Community dynamics: what happens when we rerun the tape?

The role of historical events, such as disturbances, in producing alternative developmental outcomes in forest structure has long been debated. Diversity in the assemblages of coexisting species is one measure of alternative outcomes of succession. The intermediate disturbance hypothesis proposes that a moderate disturbance level produces the highest levels of species diversity. Here, we use an agent-based model of forest development under a gradient of lightning strike frequency to analyse long-term dynamics of species coexistence in a multi-species forest. The configurations of species that result from disturbance dynamics reflect the interactions between life-history characteristics of the species and disturbance characteristics. Model results suggest that low levels of disturbance lead to highly ordered landscapes which exclude fire and are captured by late successional species. High levels of disturbance lead to oscillation between domination by early successional species and large disturbances. At intermediate levels of disturbance, the forest displays the broadest array of developmental pathways, highest entropy as measured by Shannon's index of diversity, and critical slowing near steady states. Long transients at intermediate regimes may reflect the working out of closely balanced constraints of competition between species with varying strategic adaptations to disturbance. Intermediate disturbance levels also result in the greatest number of alternative diversity configurations as outcomes of succession, reflecting an unpredictable and nonequilibrium forest dynamic.     

Modifying modifiers: what happens when interspecific interactions interact?

1. The strength of the trophic link between any given pair of species in a food web is likely to depend on the presence and/or densities of other species in the community. How these trophic interaction modifications (TIMs) interact with one another to produce a net modifying effect is an important but under-explored issue. 2. We review several specific types of TIMs that are well understood to address whether the magnitude of the net modification changes with the number of modifiers, and whether modifiers usually increase or decrease each other's effects. 3. Modifications of interactions are generally not independent. It is likely that TIMs interact antagonistically in the majority of cases; the magnitudes of TIMs decrease as more modifiers are added, or new TIMs reduce the magnitudes of modifications that are already present. 4. Individual modifications are likely to have a smaller effect in many-species systems than expected from independent combination of modifications measured in systems with relatively few species. Thus, models that lack explicit TIMs may in some cases yield adequate predictions for species-level perturbations, provided that the net effects of TIMs are implicitly included in measured interaction strengths. 5. Many types of TIMs share structural similarities. Nevertheless, a complete understanding of their effects may require theory that distinguishes different 'functional groups' of modifiers and addresses how these are structured according to trophic relationships.     

Dispersal and egg shortfall in Monarch butterflies: what happens when the matrix is cleaned up?

1. We use an individual‐based model describing the life of a monarch butterfly, which utilises milkweeds both aggregated in patches and scattered across the wider landscape as a substrate for laying eggs. The model simplifies the metapopulation of milkweed habitat patches by representing them as a proportion of the overall landscape, with the rest of the landscape considered matrix, which may contain some low density of milkweed plants. 2. The model simulates the number of eggs laid daily by a butterfly as it searches for hosts. The likelihood of finding hosts is related to the density of plants and the search ability of the butterfly. For an empty matrix, remaining in a habitat patch results in more eggs laid. However individuals that are good searchers have almost equivalent success without remaining in a habitat patch. These individuals are most affected by the presence of hosts in the matrix. 3. Given realistic values of habitat patch availability, our model shows that the presence of plants at a low density in the matrix has a substantial impact on the number of eggs laid; removing these plants can reduce lifetime potential fecundity by ca. 20%. These results have implications for monarch butterflies inhabiting agricultural landscapes, in which genetically modified soybean that is resistant to herbicides has resulted in the decimation of milkweeds over large areas.     

Physiology of tmRNA: what gets tagged and why?

Transfer-messenger RNA (tmRNA) enters stalled translational complexes and, with small protein B (SmpB), mediates peptide tagging of the nascent protein and release of the stalled ribosome. Recent studies clarify how the tmRNA system is targeted to ribosomes and suggest that tmRNA-tagging is used for both quality control and specific regulation of cellular physiology.     

Persistence of community structure: what happens when you change taxonomic scale?

It is common in community ecology to use the species as the taxonomic category of interest, yet in rich tropical assemblages containing guilds of very similar species this may not be appropriate. Such assemblages may be organized at the level of guilds rather than at the finer species level. In a ten-year study of assemblages of fish at One Tree Reef, Great Barrier Reef, we found species composition and the number of fish on a given lagoonal patch reef vary greatly across time (Sale and Douglas 1984; Sale et al. in preparation). The mean average proportional similarity of a reef's assemblage to itself at different times (censuses) is usually low at a value of around 0.5. This apparent variability may be ecologically irrelevant noise if organization is at the higher guild level. We have recast our database at the guild level to test this possibility. Thirteen guilds were defined by the diets, foraging habitats and times of the individual species comprising them. Similarity of an assemblage to itself at successive censuses was re-calculated using the number of individuals in each guild instead of the numbers in each species. This analysis yielded significantly higher levels of similarity (P<0.01) among censuses. To test whether this increase in similarity was due solely to the smaller number of categories used to calculate the similarity indices, 5 sets of randomly generated guilds were constructed using a Monte Carlo approach. No significant difference (P>0.05) was found between the average similarity among censuses when assemblages were classified into these null guilds and when they were classified according to the real guilds. These results indicate that shifting to the larger taxonomic scale of guilds does not reveal a significantly more persistent assemblage structure than that revealed when analysis is at the smaller scale of species. There is no evidence of an underlying organization of these assemblages at the guild level.     

