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Virus host shifts, where a virus transmits to and infects a novel host species, are a major source of emerging infectious disease. Genetic similarity between eukaryotic host species has been shown to be an important determinant of the outcome of virus host shifts, but it is unclear if this is the case for prokaryotes where anti-virus defences can be transmitted by horizontal gene transfer and evolve rapidly. Here, we measure the susceptibility of 64 strains of Staphylococcaceae bacteria (48 strains of Staphylococcus aureus and 16 non-S. aureus species spanning 2 genera) to the bacteriophage ISP, which is currently under investigation for use in phage therapy. Using three methods-plaque assays, optical density (OD) assays, and quantitative (q)PCR-we find that the host phylogeny explains a large proportion of the variation in susceptibility to ISP across the host panel. These patterns were consistent in models of only S. aureus strains and models with a single representative from each Staphylococcaceae species, suggesting that these phylogenetic effects are conserved both within and among host species. We find positive correlations between susceptibility assessed using OD and qPCR and variable correlations between plaque assays and either OD or qPCR, suggesting that plaque assays alone may be inadequate to assess host range. Furthermore, we demonstrate that the phylogenetic relationships between bacterial hosts can generally be used to predict the susceptibility of bacterial strains to phage infection when the susceptibility of closely related hosts is known, although this approach produced large prediction errors in multiple strains where phylogeny was uninformative. Together, our results demonstrate the ability of bacterial host evolutionary relatedness to explain differences in susceptibility to phage infection, with implications for the development of ISP both as a phage therapy treatment and as an experimental system for the study of virus host shifts.

Pre-registration of experiment designed to assess the costs of post-natal parental investment, through manipulating the duration of parental care by cross fostering chicks of different ages

Advances in spring phenology are among the clearest biological responses to climate warming. In the ephemeral temperate deciduous forest food webs, at the vanguard of research on temperature’s effect on trophic interactions, most work has focused on the average timing of phenological events. In comparison, effects of temperature on the abundance of individuals and their seasonal spread is understudied, despite the potential for profound impacts on trophic interactions. Here we use a new method to show that for the guild of forest caterpillars, warmer spring conditions not only advance the timing of the phenological distribution of abundance by -4.96 days oC-1, but also increase its height by 34% oC-1. This increase in the maximum density of caterpillars with rising temperatures is likely to have major implications for both herbivory pressure and the resources available to secondary consumers.

Genes within the major histocompatibility complex (MHC) are the most variable identified in vertebrates. Pathogen-mediated selection is believed to be the main force maintaining MHC diversity. However, relatively few studies have demonstrated contemporary selection on MHC genes. Here, we examine associations between MHC variation and several fitness measurements including total fitness and five fitness components, in 3400 wild Soay sheep (Ovis aries) monitored between 1989 and 2012. In terms of total fitness, measured as lifetime breeding success of all individuals born, we found haplotypes named C and D were associated with decreased and increased male total fitness respectively. In terms of fitness components, juvenile survival was associated with haplotype divergence while individual haplotypes (C, D and F) were associated with adult fitness components. Consistent with the increased male total fitness, the rarest haplotype D has increased in frequency throughout the study period more than expected under neutral expectations. Our results demonstrate contemporary natural selection is acting on MHC class II genes in Soay sheep and the mode of selection on specific fitness components can be different mode from selection on total fitness.

The major histocompatibility complex (MHC) is the most variable gene family known in vertebrates. Parasite-mediated selection (PMS) is believed to be the main force maintaining diversity at MHC genes, but it has proven hard to demonstrate the exact PMS regime that is acting in natural populations. Demonstrating contemporary selection on MHC alleles is not trivial, and previous work has been constrained by limited genetic tools, low sample sizes, short time scales and anticonservative statistical approaches. Here, we use a conservative statistical approach to examine associations between MHC genes and fitness components, using haplotypes of expressed MHC class II genes in a large sample of Soay sheep ( Ovis aries ) monitored over their lifetimes between 1989 and 2012. Of the eight MHC haplotypes (A-H) identified, we found that haplotype C was associated with decreased male breeding success, haplotype D was associated with increased female life span, and haplotype F was associated with decreased female life span. Consistent with the increased lifespan in females, haplotype D has increased in frequency throughout the study period. Our results suggest the existence of contemporary balancing selection on MHC class II genes in Soay sheep as might be expected under the hypotheses of rare allele advantage or fluctuating selection and do not support an effect of heterozygous advantage.

