What limits the evolutionary emergence of pathogens?

The ability of a pathogen to cause an epidemic when introduced in a new host population often relies on its ability to adapt to this new environment. Here, we give a brief overview of recent theoretical and empirical studies of such evolutionary emergence of pathogens. We discuss the effects of several ecological and genetic factors that may affect the likelihood of emergence: migration, life history of the infectious agent, host heterogeneity, and the rate and effects of mutations. We contrast different modelling approaches and indicate how details in the way we model each step of a life cycle can have important consequences on the predicted probability of evolutionary emergence. These different theoretical perspectives yield important insights into optimal surveillance and intervention strategies, which should aim for a reduction in the emergence (and re-emergence) of infectious diseases.     

What limits meiotic crossovers?

Comment on: Crismani W, et al. Science 2012; 336:1588-90.     

What limits the velocity of fast-skeletal muscle contraction in mammals?

In rat skeletal muscle the unloaded shortening velocity (Vo) is defined by the myosin isoform expressed in the muscle fibre. In 2001 we suggested that ADP release from actomyosin in solution (controlled by k(-AD)) was of the right size to limit Vo. However, to compare mechanical and solution kinetic data required a series of corrections to compensate for the differences in experimental conditions (0.5 M KCl, 22 degrees C for kinetic assays of myosin, 200 mM ionic strength, 12 degrees C to measure Vo). Here, a method was developed to prepare heavy meromyosin (HMM) from pure myosin isoforms isolated from single muscle fibres and to study k(-AD) (determined from the affinity of the acto-myosin complex for ADP, KAD) and the rate of ATP-induced acto-HMM dissociation (controlled by K1k+2) under the same experimental condition used to measure Vo). In fast-muscle myosin isolated from a wide range of mammalian muscles, k(-AD) was found to be too fast to limit Vo, whereas K1k+2 was of the right magnitude for ATP-induced dissociation of the cross-bridge to limit shortening velocity. The result was unexpected and prompted further experiments using the stopped-flow approach on myosin subfragment-1 (S1) and HMM obtained from bulk preparations of rabbit and rat muscle. These confirmed that the rate of cross-bridge dissociation by ATP limits the velocity of contraction for fast myosin II isoforms at 12 degrees C, while k(-AD) limits the velocity of slow myosin II isoforms. Extrapolating our data to 37 degrees C suggests that at physiological temperature the rate of ADP dissociation may limit Vo for both isoforms.     

What limits nitrate uptake from soil?

Abstract. An accepted view, that unless nitrate concentrations in the soil solution are very low (e.g. below 0.1–0.2 mol m^?3) the growth of high-yielding crops is not limited by the availability of nitrogen, is challenged. Conventional analyses of nutrient supply and demand, based on calculations of apparent inflow rates (uptake rates per unit total root length) are invalid. Apparent inflow rates are inversely proportional to root length. The convention of using total root length grossly overestimates the fraction of the root system active in nutrient uptake. Consequently, inflow rates based on total root lengths underestimate the true values, indicating unrealistically low nutrient concentration differentials between bulk soil and root surfaces required to drive uptake. An alternative method of analysis is suggested. This is based on total nutrient uptake rather than on inflow rate. Measurements of the former do not depend on estimates of active root length and can be made directly and reliably. The method was applied to data obtained from a pot experiment using spring wheat (Triticum aestivum L., cv. Wembley) grown in soil without nitrogen fertilizer (N₀) or with nitrogen fertilizer equivalent to 200kg N ha^?1 (N⁺). Soil nitrate concentrations calculated using the conventional method based on total root length, suggested that any increases in concentration above those measured in the N⁰ treatment should not have resulted in increased uptake and growth. However, the N⁺ plants were always bigger than those in the No treatment, refuting this suggestion. Theoretical uptakes of nitrogen (calculated initially on the basis of a fully active root system) were adjusted, by reducing the effective root length incrementally, until the theoretical uptake matched the measured net uptake of nitrogen. The mean fractions of the root systems likely to have been involved in nitrate uptake were 11% and 3.5% of the total lengths of root in the N⁰ and N⁺ treatments, respectively.     

