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[Display omitted] • New insights into the long-term evolution of Notoungulata. • Emerged lands significantly boosted notoungulate speciation rates. • Andean uplift significantly influenced notoungulate extinction rates. • Competition and predation crucially shaped notoungulate diversification dynamics. Unraveling the biotic and abiotic drivers likely influencing clades' diversification dynamics (differential speciation and extinction rates) is crucial for understanding life on Earth. Here, we present a comprehensive analysis of the diversification dynamics of notoungulates (Mammalia: Notoungulata), the most diverse and widespread Cenozoic herbivore mammals that evolved in South America (SA) but are now entirely extinct. Employing fossil occurrences restricted to the southern part of the SA and a Bayesian framework, we examined the historical speciation and extinction rates across all notoungulates, suborders, and three body size categories and tested whether these dynamics could be driven by biotic (e.g., diversity dependence, competition) and abiotic (e.g., Andean uplift and temperature changes) factors. Our findings reveal significant variability in diversification rates over time and groups driven by biotic and abiotic factors. We observed an increase in notoungulate speciation rates correlated with lower group self-diversity, likely related to limited environmental productivity and more extensive emerged continental areas that can provide increased environmental and ecological heterogeneity. In contrast, elevated extinction rates were correlated with intensified Andean uplift events, which can trigger landscape modifications and the arrival of placental carnivores after the Great American Biotic Interchange, probably due to notoungulate vulnerability to novel predation pressures. Furthermore, sparassodont diversity appears to increase speciation and extinction rates of notoungulates, although the direct mechanism relating them remains uncertain. The heterogeneity in the observed patterns of speciation and extinction across distinct size categories and taxonomic clades provides valuable perspectives on how ancient global and regional changes impacted the diversification dynamics of mammals and underscores the intricate interplay between environmental changes and biological interactions in shaping the evolution of life on Earth. [ABSTRACT FROM AUTHOR]

Theorists have identified several mechanisms through which species that compete exploitatively for resources could coexist. By contrast, under the current theory, interference competitors could coexist only in rare circumstances. Yet, some types of interference competition, such as interspecific territoriality, are common. This mismatch between theory and nature inspired us to model interference competition in an eco-evolutionary framework. We based the model on the life cycle of territorial birds and ran simulations to examine whether natural selection could rescue a superior interference competitor from extinction without driving a superior exploitative competitor extinct. We found that coexistence between interference competitors can occur over a wide range of ecologically plausible scenarios, and up to the highest levels of resource overlap. An important caveat is that coexistence requires the species to co-evolve. Reductions in population size and levels of genetic variation could destabilise coexistence between interference competitors, and thereby increase extinction rates over current estimates.

Biparental sex is widespread in nature, yet costly relative to uniparental reproduction. It is generally unclear why self-fertilizing or asexual lineages do not readily invade outcrossing populations. The Red Queen hypothesis predicts that coevolving parasites can prevent self-fertilizing or asexual lineages from invading outcrossing host populations. However, only highly virulent parasites are predicted to maintain outcrossing, which may limit the general applicability of the Red Queen hypothesis. Here, we tested whether the ability of coevolving parasites to prevent invasion of self-fertilization within outcrossing host populations was dependent on parasite virulence. We introduced wild-type Caenorhabditis elegans hermaphrodites, capable of both self-fertilization and outcrossing, into C. elegans populations fixed for a mutant allele conferring obligate outcrossing. Replicate C. elegans populations were exposed for 24 host generations to one of four strains of Serratia marcescens parasites that varied in virulence, under three treatments: a heat-killed (control, noninfectious) parasite treatment, a fixed-genotype (nonevolving) parasite treatment, and a copassaged (potentially coevolving) parasite treatment. As predicted, self-fertilization invaded C. elegans host populations in the control and fixed-parasite treatments, regardless of parasite virulence. In the copassaged treatment, selfing invaded host populations coevolving with low- to mid-virulence strains, but remained rare in hosts coevolving with highly virulent bacterial strains. Therefore, we found that only highly virulent coevolving parasites can impede the invasion of selfing. Lay Summary: The dominance of biparental sex in plant and animal populations is difficult for evolutionary biologists to explain given the high costs associated with sex. The Red Queen hypothesis provides a possible explanation, predicting that interactions with coevolving parasites produce fluctuating environments that can select for biparental sex despite the costs. However, an important limitation of the Red Queen hypothesis is that coevolving parasites might only impose sufficiently strong selection to maintain biparental sex when parasite virulence is very high. We explored this potential limitation by testing whether uniparental sex (i.e., self-fertilization) could spread into outcrossing populations of the nematode host Caenorhabditis elegans that were exposed to strains of the bacterial parasite Serratia marcescens that varied in virulence. We found that self-fertilization spread in all conditions except when the pathogen was highly virulent and coevolving. Our results support the Red Queen hypothesis by demonstrating that virulent coevolving parasites can select for biparental sex in hosts. They also highlight the limitations of the Red Queen hypothesis, showing that the conditions under which parasites can maintain biparental sex may be limited to cases of high virulence. [ABSTRACT FROM AUTHOR]