Most theoretical studies have explored the evolution of plasticity when the environment, and therefore the optimal trait value, varies in time or space. When the environment varies in time and space, we show that genetic adaptation to Markovian temporal fluctuations depends on the between-generation autocorrelation in the environment in exactly the same way that genetic adaptation to spatial fluctuations depends on the probability of philopatry. This is because both measure the correlation in parent-offspring environments and therefore the effectiveness of a genetic response to selection. If the capacity to genetically respond to selection is stronger in one dimension (e.g., space), then plasticity mainly evolves in response to fluctuations in the other dimension (e.g., time). If the relationships between the environments of development and selection are the same in time and space, the evolved plastic response to temporal fluctuations is useful in a spatial context and genetic differentiation in space is reduced. However, if the relationships between the environments of development and selection are different, the optimal level of plasticity is different in the two dimensions. In this case, the plastic response that evolves to cope with temporal fluctuations may actually be maladaptive in space, resulting in the evolution of hyperplasticity or negative plasticity. These effects can be mitigated by spatial genetic differentiation that acts in opposition to plasticity resulting in counter-gradient variation. These results highlight the difficulty of making space-for-time substitutions in empirical work but identify the key parameters that need to be measured in order to test whether space-for-time substitutions are likely to be valid.

Host shifts–where a pathogen jumps between different host species–are an important source of emerging infectious disease. With on-going climate change there is an increasing need to understand the effect changes in temperature may have on emerging infectious disease. We investigated whether species’ susceptibilities change with temperature and ask if susceptibility is greatest at different temperatures in different species. We infected 45 species of Drosophilidae with an RNA virus and measured how viral load changes with temperature. We found the host phylogeny explained a large proportion of the variation in viral load at each temperature, with strong phylogenetic correlations between viral loads across temperature. The variance in viral load increased with temperature, while the mean viral load did not. This suggests that as temperature increases the most susceptible species become more susceptible, and the least susceptible less so. We found no significant relationship between a species’ susceptibility across temperatures, and proxies for thermal optima (critical thermal maximum and minimum or basal metabolic rate). These results suggest that whilst the rank order of species susceptibilities may remain the same with changes in temperature, some species may become more susceptible to a novel pathogen, and others less so., Author summary Emerging infectious diseases are often the result of a host shift, where a pathogen jumps from one host species into another. Understanding the factors underlying host shifts is a major goal for infectious disease research. This effort has been further complicated by the fact that host-parasite interactions are now taking place in a period of unprecedented global climatic warming. Here, we ask how host shifts are affected by temperature by carrying out experimental infections using an RNA virus across a wide range of related species, at three different temperatures. We find that as temperature increases the most susceptible species become more susceptible, and the least susceptible less so. This has important consequences for our understanding of host shift events in a changing climate as it suggests that temperature changes may affect the likelihood of a host shift into certain species.

Conflict between organisms can lead to reciprocal adaptation that manifests itself as an increased evolutionary rate in genes mediating the conflict. This adaptive signature has been observed in RNA interference (RNAi) pathway genes involved in the suppression of viruses and transposable elements in Drosophila melanogaster, suggesting that a subset of Drosophila RNAi genes may be locked into an arms race with these parasites. However, it is not known whether rapid evolution of RNAi genes is a general phenomenon across invertebrates, or which RNAi genes generally evolve adaptively. Here we use population genomic data from eight invertebrate species to infer rates of adaptive sequence evolution, and to test for past and ongoing selective sweeps in RNAi genes. We assess rates of adaptive protein evolution across species using a formal meta-analytic framework to combine data across species, and by implementing a multispecies generalised linear mixed model of mutation counts. Across species, we find that RNAi genes display a greater rate of adaptive protein substitution than other genes, and that this is primarily mediated by positive selection acting on the genes most likely to defend against viruses and transposable elements. In contrast, evidence for recent selective sweeps is broadly spread across functional classes of RNAi genes, and differs substantially among species. Finally, we identify genes that exhibit elevated adaptive evolution across the analysed insect species, perhaps due to concurrent parasite-mediated arms races.

