The emergence and evolution of canine parvovirus—an example of recent host range mutation

Canine parvovirus (CPV) emerged in 1978 an a new pathogen of dogs, which spread around the world and now appears endemic in the domesticated and wild dog populations in all countries. CPV is over 98% identical in DNA sequence to viruses which had been known for many years in cats, mink and raccoons, and genetic analysis has revealed that the differences in canine host range are determined by a small number of changes in the capsid protein gene. Comparison of the atomic structures of the CPV and FPV capsids shows that the changes affecting host range and virus-specific antigenic sites are exposed on the capsid surface in three different positions within a raised region at the threefold axis of symmetry, which is also the site of major antigenic determinants on the capsid. Three types of CPV have been defined by antigenic analysis with monoclonal antibodies. The original CPV strain (called CPV type-2) was only present in nature for a few years, and by 1981 it had been largely replaced in nature by a variant of CPV (CPV type 2a), which in turn replaced between 1984 and 1990 by a further variant (CPV type-2b). Those viruses differed by less than 0.2% of their genome sequences, but in each case the replacement apparently occurred on a global scale. The true ancestry of CPV is not clear, but the apparent emergence of the new types of CPV and its subsequent evolution suggest that this is a useful model for the emergence of new viruses with extended host ranges and their continuing adaptation.     

When can host shifts produce congruent host and parasite phylogenies? A simulation approach

Congruence between host and parasite phylogenies is often taken as evidence for cospeciation. However, 'pseudocospeciation', resulting from host-switches followed by parasite speciation, may also generate congruent trees. To investigate this process and the conditions favouring its appearance, we here simulated the adaptive radiation of a parasite onto a new range of hosts. A very high congruence between the host tree and the resulting parasite trees was obtained when parasites switched between closely related hosts. Setting a shorter time lag for speciation after switches between distantly related hosts further increased the degree of congruence. The shape of the host tree, however, had a strong impact, as no congruence could be obtained when starting with highly unbalanced host trees. The strong congruences obtained were erroneously interpreted as the result of cospeciations by commonly used phylogenetic software packages despite the fact that all speciations resulted from host-switches in our model. These results highlight the importance of estimating the age of nodes in host and parasite phylogenies when testing for cospeciation and also demonstrate that the results obtained with software packages simulating evolutionary events must be interpreted with caution.     

The role of ecological feedbacks in the evolution of host defence: what does theory tell us?

Hosts have evolved a diverse range of defence mechanisms in response to challenge by infectious organisms (parasites and pathogens). Whether defence is through avoidance of infection, control of the growth of the parasite once infected, clearance of the infection, tolerance to the disease caused by infection or innate and/or acquired immunity, it will have important implications for the population ecology (epidemiology) of the host-parasite interaction. As a consequence, it is important to understand the evolutionary dynamics of defence in the light of the ecological feedbacks that are intrinsic to the interaction. Here, we review the theoretical models that examine how these feedbacks influence the nature and extent of the defence that will evolve. We begin by briefly comparing different evolutionary modelling approaches and discuss in detail the modern game theoretical approach (adaptive dynamics) that allows ecological feedbacks to be taken into account. Next, we discuss a number of models of host defence in detail and, in particular, make a distinction between 'resistance' and 'tolerance'. Finally, we discuss coevolutionary models and the potential use of models that include genetic and game theoretical approaches. Our aim is to review theoretical approaches that investigate the evolution of defence and to explain how the type of defence and the costs associated with its acquisition are important in determining the level of defence that evolves.     

Refuge evolution and the population dynamics of coupled host—parasitoid associations

Summary We have investigated the theoretical consequences of character evolution for the population dynamics of a host—parasitoid interaction, assuming a monophagous parasitoid. In the purely ecological model it is assumed that hosts can escape parasitism by being in absolute refuges. A striking property of this model is a threshold effect in control of the host by the parasitoid, when host density dependence is weak. The approximate criteria for the parasitoid to regulate the host to low densities are (1) that the parasitoid's maximum population growth rate should exceed the host's and (2) that the maximum growth rate of the host in the refuge should be less than unity. We then use this ecological framework as a basis for a model which considers evolutionary changes in quantitative characters influencing the size of the absolute refuge. For each species, an increase in its refuge-determining character comes at a cost to maximum population growth rate. We show that refuge evolution can substantially alter the population dynamics of the purely ecological model, resulting in a number of emergent and sometimes counter-intuitive properties. In general, when the host has a high carrying capacity, systems are polarized either with low or minor refuge and top-down control of the host by the parasitoid or with a refuge and bottom-up control of the host by a combination of its own density dependence and the parasitoid. A particularly tantalizing result is that co-evolutionary dynamics can modify ecologically unstable systems into ones which are either stable or quasi-stable (with bouts of unstable dynamics, punctuating long-term periods of quasi-stable behaviour). We present five quantitative criteria which must all be met for the parasitoid to be the agent responsible for control of the host at a co-evolutionary equilibrium. The apparent stringency of this full set of requirements supports the empirically-based suggestion that monophagous parasitoid-driven systems should be less common in nature than those driven by multiple forms of density dependence. Further, we apply our theory to the question of whether exploiters may harvest their victims at maximum sustainable yields and to the evolutionary stability of biological control. Finally, we present a series of testable predictions of our theory and methods useful for testing them.     