Empirical evidence of the influence of climate on plant–pathogen coevolution is limited but crucial to understand, as anthropogenic pressures including fragmentation and climate change threaten biodiversity. In this study, we tested patterns of plant–pathogen coevolution using Silphium integrifolium Michx., a native tallgrass prairie species that is undergoing domestication, and its foliar pathogens. We collected seeds from four native prairie remnants from each of three regions along an east–west precipitation gradient in central North America and used these to create three common gardens in each region. In common gardens and remnant prairie populations, we measured symptoms of foliar disease (leaf rust and leaf blotch, both caused by fungal pathogens, and Silphium clear vein (SCV), which we have evidence is associated with a virus). While we did not observe greater disease in the East common garden, we did find that on average the East populations had greater resistance to disease than West populations, consistent with an evolutionary legacy of more rapid coevolution with high precipitation. We also found strong interactions between source region and region of planting for all diseases. The Silphium rust, caused by the specialist pathogen Puccinia silphii, was better able to infect plant populations from the same region. These patterns are consistent with local adaptation of specialist pathogens to their local hosts as expected from Red Queen dynamics. For the generalist fungal pathogen driving leaf blotch, we did not observe evidence of local adaptation. However, we observed a positive correlation in the average level of leaf blotch symptoms observed in individual populations in common gardens with the levels of disease in the S. integrifolium individuals in the prairie remnants of origin, consistent with S. integrifolium genetics determining symptoms in the field. Our results are consistent with pathogen ecology being a major driver of coevolutionary dynamics along productivity gradients. As S. integrifolium is being domesticated for oilseed production, our results identify distinct targets for resistance alleles in breeding efforts and can guide pathogen management strategies. [ABSTRACT FROM AUTHOR]

The worrying phenomenon of our times is a rapid decline in the biodiversity, that is directly related to the disorder in environmental sustainability. However, the question is whether before the appearance of the Homo sapiens there was a greater eco-sustainability? Or maybe even without the presence of the man such state would be rather correlated with some natural processes, that happen independently of our interference? The paper attempts to explain the relativity of environmental sustainability described by the Red Queen Hypothesis (RQH). That model presents competition in nature, which may be extrapolated to all interactions in the world of living organisms. The RQH shows that in the evolutionary terms not keeping pace on the run threatens not only progress but also poses an increasing risk of elimination of a given individual. So in that way environmental sustainability is relative and the model explains the probability of a constant extinction, so in fact a fall. [ABSTRACT FROM AUTHOR]

Why sex has evolved and is maintained is an open question in evolutionary biology. The Red Queen hypothesis predicts that host lineages subjected to more intense parasite pressure should invest more in sexual reproduction to continuously create novel defences against their rapidly evolving natural enemies. In this comparative study across the angiosperms, we show that hermaphrodite plant species associated with higher species richness of insect herbivores evolved flowers with higher biomass allocation towards the male sex, an indication of their greater outcrossing effort. This pattern remained robust after controlling for key vegetative, reproductive and biogeographical traits, suggesting that long‐term herbivory pressure is a key factor driving the selfing–outcrossing gradient of higher plants. Although flower evolution is frequently associated with mutualistic pollinators, our findings support the Red Queen hypothesis and suggest that insect herbivores drive the sexual strategies of flowering plants and their genetic diversity. [ABSTRACT FROM AUTHOR]

Herpesviruses are ubiquitous pathogens infecting most animals. Although host immunity continually coevolves to combat virulence, viral variants with enhanced transmissibility or virulence occasionally emerge, resulting in disease burdens in host populations. Mustelid gammaherpesvirus 1 (MusGHV-1) is the only herpesvirus species identified thus far in European badgers, Meles meles. No MusGHV-1 associated pathomorbidity has been reported, but reactivation of MusGHV-1 in genital tracts is linked to impaired female reproductive success. An analysis of a short sequence from the highly conserved DNA polymerase (DNApol) gene previously identified two variants in a single host population. Here we compared genetic variance in blood samples from 66 known individuals of this same free-ranging badger population using a partial sequence comprising 2874 nucleotides of the DNApol gene, among which we identified 15 nucleotide differences resulting in 5 amino acid differences. Prevalence was 86% (59/66) for the common and 17% (11/66) for the novel variant, with 6% (4/66) of badgers presenting with coinfection. MusGHV-1 variants were distributed unevenly across the population, with individuals infected with the novel genotype clustered in 3 of 25 contiguous social groups. Individuals infected with the novel variant had significantly higher MusGHV-1 viral loads in their blood (p = 0.002) after adjusting for age (juveniles > adults, p < 0.001) and season (summer > spring and autumn, p = 0.005; mixed-effect linear regression), likely indicating higher virulence of the novel variant. Further genome-wide analyses of MusGHV-1 host resistance genes and host phenotypic variations are required to clarify the drivers and sequelae of this new MusGHV-1 variant. [ABSTRACT FROM AUTHOR]

