fitness (e.g., reproduction). Here, we examine resistance and infection costs of a generalist fungal pathogen (Metschnikowia bicuspidata) capable of infecting a number of host species. Costs were quantified as reductions in host lifespan, total reproduction, and mean clutch size as a function of pathogen exposure (resistance cost) or infection (infection cost). We provide empirical support for infection costs and modest support for resistance costs for five Daphnia host species. Specifically, only one host species examined incurred a significant cost of resistance. This species was the least susceptible to infection, suggesting the possibility that host susceptibility to infection is associated with the detectability and size of resistance cost. Host age at the time of pathogen exposure did not influence the magnitude of resistance or infection cost. Lastly, resistant hosts had fitness values intermediate between unexposed control hosts and infected hosts. Although not statistically significant, this could suggest that pathogen exposure does come at some marginal cost. Taken together, our findings suggest that infection is costly, resistance costs may simply be difficult to detect, and the magnitude of resistance cost may vary among host species as a result of host life history or susceptibility.     

Variation and multilevel selection of SARS-CoV-2

The evolution of SARS-CoV-2 remains poorly understood. Theory predicts a group-structured population with selection acting principally at two levels: the pathogen individuals and the group of pathogens within a single host individual. Rapid replication of individual viruses is selected for, but if this replication debilitates the host before transmission occurs, the entire group of viruses in that host may perish. Thus, rapid transmission can favor more pathogenic strains, while slower transmission can favor less pathogenic strains. Available data suggest that SARS-CoV-2 may follow this pattern. Indeed, high population density and other circumstances that favor rapid transmission may also favor more deadly strains. Health care workers, exposed to pathogenic strains of hospitalized patients, may be at greater risk. The low case fatality rate on the Diamond Princess cruise ship may reflect the founder effect—an initial infection with a mild strain. A vaccine made with one strain may confer limited immunity to other strains. Variation among strains may lead to the rapid evolution of resistance to therapeutics. Finally, if less pathogenic strains are largely associated with mild disease, rather than treating all SARS-CoV-2 positive individuals equally, priority could be focused on testing and contact tracing the most seriously symptomatic patients.     

Natural selection in brain evolution of early hominids

Directional effect of natural selection on the arrangement of brain of anthropoids and man is reviewed. It is demonstrated that the evolution of the human nervous system is an integrated result of several multidirectional processes. At the early stages of the evolution of primates, the general biological principles of survival of the fittest, i.e., natural selection of the most adapted variants of the brain structure prevailed. During the period of hominid specialization, natural selection led to the formation of the neocortical control of voluntary movements, memory, and mental associations. At later stages of human morphological evolution, biological mechanisms of natural selection of the brain arrangement were replaced by social mechanisms. This process initiated hominid migrations and the growth of the brain size and individual variability in human ancestors. A model of cerebral sorting is proposed to explain the mechanisms of multidirectional selection leading to an increase in brain size of early hominids.     

Natural selection and molecular evolution in PTC, a bitter-taste receptor gene

The ability to taste phenylthiocarbamide (PTC) is a classic phenotype that has long been known to vary in human populations. This phenotype is of genetic, epidemiologic, and evolutionary interest because the ability to taste PTC is correlated with the ability to taste other bitter substances, many of which are toxic. Thus, variation in PTC perception may reflect variation in dietary preferences throughout human history and could correlate with susceptibility to diet-related diseases in modern populations. To test R. A. Fisher's long-standing hypothesis that variability in PTC perception has been maintained by balancing natural selection, we examined patterns of DNA sequence variation in the recently identified PTC gene, which accounts for up to 85% of phenotypic variance in the trait. We analyzed the entire coding region of PTC (1,002 bp) in a sample of 330 chromosomes collected from African (n=62), Asian (n=138), European (n=110), and North American (n=20) populations by use of new statistical tests for natural selection that take into account the potentially confounding effects of human population growth. Two intermediate-frequency haplotypes corresponding to "taster" and "nontaster" phenotypes were found. These haplotypes had similar frequencies across Africa, Asia, and Europe. Genetic differentiation between the continental population samples was low (FST=0.056) in comparison with estimates based on other genes. In addition, Tajima's D and Fu and Li's D and F statistics demonstrated a significant deviation from neutrality because of an excess of intermediate-frequency variants when human population growth was taken into account (P<.01). These results combine to suggest that balancing natural selection has acted to maintain "taster" and "nontaster" alleles at the PTC locus in humans.     