What limits photosynthesis? Identifying the thermodynamic constraints of the terrestrial biosphere within the Earth system

Photosynthesis converts sunlight into the chemical free energy that feeds the Earth's biosphere, yet at levels much lower than what thermodynamics would allow for. I propose here that photosynthesis is nevertheless thermodynamically limited, but this limit acts indirectly on the material exchange. I substantiate this proposition for the photosynthetic activity of terrestrial ecosystems, which are notably more productive than the marine biosphere. The material exchange for terrestrial photosynthesis involves water and carbon dioxide, which I evaluate using global observation-based datasets of radiation, photosynthesis, precipitation and evaporation. I first calculate the conversion efficiency of photosynthesis in terrestrial ecosystems and its climatological variation, with a median efficiency of 0.77% (n = 13,274). The rates tightly correlate with evaporation on land (r² = 0.87), which demonstrates the importance of the coupling of photosynthesis to material exchange. I then infer evaporation from the maximum material exchange between the surface and the atmosphere that is thermodynamically possible using datasets of solar radiation and precipitation. This inferred rate closely correlates with the observation-based land evaporation dataset (r² = 0.84). When this rate is converted back into photosynthetic activity, the resulting patterns correlate highly with the observation-based dataset (r² = 0.66). This supports the interpretation that it is not energy directly that limits terrestrial photosynthesis, but rather the material exchange that is driven by sunlight. This interpretation can explain the very low, observed conversion efficiency of photosynthesis in terrestrial ecosystems as well as its spatial variations. More generally, this implies that one needs to take the necessary material flows and exchanges associated with life into account to understand the thermodynamics of life. This, ultimately, requires a perspective that links the activity of the biosphere to the thermodynamic constraints of transport processes in the Earth system.     

What limits the efficiency of double-strand break-dependent stress-induced mutation in Escherichia coli?

Stress-induced mutation is a collection of molecular mechanisms in bacterial, yeast and human cells that promote mutagenesis specifically when cells are maladapted to their environment, i.e. when they are stressed. Here, we review one molecular mechanism: double-strand break (DSB)-dependent stress-induced mutagenesis described in starving Escherichia coli. In it, the otherwise high-fidelity process of DSB repair by homologous recombination is switched to an error-prone mode under the control of the RpoS general stress response, which licenses the use of error-prone DNA polymerase, DinB, in DSB repair. This mechanism requires DSB repair proteins, RpoS, the SOS response and DinB. This pathway underlies half of spontaneous chromosomal frameshift and base substitution mutations in starving E. coli [Proc Natl Acad Sci USA 2011;108:13659-13664], yet appeared less efficient in chromosomal than F' plasmid-borne genes. Here, we demonstrate and quantify DSB-dependent stress-induced reversion of a chromosomal lac allele with DSBs supplied by I-SceI double-strand endonuclease. I-SceI-induced reversion of this allele was previously studied in an F'. We compare the efficiencies of mutagenesis in the two locations. When we account for contributions of an F'-borne extra dinB gene, strain background differences, and bypass considerations of rates of spontaneous DNA breakage by providing I-SceI cuts, the chromosome is still ～100 times less active than F. We suggest that availability of a homologous partner molecule for recombinational break repair may be limiting. That partner could be a duplicated chromosomal segment or sister chromosome.     

What causes population cycles of forest Lepidoptera?

Hypotheses for the causes of regular cycles in populations of forest Lepidoptera have invoked pathogen-insect or foliage-insect interactions. However, the available data suggest that forest caterpillar cycles are more likely to be the result of interactions with insect parasitoids, an old argument that seems to have been neglected in recent years.     

What limits clutch size? A test of the incubation‐capacity hypothesis in a high‐elevation population of Mountain Bluebirds

Most studies of factors that limit the number of eggs that birds lay have focused on the disadvantages of having too many young to feed. Less attention has been paid to the consequences of having a large number of eggs to incubate. The incubation‐capacity hypothesis proposes that females lay as many eggs as they can effectively incubate. We tested this hypothesis in 2018 in a montane population of Mountain Bluebirds (Sialia currucoides). Most females in this population lay five or six eggs; clutches of seven occur, but are rare. We added eggs to some nests, forcing females to incubate seven eggs, while leaving other nests as controls. Among females completing incubation, those with enlarged clutches hatched as many eggs as did control females, and did so in the same amount of time. This was despite an extended period of unusually cold and often wet weather that occurred when many females were incubating. Our results firmly reject the suggestion that females typically lay no more than six eggs because they cannot effectively heat seven eggs. One or more other factors must limit clutch size. One possible factor is suggested by the fact that during the period of inclement weather, more females with enlarged clutches than control females appeared to abandon nests before completing incubation. Because larger clutches require more energy to incubate, females with seven eggs during energetically stressful conditions could more quickly reach the point where they lack sufficient energy for both incubation and self‐maintenance. Such conditions may occur frequently enough in the montane environment that, on average, laying seven eggs results in reduced lifetime reproductive success.     

What are the relative costs,limits and correlates of increased degree of serotiny?

There is variability in the period that serotinous species retain seeds in protective closed cones and in the sizes of the cones. Seed predation and inter‐fire recruitment have been suggested to be reasons for this variability. I argue against these two reasons. Variation in annual rates of increase in fecundity and in numbers of flowering episodes before fire should be correlated with the degree of serotiny. These two attributes are a consequence of cone size, plant architecture and degree of serotiny.     