[Display omitted] • The Red Queen Hypothesis in virus-host interactions; viruses adapt proteins, hosts alter receptors. • Mutual adaptation shapes receptor interactions, informing disease unpredictability and interventions. • The article utilizes phylogenetics, modeling, and dynamics, focusing on Brazilian Dengue strains. • Viral quasispecies explores mutational space elegantly,linking genotype mutations to phenotype variations. • Energetic decomposition analyses identifies critical amino acids, highlighting Phe 313 in DC-SIGN interactions. The Red Queen Hypothesis (RQH), derived from Lewis Carroll's "Through the Looking-Glass", postulates that organisms must continually adapt in response to each other to maintain relative fitness. Within the context of host-pathogen interactions, the RQH implies an evolutionary arms race, wherein viruses evolve to exploit hosts and hosts evolve to resist viral invasion. This study delves into the dynamics of the RQH in the context of virus-cell interactions, specifically focusing on virus receptors and cell receptors. We observed multiple virus-host systems and noted patterns of co-evolution. As viruses evolved receptor-binding proteins to effectively engage with cell receptors, cells countered by altering their receptor genes. This ongoing mutual adaptation cycle has influenced the molecular intricacies of receptor-ligand interactions. Our data supports the RQH as a driving force behind the diversification and specialization of both viral and host cell receptors. Understanding this co-evolutionary dance offers insights into the unpredictability of emerging viral diseases and potential therapeutic interventions. Future research is crucial to dissect the nuanced molecular changes and the broader ecological consequences of this ever-evolving battle. Here, we combine phylogenetic inferences, structural modeling, and molecular dynamics analyses to describe the epidemiological characteristics of major Brazilian DENV strains that circulated from 1990 to 2022 from a combined perspective, thus providing us with a more detailed picture on the dynamics of such interactions over time. [ABSTRACT FROM AUTHOR]

Microbes inhabit virtually everywhere on and/or in our bodies, including the seminal and vaginal fluids. They have significant importance in maintaining reproductive health and protecting hosts from diseases. The exchange of microbes during sexual intercourse is one of the most direct and significant microbial transmissions between men and women. Nevertheless, the mechanism of this microbial transmission was little known. Is the transmission mode stochastic, passive diffusion similar to the random walk of particles, or driven by some deterministic forces? What is the microbial transmission probability? What are the possible evolutionary implications, particularly from the perspective of sexual reproduction (selection)? We tackle these intriguing questions by leveraging the power of Hubbell's unified neutral theory of biodiversity, specifically implemented as the HDP-MSN (hierarchical Dirichlet process approximated multi-site neutral model), which allows for constructing truly multi-site metacommunity models, simultaneously including vaginal and semen microbiomes. By reanalyzing the microbiome datasets of seminal and vaginal fluids from 23 couples both before and after sexual intercourses originally reported by Mändar and colleagues, we found that the microbial transmission between seminal and vaginal fluids is a stochastic, passive diffusion similar to the random walk of particles in physics, rather than driven by deterministic forces. The transmission probability through sexual intercourse seems to be approximately 0.05. Inspired by the results from the HDP-MSN model, we further conjecture that the stochastic drifts of microbiome transmissions during sexual intercourses can be responsible for the homogeneity between semen and vaginal microbiomes first identified in a previous study, which should be helpful for sexual reproduction by facilitating the sperm movement/survival and/or egg fertilization. This inference seems to be consistent with the classic Red Queen hypothesis, which, when extended to the co-evolutionary interactions between humans and their symbiotic microbiomes, would predict that the reproductive system microbiomes should support sexual reproduction. [ABSTRACT FROM AUTHOR]

Microbes inhabit virtually everywhere on and/or in our bodies, including the seminal and vaginal fluids. They have significant importance in maintaining reproductive health and protecting hosts from diseases. The exchange of microbes during sexual intercourse is one of the most direct and significant microbial transmissions between men and women. Nevertheless, the mechanism of this microbial transmission was little known. Is the transmission mode stochastic, passive diffusion similar to the random walk of particles, or driven by some deterministic forces? What is the microbial transmission probability? What are the possible evolutionary implications, particularly from the perspective of sexual reproduction (selection)? We tackle these intriguing questions by leveraging the power of Hubbell’s unified neutral theory of biodiversity, specifically implemented as the HDP-MSN (hierarchical Dirichlet process approximated multi-site neutral model), which allows for constructing truly multi-site metacommunity models, simultaneously including vaginal and semen microbiomes. By reanalyzing the microbiome datasets of seminal and vaginal fluids from 23 couples both before and after sexual intercourses originally reported by Mändar and colleagues, we found that the microbial transmission between seminal and vaginal fluids is a stochastic, passive diffusion similar to the random walk of particles in physics, rather than driven by deterministic forces. The transmission probability through sexual intercourse seems to be approximately 0.05. Inspired by the results from the HDP-MSN model, we further conjecture that the stochastic drifts of microbiome transmissions during sexual intercourses can be responsible for the homogeneity between semen and vaginal microbiomes first identified in a previous study, which should be helpful for sexual reproduction by facilitating the sperm movement/survival and/or egg fertilization. This inference seems to be consistent with the classic Red Queen hypothesis, which, when extended to the co-evolutionary interactions between humans and their symbiotic microbiomes, would predict that the reproductive system microbiomes should support sexual reproduction.