Does the host plant affect the benefits from mutualisms? The invasive mealybug and ghost ant association

1. The benefits to trophobionte hemipterans are affected by the ant tending level, which is a widely accepted statement. The ant tending level is closely related to multiple factors. It is clear that the ant tending level can be affected by the temporal factor, age‐specific, the density of the hemipterans, and quantity and quality of honeydew produced by hemipterans. 2. Few studies of ant–hemipteran mutualisms have reported the patterns of host plants‐dependent effects, and whether host plants influence the ant tending level that is also unclear. As such, laboratory experiments were conducted to test whether the colony growth rate of an invasive mealybug Phenacoccus solenopsis Tinsley, parasitism of Aenasius bambawalei Hayat, an dominant parasitoid of P. solenopsis, are affected by tending by ghost ants (Tapinoma melanocephalum(Fabricius)], host plants (tomato and cotton), and interactions between the two factors. The difference in the ant tending level between the host plants was also determined. 3. The results showed that mealybug colony growth and parasitism were significantly affected by ant tending and host plant separately. There were significant interactions between the independent factors on the mealybug colony growth rate and percentage parasitism. These results suggest that benefits to mealybugs are host plant‐dependent.     

Animal evolution. The end of the intermediate taxa?

Contrary to general belief, there has not been a reliable, global phylogeny of animals at hand within the past few decades. Recent progress in molecular phylogeny is rapidly changing the situation and has provided trees that constitute a reference frame for discussing the still controversial evolution of body plans. These trees, once purged of their possible artefacts, have already yielded confirmation of traditional, anatomically based, phylogenies as well as several new and quite significant results. Of these, one of the most striking is the disappearance of two superphyla (acoelomates such as flatworms, pseudocoelomates such as nematodes) previously thought to represent grades of intermediate complexity between diploblasts (organisms with two germ layers) and triploblasts (organisms with three germ layers). The overall image now emerging is of a fairly simple global tree of metazoans, comprising only a small number of major branches. The topology nicely accounts for the striking conservation of developmental genes in all bilaterians and suggests a new interpretation of the 'Cambrian explosion' of animal diversity.     

The “survivor effect” and the evolution of parthenogenesis and self-fertilization

Parthenogenetic or self-fertilizing species are often reduced to small numbers of survivors or colonists. These types of reproduction may therefore evolve because they eliminate problems of finding a mate. It is argued here that outbreeding populations which are often reduced to a few survivors will experience heavy offspring losses when population expansion occurs. This ‘survivor effect’ results from the production of many individuals homozygous for deleterious mutations (i.e. inbreeding depression). Parthenogenetic and selfing species do not experience a “survivor effect”. This effect together with mate-finding problems will tend to cause the evolution of parthenogenesis and selfing in weedy or colonizing species.     

The serpent and the egg: unidirectional evolution of reproductive mode in vipers?

Dollo’s law, that complex characters are not regained in evolution, is a pattern applied to many systems. Recent work has evaluated unidirectional evolution in a number of contexts, and several violations of this law have been documented. These methods have also been criticized for potentially overestimating reversals. We test the hypothesis that the ancestral reproductive mode of oviparity can be regained in vipers, in opposition to Dollo’s law. We use model comparison and ancestral character state reconstruction methods that address recent criticisms, and find evidence both supporting and refuting Dollo’s predictions from different analyses. We discuss our results in the context of unidirectional evolution and review factors required for strong inference of violations of Dollo’s law.     

Can females benefit from selfing avoidance? Genetic associations and the evolution of plant gender

Evolutionary stability of dioecy and nuclear gynodioecy in higher plants requires that females produce over twice as many successful seeds as hermaphrodites. This fitness differential is widely thought to derive primarily from the advantages of outcrossing caused by high selfing rates and inbreeding depression in the hermaphrodite. This study hypothesized that (i) extraordinarily high deleterious mutation rates are necessary to double female seed success due to outcrossing, and (ii) the large difference in outcrossing rates between sex morphs causes differential purging of these mutations, resulting in additional genetic selection on male sterility. Using genetically explicit models, I showed that the phenotypic outcrossing advantage requires at least one new highly recessive deleterious mutation per genome per generation, regardless of selection coefficient. However, under this mutational regime, differential purging created strong genetic selection against recessive male sterility that overwhelmed the phenotypic selection in favour of outcrossing. In very small populations and for dominant male sterility, this genetic selection was weaker or absent. This first genetically explicit study of the outcrossing advantage of unisexual females may shed new light on both the genetic and selective conditions for the evolution of gynodioecy and dioecy.     

