Alastair Grant

Elasticity analysis as an important tool in evolutionary and population ecology.

Elasticity analysis estimates the proportional change in the population growth rate for a proportional change in a vital rate (i.e. survival, growth or reproduction). It can be used to pinpoint those parts of an organisms life history that should be the focus of management effort, or those that contribute most to fitness. Recent theoretical work has emphasized some limitations of the technique, has overcome other problems, and has shown that it is robust to some violations of its underlying assumptions. Thus, although care is needed, elasticity analysis is a simple first step in answering important questions in evolutionary and population ecology.

HURRICANES AND CARIBBEAN CORAL REEFS: IMPACTS, RECOVERY PATTERNS, AND ROLE IN LONG-TERM DECLINE

The decline of corals on tropical reefs is usually ascribed to a combination of natural and anthropogenic factors, but the relative importance of these causes remains unclear. In this paper, we attempt to quantify the contribution of hurricanes to Caribbean coral cover decline over the past two decades using meta-analyses. Our study included published and unpublished data from 286 coral reef sites monitored for variable lengths of time between 1980 and 2001. Of these, 177 sites had experienced hurricane impacts during their period of survey. Across the Caribbean, coral cover is reduced by ∼17%, on average, in the year following a hurricane impact. The magnitude of this immediate loss increases with hurricane intensity and with the time elapsed since the last impact. In the following year, no further loss is discernible, but the decline in cover then resumes on impacted sites at a rate similar to the regional background rate of decline for nonimpacted sites. There is no evidence of recovery to a pre-storm state for at least eight years after impact. Overall, coral cover at sites impacted by a hurricane has declined at a significantly faster rate (6% per annum) than nonimpacted sites (2% per annum), due almost exclusively to higher rates of loss in the year after impact in the 1980s. While hurricanes, through their immediate impacts, appear to have contributed to changing coral cover on many Caribbean reefs in the 1980s, the similar decline in coral cover at impacted and nonimpacted sites in the 1990s suggests that other stressors are now relatively more important in driving the overall pattern of change in coral cover in this region. The overall lack of post-hurricane recovery points to a general impairment of the regeneration potential of Caribbean coral reefs.

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

Plant–microbe interactions in the rhizosphere have important roles in biogeochemical cycling, and maintenance of plant health and productivity, yet remain poorly understood. Using RNA-based metatranscriptomics, the global active microbiomes were analysed in soil and rhizospheres of wheat, oat, pea and an oat mutant (sad1) deficient in production of anti-fungal avenacins. Rhizosphere microbiomes differed from bulk soil and between plant species. Pea (a legume) had a much stronger effect on the rhizosphere than wheat and oat (cereals), resulting in a dramatically different rhizosphere community. The relative abundance of eukaryotes in the oat and pea rhizospheres was more than fivefold higher than in the wheat rhizosphere or bulk soil. Nematodes and bacterivorous protozoa were enriched in all rhizospheres, whereas the pea rhizosphere was highly enriched for fungi. Metabolic capabilities for rhizosphere colonisation were selected, including cellulose degradation (cereals), H2 oxidation (pea) and methylotrophy (all plants). Avenacins had little effect on the prokaryotic community of oat, but the eukaryotic community was strongly altered in the sad1 mutant, suggesting that avenacins have a broader role than protecting from fungal pathogens. Profiling microbial communities with metatranscriptomics allows comparison of relative abundance, from multiple samples, across all domains of life, without polymerase chain reaction bias. This revealed profound differences in the rhizosphere microbiome, particularly at the kingdom level between plants.

HOW TO KEEP FIT IN THE REAL WORLD: ELASTICITY ANALYSES AND SELECTION PRESSURES ON LIFE HISTORIES IN A VARIABLE ENVIRONMENT

Most life-history theory assumes the environment is invariant. For the first time, analytical and numerical techniques were employed to investigate the impact of environmental variability on selection pressures (elasticities = proportional sensitivities) on a range of life histories. We find that the impact of variability is influenced significantly by the amount of variability an organism experiences (more variability affects selection pressures more), the correlations between variations among the vital rates (negative correlations are more likely to relax selection on fecundities and increase it on survival rates), and the life history in question (shorter life histories are more affected). In addition, the impact of a variable environment on the elasticities of life histories is sensitive to the sampling distribution used to generate the variability, and it is particularly sensitive to extreme values, such as those caused by occasional catastrophic events. The elasticities of life histories in highly variable environments may bear little relationship to those in a constant environment. In detailed optimality or evolutionarily stable strategy (ESS) modeling, variability in vital rates as small as a standard deviation being 10%-15% of the mean may appreciably alter the conclusions. Thus, it may be very important to consider the possible impact of environmental stochasticity and not to assume that it has no effect.