Viruses and hosts must navigate environments in which each tries to outcompete the other for survival or to coexist within the same spaces. In Lewis Carrol's Through the Looking Glass , the Red Queen tells Alice, "Now, here, you see, it takes all the running you can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!" Borrowing from this idea, the Red Queen hypothesis asserts that organisms, such as viruses, must continuously adapt to environmental pressures to survive. In this commentary, we draw parallels between the Red Queen hypothesis and the experiences scientists of color navigate to thrive in academic spaces. In both phenomena, adapting to environmental pressures is necessary for survival. We identify the various pressures and bottlenecks faced by historically underrepresented groups in academia, as well as the adaptation strategies they must implement to persist in academia. [ABSTRACT FROM AUTHOR]

Toward a coevolutionary sustainable world Control and reduce gene flow To reduce the risks of future outbreaks of novel pathogens, we must control the gene flow of pathogens. Keywords: Coevolution; Red Queen hypothesis; One Health; mutation; gene flow; zoonosis; pandemic; EIDs; SARS-CoV-2; COVID-19; COVID status certification; Digital Green Certificate; immunity-based license; vaccination EN Coevolution Red Queen hypothesis One Health mutation gene flow zoonosis pandemic EIDs SARS-CoV-2 COVID-19 COVID status certification Digital Green Certificate immunity-based license vaccination 1288 1295 8 12/30/21 20211201 NES 211201 Introduction I "Nothing in biology makes sense except in the light of evolution" i [[1]] and this is no less true for viral pathogens than it is for their host species. (d) Habitat destruction, illegal wildlife trade and human activities have increased gene flow and brought many species into contact, which is facilitating spillover and hybridization of pathogens[[16]]. (f) Close contact between livestock and humans can lead to spillovers, which make zoonotic hybrid pathogens a significant threat to human health now and in the future[[40]] Recombination By mixing the already available genetic variation into new combinations, recombination can also generate evolutionary novelty. [Extracted from the article]

Herpesviruses are ubiquitous pathogens infecting most animals. Although host immunity continually coevolves to combat virulence, viral variants with enhanced transmissibility or virulence occasionally emerge, resulting in disease burdens in host populations. Mustelid gammaherpesvirus 1 (MusGHV-1) is the only herpesvirus species identified thus far in European badgers, Meles meles. No MusGHV-1 associated pathomorbidity has been reported, but reactivation of MusGHV-1 in genital tracts is linked to impaired female reproductive success. An analysis of a short sequence from the highly conserved DNA polymerase (DNApol) gene previously identified two variants in a single host population. Here we compared genetic variance in blood samples from 66 known individuals of this same free-ranging badger population using a partial sequence comprising 2874 nucleotides of the DNApol gene, among which we identified 15 nucleotide differences resulting in 5 amino acid differences. Prevalence was 86% (59/66) for the common and 17% (11/66) for the novel variant, with 6% (4/66) of badgers presenting with coinfection. MusGHV-1 variants were distributed unevenly across the population, with individuals infected with the novel genotype clustered in 3 of 25 contiguous social groups. Individuals infected with the novel variant had significantly higher MusGHV-1 viral loads in their blood (p = 0.002) after adjusting for age (juveniles > adults, p < 0.001) and season (summer > spring and autumn, p = 0.005; mixed-effect linear regression), likely indicating higher virulence of the novel variant. Further genome-wide analyses of MusGHV-1 host resistance genes and host phenotypic variations are required to clarify the drivers and sequelae of this new MusGHV-1 variant.