Host location and selection cues in a generalist tachinid parasitoid

Tachinid flies are diverse and ecologically important insect parasitoids. However, the means by which tachinid species locate and select hosts are poorly known. Many tachinids exhibit unusually wide host ranges and they also possess well-developed visual systems. These characteristics suggest that tachinids differ from parasitic wasps in their reliance on various sensory modes and types of cues. A series of behavioral assays using the generalist tachinid Exorista mella Walker (Diptera: Tachinidae) were conducted to examine what types of cues this parasitoid uses to locate and accept hosts, and how the cues used may reflect its ecological relationships with hosts. Female E. mella responded strongly to host motion in assays using both live hosts and host corpses, and this cue is shown to be an important elicitor of attack behavior. Females also responded to volatile chemicals associated with damaged food plants of their host in an olfactometer. Flies responded only weakly to direct visual contact with stationary hosts and odors directly associated with hosts. The behavior of female E. mella changed with experience such that more experienced flies recognized and attacked hosts more readily than did inexperienced flies. The use of general olfactory and visual cues by E. mella may be an effective strategy by this polyphagous parasitoid to locate a broad range of potential hosts.     

Partial host fidelity in nest selection by the shiny cowbird (Molothrus bonariensis), a highly generalist avian brood parasite

Obligate avian brood parasites can be host specialists or host generalists. In turn, individual females within generalist brood parasites may themselves be host specialists or generalists. The shiny cowbird Molothrus bonariensis is an extreme generalist, but little is known about individual female host fidelity. We examined variation in mitochondrial control region sequences from cowbird chicks found in nests of four common Argentinean hosts. Haplotype frequency distributions differed among cowbird chicks from nests of these hosts, primarily because eggs laid in nests of house wrens Troglodytes aedon differed genetically from those laid in nests of the other three hosts (chalk-browed mockingbird Mimus saturninus, brown-and-yellow marshbird Pseudoleistes virescens, and rufous-collared sparrow Zonotrichia capensis). These differences in a maternally inherited marker indicate the presence of a nonrandom laying behaviour in the females of this otherwise generalist brood parasite, which may be guided by choice for nest type, as house wrens nest in cavities whereas the other three species are open cup nesters.     

Factors affecting host range in a generalist seed pathogen of semi-arid shrublands

Generalist pathogens can exhibit differential success on different hosts, resulting in complex host range patterns. Several factors operate to reduce realized host range relative to potential host range, particularly under field conditions. We explored factors influencing host range of the naturally occurring generalist ascomycete grass seed pathogen Pyrenophora semeniperda. We measured potential host range in laboratory experiments at high inoculum loads with 26 grass species, including the primary host Bromus tectorum, and developed models to predict susceptibility and tolerance based on host traits, including germination speed, seed hardness, seed size, and phylogenetic relations. We also examined pathogen and host density effects on infection and mortality. All species tested were at least somewhat susceptible to the pathogen at high inoculum loads, but both infection and mortality varied widely. Species more closely related to the original host (B. tectorum) were more susceptible to infection, whereas species with slower germination were less tolerant and therefore more likely to suffer mortality. Infection and mortality were sharply reduced as inoculum load was reduced. Intermediate loads had major negative impacts on dormant B. tectorum seeds but generally minimal effects on native species. In addition, field seed bank studies determined that P. semeniperda rarely exploits native grass species as hosts. This marked reduction in realized host range relative to potential host range indicates that laboratory host range studies are potentially a poor predictor of either the current or possible future realized host range for wildland plant pathogens.     