An assessment of metal contamination of sediments in the humber estuary, U.K.

Abstract It is difficult to make an overall assessment of the degree of metal contamination in estuarine and marine sediments. This is a consequence of variations in analytical procedures between studies and the presence of an unknown natural background in the sediment. Measurement of total (rather than extractable) metal and normalization of concentrations as ratios to an element associated with clays provides a solution to the first difficulty. Expressing these values as enrichment factors relative to pre-industrial sediments from the same environment solves the second. Levels of anthropogenic enrichment of intertidal sediments in the Humber Estuary have been assessed relative to a baseline provided by sediments deposited in the Humber approximately 5000 years B.P. A sample of consolidated Holocene mud estimated to be at least 100 years old confirmed the appropriateness of this baseline. Normalization relative to Rb, which is not anthropogenically enriched, was the most suitable way to adjust for grain size. Levels of Ti, Fe, P, V, Cr, Mn, Ni, Cu, Zn, As, Y, Nb and Pb are elevated above this baseline. The most marked enrichments (between 3·5- and 6-fold) are of P, As, Pb, Cu and Zn. Normalized concentrations were spatially rather uniform with two exceptions. A single sample from the north bank showed elevated levels of Pb, Cu, Zn and Cr. An area receiving effluents from an industrialized zone on the south bank, including two titanium dioxide processing factories, showed high levels of a number of elements, particularly Nb. It is suggested that Nb may be a valuable tracer for effluents from the sulphate process of TiO 2 extraction.

ELASTICITY ANALYSIS FOR DENSITY-DEPENDENT POPULATIONS IN STOCHASTIC ENVIRONMENTS

Elasticities of λ indicate the influence of demographic parameters on both individual fitness and population growth for a population with density-independent growth. Here we discuss the extension of elasticity analysis to populations with density-dependent demographic parameters and examine the circumstances in which the standard density-independent analysis gives useful information for populations that are, in reality, density dependent. In the presence of density dependence the fitness of one strategy depends upon what the rest of the population is doing. Elasticities of fitness must therefore be calculated using invasibility methods, and the resulting elasticities of the invasion exponent ϑ are not necessarily identical with elasticities of mean or equilibrium population size. The former are of interest in evolutionary studies; the latter in population management. If a population has a stable equilibrium and density dependence is a function of the total number of individuals in the population, then ela...

Assessment of the phase selectivity of the European Community Bureau of Reference (BCR) sequential extraction procedure for metals in sediment

Sequential extractions potentially offer useful information on how metals are bound to sediment. For example, reagents used in such extractions may be expected to selectively release metal bound to carbonates, iron and manganese oxides or organic/sulphidic material. However, various criticisms have been levelled at sequential methods, including that of inaccuracy in releasing metal from specific geochemical phases. This study examines specificity by analysing individual mineral phases previously equilibrated with metal-spiked artificial sea water. Substrates were then sequentially extracted according to the three-step BCR procedure. The distribution of recovered metal between extracts was compared to that expected if reagents were acting on a specific phase. Acetic acid released most of the metal associated with calcium carbonate, kaolinite, potassium felspar and ferrihydrite. Hydroxylamine hydrochloride contained most of the recovered metal from montmorillonite and manganese dioxide, as well as nickel from humic acid. Iron oxides are expected to be attacked by this reducing agent, but the majority of the metal had already been removed by the first extract (acetic acid). This may reflect the high absorption capacity of ferrihydrite. Zinc on humic acid was split between the first two reagents. The third extraction, hydrogen peroxide/ammonium acetate, which might be expected to release metal from organic or sulphidic material, only significantly recovered the added copper from humic acid. Total recoveries of the added metal were high, except from humic acid, felspar and montmorillonite, suggesting strong metal binding by these substrates. Variability between carefully controlled experiments raises some questions about the reproducibility of the extraction procedure which may be exacerbated when applying the method to real sediments.