The Red Queen hypothesis depicts evolution as the continual struggle to adapt. According to this hypothesis, new genes, especially those originating from nongenic sequences (i.e. de novo genes), are eliminated unless they evolve continually in adaptation to a changing environment. Here, we analyze two Drosophila de novo miRNAs that are expressed in a testis-specific manner with very high rates of evolution in their DNA sequence. We knocked out these miRNAs in two sibling species and investigated their contributions to different fitness components. We observed that the fitness contributions of miR-975 in Drosophila simulans seem positive, in contrast to its neutral contributions in D. melanogaster , whereas miR-983 appears to have negative contributions in both species, as the fitness of the knockout mutant increases. As predicted by the Red Queen hypothesis, the fitness difference of these de novo miRNAs indicates their different fates. [ABSTRACT FROM AUTHOR]

The "law of constant extinction," proposed by Van Valen, states that long and short‐lived taxa have equal chances of going extinct. This pattern of age‐independent extinction was originally inferred using the fossil record of several different taxa and relied on survivorship curves built from the literal reading of the fossil record. Van Valen's seminal work was mostly done at higher taxonomic levels, hence its prevalence at the species level could not be directly inferred. The surprisingly few subsequent studies done at the species level have challenged the prevalence of age‐independent extinction, but those have, for the most part, failed to explicitly incorporate inherent biases of the fossil record. Using a recent Bayesian framework that accounts for several of those biases, including the fact that very short‐living lineages might never make to the record itself, we showed that Ruminantia species present age‐dependent extinction, where extinction probability decreases with species age. An analysis at the genus level suggested age‐independent extinction but further examination suggested that the pattern might be more complex than previously reported by Van Valen. Our results indicate that different taxonomic levels may present different extinction regimes, which could justify the development of new macroevolutionary theory and methods. [ABSTRACT FROM AUTHOR]

Species diversity patterns are governed by complex interactions among biotic and abiotic factors over time and space, but are essentially the result of the diversification dynamics (differential speciation and extinction rates) over the long‐term evolutionary history of a clade. Previous studies have suggested that temporal variation in global temperature drove long‐term diversity changes in Crocodylia, a monophyletic group of large ectothermic organisms. We use a large database of crocodylian fossil occurrences (192 spp.) and body mass estimations, under a taxic approach, to characterize the global diversification dynamics of crocodylians since the Cretaceous, and their correlation with multiple biotic and abiotic factors in a Bayesian framework. The diversification dynamic of crocodylians, which appears to have originated in the Turonian (c. 92.5 Ma), is characterized by several phases with high extinction and speciation rates within a predominantly low long‐term mean rate. Our results reveal long‐term diversification dynamics of Crocodylia to be a highly complex process driven by a combination of biotic and abiotic factors which influenced the speciation and extinction rates in dissimilar ways. Higher crocodylian extinction rates are related to low body mass disparity, indicating selective extinctions of taxa at both ends of the body mass spectrum. Speciation rate slowdowns are noted when the diversity of the clade is high and the warm temperate climatic belt is reduced. Our finding supports the idea that temporal variations of body mass disparity, self‐diversity, and the warm climate belt size provided more direct mechanistic explanations for crocodylian diversification than do proxies of global temperature. [ABSTRACT FROM AUTHOR]

Definitions of macroevolution fall into three categories: (1) evolution of taxa of supraspecific rank; (2) evolution on the grand time‐scale; and (3) evolution that is guided by sorting of interspecific variation (as opposed to sorting of intraspecific variation in microevolution). Here, it is argued that only definition 3 allows for a consistent separation of macroevolution and microevolution. Using this definition, speciation has both microevolutionary and macroevolutionary aspects: the process of morphological transformation is microevolutionary, but the variation among species that it produces is macroevolutionary, as is the rate at which speciation occurs. Selective agents may have differential effects on intraspecific and interspecific variation, with three possible situations: effect at one level only, effect at both levels with the same polarity but potentially different intensity, and effects that oppose between levels. Whereas the impact of all selective agents is direct in macroevolution, microevolution requires intraspecific competition as a mediator between selective agents and evolutionary responses. This mediating role of intraspecific competition occurs in the presence of sexual reproduction and has therefore no analogue at the macroevolutionary level where species are the evolutionary units. Competition between species manifests both on the microevolutionary and macroevolutionary level, but with different effects. In microevolution, interspecific competition spurs evolutionary divergence, whereas it is a potential driver of extinction at the macroevolutionary level. Recasting the Red Queen hypothesis in a macroevolutionary framework suggests that the effects of interspecific competition result in a positive correlation between origination and extinction rates, confirming empirical observations herein referred to as Stanley's rule. [ABSTRACT FROM AUTHOR]

Abstract Background The persistence of high genetic variability in natural populations garners considerable interest among ecologists and evolutionary biologists. One proposed hypothesis for the maintenance of high levels of genetic diversity relies on frequency-dependent selection imposed by parasites on host populations (Red Queen hypothesis). A complementary hypothesis suggests that a trade-off between fitness costs associated with tolerance to stress factors and fitness costs associated with resistance to parasites is responsible for the maintenance of host genetic diversity. Results The present study investigated whether host resistance to parasites is traded off with tolerance to environmental stress factors (high/low temperatures, high salinity), by comparing populations of the freshwater snail Melanoides tuberculata with low vs. high clonal diversity. Since polyclonal populations were found to be more parasitized than populations with low clonal diversity, we expected them to be tolerant to environmental stress factors. We found that clonal diversity explained most of the variation in snail survival under high temperature, thereby suggesting that tolerance to high temperatures of clonally diverse populations is higher than that of populations with low clonal diversity. Conclusions Our results suggest that resistance to parasites may come at a cost of reduced tolerance to certain environmental stress factors.