Positive selection operates continuously on hemagglutinin during evolution of H3N2 human influenza A virus

It has been proposed that antigenic evolution of hemagglutinin 1 (HA1) for H3N2 human influenza A virus was punctuated. In the population genetic analysis, however, it was controversial whether positive selection operated on HA1 in a punctuated manner for the branches of the phylogenetic tree where transitions to new antigenic clusters occurred (C branches), or continuously. In the molecular evolutionary analysis, positive selection was detected for the trunk (T) branches but the relationship between antigenic evolution and positive selection was unclear. Here molecular evolutionary analysis was conducted to examine natural selection operating on HA1 of H3N2 human influenza A virus by dividing HA1 into epitopes A-E and other sites, as well as dividing the phylogenetic tree into the C branches overlapping with the T branches (C-T branches), those not overlapping with the T branches (C-NT branches), the T branches not overlapping with the C branches (NC-T branches), and other branches (NC-NT branches). Positive selection was detected for C, T, and NC-T branches, whereas evolution for the NC-NT branches appeared to be mainly neutral. Positive selection appeared to have operated throughout the trunk, which covered the entire time period of the phylogenetic tree, suggesting that positive selection operated continuously on HA1 during evolution of H3N2 human influenza A virus.     

Context-dependent transmission of a generalist plant pathogen: host species and pathogen strain mediate insect vector competence

The specificity of pathogen–vector–host interactions is an important element of disease epidemiology. For generalist pathogens, different pathogen strains, vector species, or host species may all contribute to variability in disease incidence. One such pathogen is Xylella fastidiosa Wells et al., a xylem-limited bacterium that infects dozens of crop, ornamental, and native plants in the USA. This pathogen also has a diverse vector complex and multiple biologically distinct strains. We studied the implications of diversity in this pathogen–vector–host system, by quantifying variability in transmission efficiency of different X. fastidiosa strains (isolates from almond and grape genetic groups) for different host plants (grape, almond, and alfalfa) by two of the most important vectors in California: glassy-winged sharpshooter [ Homalodisca vitripennis (Germar)] and green sharpshooter ( Draeculacephala minerva Ball) (both Hemiptera: Cicadellidae). Transmission of isolates of the almond strain by H. vitripennis did not differ significantly, whereas transmission varied significantly among isolates from the grape strain (15–90%). Host plant species did not affect H. vitripennis transmission. Conversely, D. minerva efficiency was mediated by both host plant species and pathogen strain. No acquisition of an almond isolate occurred regardless of plant type (0/122), whereas acquisition of a grape isolate from alfalfa was 10-fold higher than from grape or almond plants. These results suggest that pathogen, vector, and host diversity impose contingencies on the transmission ecology of this complex disease system. Studies aimed at the development of management strategies for X. fastidiosa diseases should consider the complexity of these interactions as they relate to disease spread.     

Roost use by long-tailed bats in South Canterbury: examining predictions of roost-site selection in a highly fragmented landscape

We studied the roosting ecology of the long-tailed bat (Chalinolobus tuberculatus) during the springautumn months from 1998–2002 at Hanging Rock in the highly fragmented landscape of South Canterbury, South Island, New Zealand. We compared the structural characteristics and microclimates of roost sites used by communally and solitary roosting bats with those of randomly available sites, and roosts of C. tuberculatus occupying unmodified Nothofagus forest in the Eglinton Valley, Fiordland. Roosting group sizes and roost residency times were also compared. We followed forty radio-tagged bats to 94 roosts (20% in limestone crevices, 80% in trees) at Hanging Rock. Roosts were occupied for an average of 1 day and 86% were only used once during the study period. Colony size averaged 9.8 ± 1.1 bats (range 2–38) and colonies were dominated by breeding females and young. Indigenous forest, shrubland remnants and riparian zones were preferred roosting habitats. Communally roosting bats selected roosts in split trunks of some of the largest trees available. Selection of the largest available trees as roost sites is similar to behaviour of bat species occupying unmodified forested habitats. Temperatures inside 12 maternity roosts measured during the lactation period were variable. Five roosts were well insulated from ambient conditions and internal temperatures were stable, whereas the temperatures inside seven roosts fluctuated in parallel with ambient temperature. Tree cavities used by bats at Hanging Rock were significantly nearer ground level, had larger entrance dimensions, were less well insulated, and were occupied by fewer bats than roosts in the Eglinton Valley. These characteristics appear to expose their occupants to unstable microclimates and to a higher risk of threats such as predation. We suggest that roosts at Hanging Rock are of a lower quality than those in the Eglinton Valley, and that roost quality may be one of the contributory factors in the differential reproductive fitness observed in the two bat populations. The value of introduced willows (especially Salix fragilis) as bat roosts should be acknowledged. We recommend six conservation measures to mitigate negative effects of deterioration of roosting habitat: protection and enhancement of the quality of existing roosts, replanting within roosting habitat, provision of high quality artificial roosts, predator control, and education of landowners and statutory bodies.     