The terrestrial evolution of metabolism and life – by the numbers

Background  

Allometric scaling relating body mass to metabolic rate by an exponent of the former (Kleiber's Law), commonly known as quarter-power scaling (QPS), is controversial for claims made on its behalf, especially that of its universality for all life. As originally formulated, Kleiber was based upon the study of heat; metabolic rate is quantified in watts (or calories per unit time). Techniques and technology for metabolic energy measurement have been refined but the math has not. QPS is susceptible to increasing deviations from theoretical predictions to data, suggesting that there is no single, universal exponent relevant to all of life. QPS's major proponents continue to fail to make good on hints of the power of the equation for understanding aging.     

An engram found? Evaluating the evidence from fruit flies

Is it possible to localize a memory trace to a subset of cells in the brain? If so, it should be possible to show: first, that neuronal plasticity occurs in these cells. Second, that neuronal plasticity in these cells is sufficient for memory. Third, that neuronal plasticity in these cells is necessary for memory. Fourth, that memory is abolished if these cells cannot provide output during testing. And fifth, that memory is abolished if these cells cannot receive input during training. With regard to olfactory learning in flies, we argue that the notion of the olfactory memory trace being localized to the Kenyon cells of the mushroom bodies is a reasonable working hypothesis.     

What's in a genome? The C-value enigma and the evolution of eukaryotic genome content

Some notable exceptions aside, eukaryotic genomes are distinguished from those of Bacteria and Archaea in a number of ways, including chromosome structure and number, repetitive DNA content, and the presence of introns in protein-coding regions. One of the most notable differences between eukaryotic and prokaryotic genomes is in size. Unlike their prokaryotic counterparts, eukaryotes exhibit enormous (more than 60 000-fold) variability in genome size which is not explained by differences in gene number. Genome size is known to correlate with cell size and division rate, and by extension with numerous organism-level traits such as metabolism, developmental rate or body size. Less well described are the relationships between genome size and other properties of the genome, such as gene content, transposable element content, base pair composition and related features. The rapid expansion of ‘complete’ genome sequencing projects has, for the first time, made it possible to examine these relationships across a wide range of eukaryotes in order to shed new light on the causes and correlates of genome size diversity. This study presents the results of phylogenetically informed comparisons of genome data for more than 500 species of eukaryotes. Several relationships are described between genome size and other genomic parameters, and some recommendations are presented for how these insights can be extended even more broadly in the future.     

Is genome size of Lepidoptera linked to host plant range?

Genome size varies considerably among organisms, largely as the result of differences in the content of non‐coding and/or repetitive DNA, such as introns, pseudogenes, or transposable elements, as well as whole‐genome duplications. Genome size is known to correlate with metabolic rates. Because polyphagy also affects the metabolism, a correlation between diet specialization and genome size can be expected. To test this hypothesis, a study was undertaken with five closely related species of stem borers which are easy to rear under artificial conditions, namely Busseola fusca (Fuller), Busseola segeta (Bowden), Busseola nairobica Le Ru, Sesamia calamistis Hampson, and Sesamia nonagrioides Lefebvre (all Lepidoptera: Noctuidae). However, as the number of species was too low for correlating diet with genome size in Lepidoptera in general, literature data from 16 Lepidoptera species were used in addition. The results pointed to a relationship between genome size and the insect's host plant range in Lepidoptera, but below the family level only, with larger genomes in polyphagous compared to specialist species. In addition, the genome size appeared to be influenced not only by host plant range but also by environmental/climatic conditions. Studies to test this hypothesis should be done strictly below the family level.     

The evolution of photosynthesis…again?

‘Replaying the tape’ is an intriguing ‘would it happen again?’ exercise. With respect to broad evolutionary innovations, such as photosynthesis, the answers are central to our search for life elsewhere. Photosynthesis permits a large planetary biomass on Earth. Specifically, oxygenic photosynthesis has allowed an oxygenated atmosphere and the evolution of large metabolically demanding creatures, including ourselves. There are at least six prerequisites for the evolution of biological carbon fixation: a carbon-based life form; the presence of inorganic carbon; the availability of reductants; the presence of light; a light-harvesting mechanism to convert the light energy into chemical energy; and carboxylating enzymes. All were present on the early Earth. To provide the evolutionary pressure, organic carbon must be a scarce resource in contrast to inorganic carbon. The probability of evolving a carboxylase is approached by creating an inventory of carbon-fixation enzymes and comparing them, leading to the conclusion that carbon fixation in general is basic to life and has arisen multiple times. Certainly, the evolutionary pressure to evolve new pathways for carbon fixation would have been present early in evolution. From knowledge about planetary systems and extraterrestrial chemistry, if organic carbon-based life occurs elsewhere, photosynthesis—although perhaps not oxygenic photosynthesis—would also have evolved.