Bifidobacteria are commensal microorganisms that inhabit a wide range of hosts, including insects, birds and mammals. The mechanisms responsible for the adaptation of bifidobacteria to various hosts during the evolutionary process remain poorly understood. Previously, we reported that the species-specific PFNA gene cluster is present in the genomes of various species of the Bifidobacterium genus. The cluster contains signal transduction and adhesion genes that are presumably involved in the communication between bifidobacteria and their hosts. The genes in the PFNA cluster show high sequence divergence between bifidobacterial species, which may be indicative of rapid evolution that drives species-specific adaptation to the host organism. We used the maximum likelihood approach to detect positive selection in the PFNA genes. We tested for both pervasive and episodic positive selection to identify codons that experienced adaptive evolution in all and individual branches of the Bifidobacterium phylogenetic tree, respectively. Our results provide evidence that episodic positive selection has played an important role in the divergence process and molecular evolution of sequences of the species-specific PFNA genes in most bifidobacterial species. Moreover, we found the signatures of pervasive positive selection in the molecular evolution of the tgm gene in all branches of the Bifidobacterium phylogenetic tree. These results are consistent with the suggested role of PFNA gene cluster in the process of specific adaptation of bifidobacterial species to various hosts. [ABSTRACT FROM AUTHOR]

Red Queen dynamics, involving coevolutionary interactions between species, are ubiquitous, shaping the evolution of diverse biological systems. To date, information on the underlying selection dynamics and the involved genome regions is mainly available for bacteria-phage systems or only one of the antagonists of a eukaryotic host-pathogen interaction. We add to our understanding of these important coevolutionary interactions using an experimental host-pathogen model, which includes the nematode Caenorhabditis elegans and its pathogen Bacillus thuringiensis. We combined experimental evolution with time-shift experiments, in which a focal host or pathogen is tested against a coevolved antagonist from the past, present, or future, followed by genomic analysis. We show that (i) coevolution occurs rapidly within few generations, (ii) temporal coadaptation at the phenotypic level is found in parallel across replicate populations, consistent with antagonistic frequency-dependent selection, (iii) genomic changes in the pathogen match the phenotypic pattern and include copy number variations of a toxin-encoding plasmid, and (iv) host genomic changes do not match the phenotypic pattern and likely involve selective responses at more than one locus. By exploring the dynamics of coevolution at the phenotypic and genomic level for both host and pathogen simultaneously, our findings demonstrate a more complex model of the Red Queen, consisting of distinct selective processes acting on the two antagonists during rapid and reciprocal coadaptation. [ABSTRACT FROM AUTHOR]

Asexual lineages should rapidly replace sexual populations. Why sex then? The Red Queen hypothesis proposes that parasite-mediated selection against common host genotypes could counteract the per capita birth rate advantage of asexuals. Under the Red Queen hypothesis, fluctuations in parasite-mediated selection can drive fluctuations in the asexual population, leading to the coexistence of sexual and asexual reproduction. Does shifting selection by parasites drive fluctuations in the fitness and frequency of asexuals in nature? Combining long-term field data with mesocosm experiments, we detected a shift in the direction of parasite selection in the snail Potamopyrgus antipodarum and its coevolving parasite, Microphallus sp. In the early 2000s, asexuals were more infected than sexuals. A decade later, the asexuals had declined in frequency and were less infected than sexuals. Over time, the mean infection prevalence of asexuals equaled that of sexuals but varied far more. This variation in asexual infection prevalence suggests the potential for parasite-mediated fluctuations in asexual fitness. Accordingly, we detected fitness consequences of the shift in parasite selection: when they were less infected than sexuals, asexuals increased in frequency in the field and in paired mesocosms that isolated the effect of parasites. The match between field and experiment argues that coevolving parasites drive temporal change in the relative fitness and frequency of asexuals, potentially promoting the coexistence of reproductive modes in P. antipodarum. [ABSTRACT FROM AUTHOR]

Winnerless coevolution of hosts and parasites could exhibit Red Queen dynamics, which is characterized by parasite-driven cyclic switching of expressed host phenotypes. We hypothesize that the application of antibiotics to suppress the reproduction of parasites can provide an opportunity for the hosts to escape such winnerless coevolution. Here, we formulate a minimal mathematical model of host–parasite interaction involving multiple host phenotypes that are targeted by adapting parasites. Our model predicts the levels of antibiotic effectiveness that can steer the parasite-driven cyclic switching of host phenotypes (oscillations) to a stable equilibrium of host survival. Our simulations show that uninterrupted application of antibiotic with high-level effectiveness (greater than 85%) is needed to escape the Red Queen dynamics. Interrupted and low level of antibiotic effectiveness are indeed useless to stop host–parasite coevolution. This study can be a guide in designing good practices and protocols to minimize the risk of further progression of parasitic infections.