Phytochromes function as thermosensors in Arabidopsis

Combining heat and light responses Plants integrate a variety of environmental signals to regulate growth patterns. Legris et al. and Jung et al. analyzed how the quality of light is interpreted through ambient temperature to regulate transcription and growth (see the Perspective by Halliday and Davis). The phytochromes responsible for reading the ratio of red to far-red light were also responsive to the small shifts in temperature that occur when dusk falls or when shade from neighboring plants cools the soil. Science, this issue p. 897, p. 886; see also p. 832 Red-light photoreceptors also act as temperature sensors in plants. Plants are responsive to temperature, and some species can distinguish differences of 1°C. In Arabidopsis, warmer temperature accelerates flowering and increases elongation growth (thermomorphogenesis). However, the mechanisms of temperature perception are largely unknown. We describe a major thermosensory role for the phytochromes (red light receptors) during the night. Phytochrome null plants display a constitutive warm-temperature response, and consistent with this, we show in this background that the warm-temperature transcriptome becomes derepressed at low temperatures. We found that phytochrome B (phyB) directly associates with the promoters of key target genes in a temperature-dependent manner. The rate of phyB inactivation is proportional to temperature in the dark, enabling phytochromes to function as thermal timers that integrate temperature information over the course of the night.

Does environmental stochasticity matter? Analysis of red deer life-histories on Rum.

SummaryMost life-history theory assumes that short-term variation in an organisms environment does not affect the survivorships and fecundities of the organisms. This assumption is rarely met. Here we investigate the population and evolutionary biology of red deer,Cervus elephas, to see if relaxation of this assumption is likely to make significant differences to the predicted evolutionary biology of this species. To do this we used 21 years of data from a population of deer on Rum, Western Isles, Scotland. Population growth rates in a stochastic environment were estimated using Tuljapurkars small noise approximation, confirmed by bootstrap simulation. Numerical differentiation was used to see if the selection pressures (i.e. sensitivities of population growth rate to changes in the vital rates) differ between the stochastic and deterministic cases. The data also allow the costs of reproduction to be estimated. These costs, incorporated as trade-offs into the sensitivity analysis, allow investigation of evolutionary benefits of different life-history tactics. Environmentally induced stochastic variation in the red deer vital rates causes a slight reduction (≃ 1%) in the predicted population growth rate and has little impact on the estimated selection pressures on the deers life-history. We thus conclude that, even though density-independent stochastic effects on the population are marked, the deers fitness is not markedly affected by these and they are adapted to the average conditions they experience. However, the selected life-history is sensitive to the trade-offs between current fecundity, survivorship and future fecundity and it is likely that the environmental variance will affect these trade-offs and, thus, affect the life-history favoured by selection. We also show that the current average life-history is non-optimal and suggest this is a result of selection pressures exerted by culling and predation, now much reduced. As the use of stochastic or deterministic methods provide similar estimates in this case, the use of the latter is justified. Thus,r (the annual per capita rate of population growth) is an appropriate measure of fitness in a population with stochastic numerical fluctuations. In a population of constant size lifetime reproductive success is the obvious measure of fitness to use.

Population consequences of chronic toxicity: incorporating density dependence into the analysis of life table response experiments

Data from chronic toxicity tests are usually analysed by calculating how the toxicant reduces population growth rate. The contribution of effects on different parts of the life history to this reduction can be determined using sensitivity analyses and life table response experiments (LTREs). These provide a convenient descriptor of what happens within the laboratory toxicity test, but are only a good predictor of likely consequences in the field if density dependence of population dynamics can be ignored. Here I show how sensitivity analysis and LTREs can be applied to density dependent populations and illustrate the methods with data on the toxicity of dieldrin to Eurytemora affinis. I also outline the extension of the approach to populations which experience variations in vital rates. Stationary population sizes in density dependent populations at equilibrium mean that vital rates late in life are usually more important than in the density independent analysis. Substantial reductions in some vital rates can have little impact on the population if they are compensated by reductions in the intensity of density dependence. This represents one aspect of the assimilative capacity of ecological systems.