What changed the demography of an introduced population of an herbivorous lady beetle?

1. The population dynamics of an introduced population of Epilachna niponica (Lewis) (Coleoptera: Coccinellidae) was investigated for a 7-year period following its introduction to a site outside of its natural range. A population from Asiu Experimental Forest was introduced to Kyoto University Botanical Garden, 10 km south of its natural distribution.
2. Arthropod predation was much lower in the introduced than in the source population. As a result of the lower predation in the Botanical Garden, larvae reached densities five times higher than in the Asiu Forest and host plants were frequently defoliated. Food shortage caused larval deaths from starvation and increased dispersal.
3. The density of the introduced population was much more variable than that of the source population. The variation in population density in both the introduced and source populations is limited by density-dependent reduction in fecundity and female survival. However, variation in the introduced population's density was increased due to host plant defoliation that resulted in overcompensating density-dependent mortality. In years with high larval density plants were defoliated and this increased adult mortality during the prehibernation period. Besides, the density-dependent regulatory mechanisms that produce population stability were weaker in the introduced population than in the source population.     

What limits herb biomass in grasslands: competition or herbivory?

Competition and herbivory are two of the main forces shaping plant communities. Although several studies have investigated their impact on plant populations separately, few investigations have examined how they might interact. With the purpose of clarifying the combined roles of competition and herbivory on herb biomass in a grassland, we assessed the effects of different herbivores with reduced grass competition. We conducted a field experiment in 2000-2001 in a British acid grassland (Oak Mead), where we experimentally reduced grass biomass and excluded rabbits, insects and molluscs in a factorial design. Removing the grasses from Oak Mead dramatically increased herb biomass and total above-ground biomass. Herbivore exclusions (i.e. rabbits, insects and molluscs) did not affect total above-ground biomass, but they altered relative abundance of several species. Grass removal and rabbit exclusion had positive interactions on biomass of several herb species, and there were some subtle interactions between different herbivore groups: monocots benefitted when both rabbits and molluscs were excluded, and some herb species had greater biomass when insects and rabbits were absent. We then compared the results with a 10-year experiment that manipulated similar variables in neighbouring grassland (Nashs Field). The comparison between Oak Mead and Nashs Field showed that cessation of herbicide application returns the system to its previous state of grass dominance after 3 years. Therefore, even when herbs were more abundant, they could not prevent reinvasion of the grasses once external factors were removed.     

What can genetics tell us about population connectivity?

Genetic data are often used to assess ‘population connectivity’ because it is difficult to measure dispersal directly at large spatial scales. Genetic connectivity, however, depends primarily on the absolute number of dispersers among populations, whereas demographic connectivity depends on the relative contributions to population growth rates of dispersal vs. local recruitment (i.e. survival and reproduction of residents). Although many questions are best answered with data on genetic connectivity, genetic data alone provide little information on demographic connectivity. The importance of demographic connectivity is clear when the elimination of immigration results in a shift from stable or positive population growth to negative population growth. Otherwise, the amount of dispersal required for demographic connectivity depends on the context (e.g. conservation or harvest management), and even high dispersal rates may not indicate demographic interdependence. Therefore, it is risky to infer the importance of demographic connectivity without information on local demographic rates and how those rates vary over time. Genetic methods can provide insight on demographic connectivity when combined with these local demographic rates, data on movement behaviour, or estimates of reproductive success of immigrants and residents. We also consider the strengths and limitations of genetic measures of connectivity and discuss three concepts of genetic connectivity that depend upon the evolutionary criteria of interest: inbreeding connectivity, drift connectivity, and adaptive connectivity. To conclude, we describe alternative approaches for assessing population connectivity, highlighting the value of combining genetic data with capture‐mark‐recapture methods or other direct measures of movement to elucidate the complex role of dispersal in natural populations.     

What do simple models reveal about the population dynamics of a cooperatively breeding species?

Research on cooperatively breeding species has shown that their population dynamics differ from those of conventional breeders. Populations of cooperators are structured into groups, and group‐level Allee effects are likely common. We assess the ability of phenomenological models, lacking explicit group structure, to describe population dynamics in cooperative meerkats Suricata suricatta, and we assess potential Allee effects at the population level. Using maximum likelihood model fitting and information theoretic model selection, applied to time series data from a wild meerkat population, we find simple models that incorporate rainfall and conventional density dependence to be the most parsimonious of the models considered. Detecting no population‐level Allee effect, we conclude that explicit consideration of population structure will be key to understanding the mechanisms behind population dynamics in cooperatively breeding species.