Abstract: We studied parasitism rate by the terrestrial mite Leptus killingtoni Turk (Acari: Erythraeidae) on asexual parthenogenetic damselflies, Ischnura hastata (Say), and sexual Ischnura pumilio (Charpentier) (Odonata: Coenagrionidae) on Pico island (Azores, Portugal). We sampled 52 water bodies on the island and recorded whether Ischnura specimens were parasitized. Half of the water bodies had either dried up or were almost dry or did not have Ischnura populations. In the remaining 23 ponds, mite parasitism was extremely low, with only 3.6% of I. hastata females bearing one or more mites. Ischnura pumilio was rare on the island (61 specimens examined) and had also very few parasites (9.8% parasitism). We examined the biology of the mite and its effects on the host, by studying mite attachment behavior and seasonal abundance, in an intensive study of one pond (Lagoa do Landroal). At this pond, mite prevalence peaked at the start of the sampling period, with 32% of females of I. hastata parasitized and decreased continuously until the end of the study, when only 2% were parasitized. The analysis of mark–recapture histories of 1 748 females of I. hastata indicates that mites did not affect female survival or recapture rate. Our results suggest that L. killingtoni is unlikely to represent a significant selective factor for odonates on the island of Pico, if its density is as low as during the period of our study, although it could be relevant when it is locally abundant or during periods of outbreak. [ABSTRACT FROM AUTHOR]

Abstract: Asexual lineages can grow at a faster rate than sexual lineages. Why then is sexual reproduction so widespread? Much empirical evidence supports the Red Queen hypothesis. Under this hypothesis, coevolving parasites favour sexual reproduction by adapting to infect common asexual clones and driving them down in frequency. One limitation, however, seems to challenge the generality of the Red Queen: in theoretical models, parasites must be very virulent to maintain sex. Moreover, experiments show virulence to be unstable, readily shifting in response to environmental conditions. Does variation in virulence further limit the ability of coevolving parasites to maintain sex? To address this question, we simulated temporal variation in virulence and evaluated the outcome of competition between sexual and asexual females. We found that variation in virulence did not limit the ability of coevolving parasites to maintain sex. In fact, relatively high variation in virulence promoted parasite‐mediated maintenance of sex. With sufficient variation, sexual females persisted even when mean virulence fell well below the threshold virulence required to maintain sex under constant conditions. We conclude that natural variation in virulence does not limit the relevance of the Red Queen hypothesis for natural populations; on the contrary, it could expand the range of conditions over which coevolving parasites can maintain sex. [ABSTRACT FROM AUTHOR]

Background: The persistence of high genetic variability in natural populations garners considerable interest among ecologists and evolutionary biologists. One proposed hypothesis for the maintenance of high levels of genetic diversity relies on frequency-dependent selection imposed by parasites on host populations (Red Queen hypothesis). A complementary hypothesis suggests that a trade-off between fitness costs associated with tolerance to stress factors and fitness costs associated with resistance to parasites is responsible for the maintenance of host genetic diversity. Results: The present study investigated whether host resistance to parasites is traded off with tolerance to environmental stress factors (high/low temperatures, high salinity), by comparing populations of the freshwater snail Melanoides tuberculata with low vs. high clonal diversity. Since polyclonal populations were found to be more parasitized than populations with low clonal diversity, we expected them to be tolerant to environmental stress factors. We found that clonal diversity explained most of the variation in snail survival under high temperature, thereby suggesting that tolerance to high temperatures of clonally diverse populations is higher than that of populations with low clonal diversity. Conclusions: Our results suggest that resistance to parasites may come at a cost of reduced tolerance to certain environmental stress factors. [ABSTRACT FROM AUTHOR]

Host-parasite systems provide convincing examples of Red Queen co-evolutionary dynamics. Yet, a key process underscored in Van Valen's theory - that arms race dynamics can result in extinction - has never been documented. One reason for this may be that most sampling designs lack the breadth needed to illuminate the rapid pace of adaptation by pathogen populations. In this study, we used a 25-year temporal sampling to decipher the demographic history of a plant pathogen: the poplar rust fungus, Melampsora larici-populina. A major adaptive event occurred in 1994 with the breakdown of R7 resistance carried by several poplar cultivars widely planted in Western Europe since 1982. The corresponding virulence rapidly spread in M. larici-populina populations and nearly reached fixation in northern France, even on susceptible hosts. Using both temporal records of virulence profiles and temporal population genetic data, our analyses revealed that (i) R7 resistance breakdown resulted in the emergence of a unique and homogeneous genetic group, the so-called cultivated population, which predominated in northern France for about 20 years, (ii) selection for Vir7 individuals brought with it multiple other virulence types via hitchhiking, resulting in an overall increase in the population-wide number of virulence types and (iii) - above all - the emergence of the cultivated population superseded the initial population which predominated at the same place before R7 resistance breakdown. Our temporal analysis illustrates how antagonistic co-evolution can lead to population extinction and replacement, hence providing direct evidence for the escalation process which is at the core of Red Queen dynamics. [ABSTRACT FROM AUTHOR]