"We propose to change the default P-value threshold forstatistical significance for claims of new discoveries from 0.05 to 0.005."

1. In many birds, hatching asynchrony is a common phenomenon, primarily driven by patterns of incubation behaviour. However, experimental results in blue tits (Cyanistes caeruleus) have shown that asynchrony is reduced by intrinsic properties of later eggs that accelerate pre-natal development.2. These intrinsic differences between early and late eggs could be driven by changes in resource availability to females, which are then passively passed onto the egg. Alternatively, it may be due to an anticipatory maternal effect, wherein some signal or resource is actively placed within the egg, which is beneficial to those eggs laid late within the clutch. 3. In order to distinguish between these hypotheses we designed a supplementary feeding experiment, wherein females were provided with food at certain times during the laying phase. This had no discernible effect on development rate, or other egg characteristics, consistent with anticipatory maternal effects.4. Using a larger data set we also tested whether natural environmental variation (weather) during egg formation affected maternal investment in eggs. Similarly, egg characteristics were found to be relatively insensitive to the environmental variation, supporting the experimental results.

One consequence of rising spring temperatures is that the optimum timing of key life history events may advance. Where this is the case, a population’s fate may depend on the degree to which it is able to track a change in the optimum timing either via plasticity or via adaptation. Estimating the effect that temperature change will have on optimum timing using standard approaches is logistically challenging, with the result that very few estimates of this important parameter exist. Here we adopt an alternative statistical method that substitutes space for time to estimate the temperature-sensitivity of the optimum timing of 22 plant species based on >200,000 spatiotemporal phenological observations from across the UK. We find that first leafing and flowering dates are sensitive to forcing (spring) temperatures, with optimum timing advancing by 3 days°C-1 and plastic responses to forcing between -3 and -8 days°C-1. Chilling (autumn/winter) temperatures and photoperiod tend to be important cues for species with early and late phenology respectively. For most species we find that plasticity is adaptive and for seven species plasticity is sufficient to track geographic variation in the optimum phenology. For four species we find that plasticity is significantly steeper than the optimum slope that we estimate between forcing temperature and phenology, and we examine possible explanations for this countergradient pattern, including local adaptation.

Projecting the fates of populations under climate change is one of global change biology’s foremost challenges. Here we seek to identify the contributions that temperature-mediated local adaptation and plasticity make to spatial variation in British bird nesting phenology, a phenotypic trait showing strong responses to warming. We apply a mixed modeling framework to a Britain-wide spatiotemporal dataset comprising >100,000 records of first egg dates from four single-brooded passerine bird species. The average temperature during a specific time period (sliding-window) strongly predicts spatiotemporal variation in lay date. All four species exhibit phenological plasticity, advancing lay date by 2–5 days°C-1. The initiation of this sliding-window is delayed further north, which may be a response to a photoperiod threshold. Using clinal trends in phenology and temperature we are able to estimate the temperature sensitivity of selection on lay date (B), but our estimates are highly sensitive to the temporal position of the sliding-window. If the sliding-window is of fixed duration with a start date determined by photoperiod we find B is tracked by phenotypic plasticity. If, instead, we allow the start and duration of the sliding-window to change with latitude, we find plasticity does not track B, though at odds with theoretical expectations, our estimates of B differ across latitude versus longitude. We argue that a model combining photoperiod and mean temperature is most consistent with current understanding of phenological cues in passerines, the results of which suggest that each species could respond to projected increases in spring temperatures through plasticity alone. However, our estimates of B require further validation.