Haldane's rule in marsupials: what happens when both sexes are functionally hemizygous?

During the process of speciation, diverging taxa often hybridize and produce offspring wherein the heterogametic sex (i.e., XY or ZW) is unfit (Haldane's rule). Dominance theory seeks to explain Haldane's rule in terms of the difference in X-linked dominance regimes experienced by the sexes. However, X inactivation in female mammals extends the effects of hemizygosity to both sexes. Here, we highlight where the assumptions of dominance theory are particularly problematic in marsupials, where X inactivation uniformly results in silencing the paternal X. We then present evidence of Haldane's rule for sterility but not for viability in marsupials, as well as the first violations of Haldane's rule for these traits among all mammals. Marsupials represent a large taxonomic group possessing heteromorphic sex chromosomes, where the dominance theory cannot explain Haldane's rule. In this light, we evaluate alternative explanations for the preponderance of male sterility in interspecific hybrids, including faster male evolution, X-Y interactions, and genomic conflict hypotheses.     

What happens when tendons bend and twist? Proteoglycans

When tendons must bend or twist in order to fulfil their function of attaching muscle to bone they are subjected to forces that could damage the tendon. However, there are concomitant protective changes in the structure of the tendon at the location of bending. One of these changes involves increased synthesis and accumulation of the large proteoglycan aggrecan. The accumulation of aggrecan can protect the tendon by providing compressive stiffness, by allowing collagen fascicles to slide relative to one another, and by protecting vascular elements.     

Avian sex determination: what, when and where?

Sex is determined genetically in all birds, but the underlying mechanism remains unknown. All species have a ZZ/ZW sex chromosome system characterised by female (ZW) heterogamety, but the chromosomes themselves can be heteromorphic (in most birds) or homomorphic (in the flightless ratites). Sex in birds might be determined by the dosage of a Z-linked gene (two in males, one in females) or by a dominant ovary-determining gene carried on the W sex chromosome, or both. Sex chromosome aneuploidy has not been conclusively documented in birds to differentiate between these possibilities. By definition, the sex chromosomes of birds must carry one or more sex-determining genes. In this review of avian sex determination, we ask what, when and where? What is the nature of the avian sex determinant? When should it be expressed in the developing embryo, and where is it expressed? The last two questions arise due to evidence suggesting that sex-determining genes in birds might be operating prior to overt sexual differentiation of the gonads into testes or ovaries, and in tissues other than the urogenital system.     

Chemical genomics: what will it take and who gets to play?

Chemical genomics requires continued advances in combinatorial chemistry, protein biochemistry, miniaturization, automation, and global profiling technology. Although innovation in each of these areas can come from individual academic labs, it will require large, well-funded centers to integrate these components and freely distribute both data and reagents.     

Trade‐offs between eating and moving: what happens to the locomotion of slender arboreal snakes when they eat big prey?

The capacity to consume large prey evolved long ago in snakes. Subsequently, many specialized arboreal snake species convergently evolved slender bodies, presumably well‐suited for moving on thin branches and steep slopes, although how this accentuates changes in their shape and weight after eating and creates trade‐offs with locomotor performance is poorly understood. Hence, we tested whether the performance and modes of locomotion of a specialized arboreal snake (Boiga irregularis) changed after eating one or two mice when crawling on cylinders with and without pegs and on horizontal or 45° slopes. On surfaces with pegs: (1) only lateral undulation was used; (2) speed decreased with increased meal size; and (3) unexpectedly, more sideways toppling occurred than without pegs. On the horizontal cylinders without pegs, most unfed snakes used lateral undulation with continuous sliding contact, whereas, after eating two mice, most snakes periodically stopped and gripped the cylinder with speeds of concertina locomotion similar to those for the lateral undulation of unfed snakes. Thus, the behaviour of switching to a gripping mode of locomotion (concertina) circumvented some of the constraints of a slender limbless body plan, for which bulky meals alter shape and can impede the movement of the propulsive structures. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 114 , 446–458.     

Stability diagram and unfolding of a modified cytochrome c: what happens in the transformation regime?

We determined the stability diagram of a modified cytochrome c protein in a glycerol water mixture by measuring the first and the second moment of the fluorescence from the chromophore as a function of temperature and pressure. Temperature and pressure were varied between 273 and 363 K and 0.0001 and 1 GPa, respectively. The shift of the fluorescence maximum showed a characteristic sigmoid-like pattern from which information on the microscopic processes during unfolding is obtained: as the transformation regime is entered, the fluorescence shows a significant blue shift. The conclusion is that water molecules get into contact with the chromophore. They lead to strong electrostatic contributions in the solvent shift, which counteract the red shifting dispersion interactions. Assuming that there are just two relevant states that determine the stability diagram, the complete set of thermodynamic parameters can be determined from the data. However, under certain pressure-temperature conditions the fluorescence pattern is more complicated, pointing toward reentrant transitions and, possibly, to consecutive steps in the unfolding process.