Given the cost of sex, outcrossing populations should be susceptible to invasion and replacement by self-fertilization or parthenogenesis. However, biparental sex is common in nature, suggesting that cross-fertilization has substantial short-term benefits. The Red Queen hypothesis (RQH) suggests that coevolution with parasites can generate persistent selection favoring both recombination and outcrossing in host populations. We tested the prediction that coevolving parasites can constrain the spread of self-fertilization relative to outcrossing. We introduced wild-type Caenorhabditis elegans hermaphrodites, capable of both self-fertilization, and outcrossing, into C. elegans populations that were fixed for a mutant allele conferring obligate outcrossing. Replicate C. elegans populations were exposed to the parasite Serratia marcescens for 33 generations under three treatments: a control (avirulent) parasite treatment, a fixed (nonevolving) parasite treatment, and a copassaged (potentially coevolving) parasite treatment. Self-fertilization rapidly invaded C. elegans host populations in the control and the fixed-parasite treatments, but remained rare throughout the entire experiment in the copassaged treatment. Further, the frequency of the wild-type allele (which permits selfing) was strongly positively correlated with the frequency of self-fertilization across host populations at the end of the experiment. Hence, consistent with the RQH, coevolving parasites can limit the spread of self-fertilization in outcrossing populations. [ABSTRACT FROM AUTHOR]

Mistletoe can have a major impact on the fitness of the host plant. If there is more than one species of mistletoe on the same host tree, the overall impact might be amplified. We report the occurrence of more than one species of mistletoe on the same host tree. Although it is not a rule in the field, to our knowledge, there have been no studies of this topic. In most cases, two species of mistletoe were recorded on the same host tree, although we recorded three species of mistletoe on one occasion. This demonstrates that different species of mistletoe can be compatible with the same host species. Therefore, compatibility (structural and physiological) might be an important factor for the occurrence of mistletoe. Recent studies have shown that if the mistletoe does not "recognize" the host species, the deposited seeds will germinate but the haustorium will not penetrate the host branch. This is probably the primary mechanism in the establishment of more than one species of mistletoe on the same host, which can trigger a cascade of harmful effects for the host species.

Evolutionary biology has yet to reconcile the ubiquity of sex with its costs relative to asexual reproduction. Here, we test the hypothesis that coevolving parasites maintain sex in their hosts. Specifically, we examined the distributions of sexual reproduction and susceptibility to local parasites within a single population of freshwater snails ( Potamopyrgus antipodarum). Susceptibility to local trematode parasites (Microphallus sp.) is a relative measure of the strength of coevolutionary selection in this system. Thus, if coevolving parasites maintain sex, sexual snails should be common where susceptibility is high. We tested this prediction in a mixed population of sexual and asexual snails by measuring the susceptibility of snails from multiple sites in a lake. Consistent with the prediction, the frequency of sexual snails was tightly and positively correlated with susceptibility to local parasites. Strikingly, in just two years, asexual females increased in frequency at sites where susceptibility declined. We also found that the frequency of sexual females covaries more strongly with susceptibility than with the prevalence of Microphallus infection in the field. In linking susceptibility to the frequency of sexual hosts, our results directly implicate spatial variation in coevolutionary selection in driving the geographic mosaic of sex. [ABSTRACT FROM AUTHOR]

The RQH (Red Queen hypothesis), which argues that hosts need to be continuously finding new ways to avoid parasites that are able to infect common host genotypes, has been at the center of discussions on the maintenance of sex. This is because diversity is favored under the host-parasite coevolution based on negative frequency-dependent selection, and sexual reproduction is a mechanism that generates genetic diversity in the host population. Together with parasite infections, sexual organisms are usually under sexual selection, which leads to mating skew or mating success biased toward males with a particular phenotype. Thus, strong mating skew would affect genetic variance in a population and should affect the benefit of the RQH. However, most models have investigated the RQH under a random mating system and not under mating skew. In this study, I show that sexual selection and the resultant mating skew may increase parasite load in the hosts. An IBM (individual-based model), which included host-parasite interactions and sexual selection among hosts, demonstrates that mating skew influenced parasite infection in the hosts under various conditions. Moreover, the IBM showed that the mating skew evolves easily in cases of male-male competition and female mate choice, even though it imposes an increased risk of parasite infection on the hosts. These findings indicated that whether the RQH favored sexual reproduction depended on the condition of mating skew. That is, consideration of the host mating system would provide further understanding of conditions in which the RQH favors sexual reproduction in real organisms. [ABSTRACT FROM AUTHOR]