The use of SARS-CoV-2-related coronaviruses from bats and pangolins to polarize mutations in SARS-Cov-2

正Dear Editor,The coronavirus disease 2019 (COVID-19) caused by the SARS-CoV-2 coronavirus has become a global pandemic.The SARS-CoV-2 genome has a similarity of 96.2%to that of RaTG13, a bat SARS-CoV-2-related coronavirus detected in Rhinolophus affinis (Paraskevis et al., 2020; Zhou et al.,2020). The SARS-CoV-2 genome also has 85.5%-92.4%     

Maladaptation in wild populations of the generalist plant pathogen Pseudomonas syringae

Multihost pathogens occur widely on both natural and agriculturally managed hosts. Despite the importance of such generalists, evolutionary studies of host-pathogen interactions have largely focused on tightly coupled interactions between species pairs. We characterized resistance in a collection of Arabidopsis thaliana hosts, including 24 accessions collected from the Midwest USA and 24 from around the world, and patterns of virulence in a collection of Pseudomonas syringae strains, including 24 strains collected from wild Midwest populations of A. thaliana (residents) and 18 from an array of cultivated species (nonresidents). All of the nonresident strains and half of the resident strains elicited a resistance response on one or more A. thaliana accessions. The resident strains that failed to elicit any resistance response possessed an alternative type III secretion system (T3SS) that is unable to deliver effectors into plant host cells; as a result, these seemingly nonpathogenic strains are incapable of engaging in gene for gene interactions with A. thaliana. The remaining resident strains triggered greater resistance compared to nonresident strains, consistent with maladaptation of the resident bacterial population. We weigh the plausibility of two explanations: general maladaptation of pathogen strains and a more novel hypothesis whereby community level epidemiological dynamics result in adaptive dynamics favoring ephemeral hosts like A. thaliana.     

Mutation, selection and the future of human evolution

Several recent analyses provide growing evidence of the influence of positive selection acting in the ancestors of modern humans. Additionally, the best way to explain current fluctuations in neutral variation across the genome is by including negative selection against a high rate of deleterious mutants. We suggest that explaining these predicted high deleterious mutation rates in humans could require the inclusion of additional factors, such as inbreeding and prezygotic selection, in addition to rank-order selection and fitness interactions among mutations. We also suggest that some forms of selection, rather than being relaxed in modern humans, are probably still acting and might intensify in the near future, and make some predictions about the next several millennia of human evolution.     

Natural selection and the joint evolution of toleranceand resistance as plant defenses

Plants can defend themselves against the damaging effects of herbivory in at least two ways. Resistant plants avoid or deter herbivores and are therefore fed upon less than susceptible plants. Tolerant plants are not eaten less than plants with little tolerance, but the effects of herbivore damage are not so detrimental to a tolerant plant as they are to a less tolerant plant. Biologists have suggested that these two strategies might represent two alternative and redundant defenses against herbivory since they appear to serve the same function for plants. I explore the relationship between resistance and tolerance, particularly with regards to how the joint evolution of these two traits will influence the evolution of plant defense. Although I briefly review some of the contributions of theory to the study of tolerance, I concentrate on an empirical, ecological genetic approach to the study of the evolution of these characters and the coevolution of tolerance and herbivores. In order to understand the evolution of any trait, we must understand the evolutionary forces acting on the trait. Specifically, we must understand how natural selection acts on tolerance. I review several studies that have specifically measured the form of selection acting on tolerance and tested the hypothesis that resistance and tolerance are alternative strategies. I also present a statistical analysis that does not support the hypothesis that herbivores are selective agents on tolerance. Finally, I consider a variety of constraints that possibly restrict the evolution of tolerance. This revised version was published online in July 2006 with corrections to the Cover Date.