Improving Bayesian isotope mixing models: a response to Jackson et al. (2009)

We recently described a Bayesian framework for stable isotope mixing models and provided a software tool, MixSIR, for conducting such analyses (Ecol. Lett., 2008; 11 :470). Jackson et al. (Ecol. Lett., 2009; 12:E1) criticized the performance of our software based on tests using simulated data. However, their simulation data were flawed, rendering claims of erroneous behaviour inaccurate. A re‐evaluation of the MixSIR source code did, however, uncover two minor coding errors, which we have fixed. When data are correctly simulated according to eqns  (1)–(4) in Jackson et al. (2009) , MixSIR consistently and accurately estimated the proportional contribution of prey to a predator diet, and was surprisingly robust to additional unquantified error. Jackson et al. (2009) also suggested we use a Dirichlet prior on the source proportion parameters, which we agree with. Finally, Jackson et al. (2009) propose adding additional error parameters to our mixing model framework. We caution that such increases in model complexity should be evaluated based on data support.     

Diet diversity among five co-existing fish species in a tropical river: integration of dietary and stable isotope data

Diets were estimated from stomach contents and the MixSIR model using stable isotope values for five co-existing and abundant benthic fishes in relation to potential prey from a riffle habitat in a tropical river in eastern Thailand. Collectively, aquatic insects were of greatest dietary importance based on stomach contents and, except for one fish species, predicted from the MixSIR. The most prominent functional feeding insect groups in fish diets were collector-filterers and scrapers and, to a lesser extent, predators. MixSIR predicted shrimp to be the most important single dietary constituent for all fishes in contrast to stomach contents, which indicated they are a major item for only one species. MixSIR predicted plant material to be more important in fish diets than stomach contents where the composition of detritus was a concern. Differences in temporal feeding schedules, prey availability, species adaptations and others are important in understanding diet and in the construction of food webs. Stable isotope and dietary analysis provides a more accurate assessment of the food web structure and dynamics of tropical river ecosystems than either method alone.     

基于稳定氧同位素确定植物水分来源不同方法的比较

利用稳定同位素技术确定植物水分来源,对提高生态水文过程的认识和对干旱半干旱区的生态管理至关重要。目前基于稳定同位素技术确定植物水分来源的方法众多,但不同方法之间对比的研究较少。本研究基于原位样品采集,室内实验测试,利用直接对比法、多元线性混合模型(IsoSource)、贝叶斯混合模型(MixSIR、MixSIAR)和吸水深度模型分析植物水分来源,并对比各方法的优缺点。结果表明:相对于多元线性混合模型(IsoSource)而言,贝叶斯混合模型(MixSIR、MixSIAR)具有更好的水源区分性能,但对数据要求较高,且植物木质部水和潜在水源同位素组成的标准差越小,模型运行结果的可信度更高。本研究中贝叶斯混合模型(MixSIR)为最优解。在利用稳定氢氧同位素技术确定植物水分来源时,可先通过直接对比法定性判断植物可能利用的潜在水源,然后再用多元线性混合模型(IsoSource)、贝叶斯混合模型(MixSIR、MixSIAR)计算出各潜在水源对植物的贡献率和贡献范围,必要时可评估模型性能,选择出最优模型,定量分析植物的水分来源。若植物主要吸收利用不同土层深度的土壤水,可结合吸水深度模型计算出植物...     

Diverse diet compositions among harpaline ground beetle species revealed by mixing model analyses of stable isotope ratios

1. Species diversities of some insect lineages have been attributed to differentiation of feeding habits among species. Our objective was to determine variation in diet composition among harpaline ground beetle species occurring in a riverside grassland. 2. We examined the diet compositions of 14 species from six genera in the spring and 10 species from two genera in the autumn. We performed measurements of nitrogen and carbon stable isotope ratios in consumers and in their potential food items, and estimated relative contributions of different food items with two mixing models, IsoSource and MixSIR. 3. IsoSource and MixSIR software gave similar results, but IsoSource tended to calculate higher contributions of principal food items and smaller percentile ranges than MixSIR. Among harparine beetle species, there were diverse food utilisation patterns among four food categories (detritivorous invertebrates, herbivorous invertebrates, C3 plants, and C4 plants). Detritivores comprised the main diets of abundant harpaline species in the spring, whereas abundant harpaline species in the autumn were primarily herbivores feeding on C4 plants, or omnivores feeding on herbivorous invertebrates and C3 plants. Seasonal changes in food use were related to seasonal changes in the abundance of each food resource. 4. Mixing model analysis of stable isotope ratios is a convenient and effective method for roughly estimating diets of many species with diverse food habits (such as ground beetles). This method can contribute to determining the trophic relationships of related insects in one ecosystem.     

The politics of assessing risk for biological invasions: the USA as a case study

The current regulation of biological invasions rests on an unwarranted presumption (that the invader will cause no harm) and on risk assessment procedures that are narrowly focused, subjective, often arbitrary and unquantified, and subject to political interference. Although this current approach dominates international treaties and most national policies, it has not stemmed the rising tide of biological invasions, as evidenced by several examples from the USA. Technical advances in measuring and predicting impacts of introduced species will improve risk assessments. Additionally, focusing squarely on the risks associated not only with a proposed species introduction, but also on the goals of the introduction and on alternative ways of achieving them, would lead to more-informed decisions permitting the introduction of a species and fewer problematic invaders. In assessing the alternatives to introductions, the precautionary principle should be given heavy weight, as should the distribution of possible costs and benefits.     

Fire and the chemistry of a South African mountain stream

The effects of a late-summer prescribed burn on the chemistry of a second-order mountain stream in the south-western Cape, South Africa, were investigated. Nitrate concentrations in stream water were significantly higher during the winter of the post-burn year. Increased concentrations of chloride, bicarbonate, polyphenols and potassium and decreased sodium concentrations were also recorded. Concentrations of ammonium, phosphate, calcium, magnesium, total dissolved solids and hydrogen ions were not significantly affected by the burn. Ionic export from the catchment was generally greater in the post-burn year. Apart from nitrate, however, values probably lie within the natural range of year-to-year variation. It is predicted that enhanced losses of nitrate will decrease progressively with the recovery of the vegetation and the re-establishment of soil/plant nutrient cycles. Atmospheric losses of nutrients in smoke were unquantified, but may be of more significance to site productivity than losses through surface runoff, which, in the case of nitrogen, appear to be compensated by precipitation inputs.     

A Fatty Acid Based Bayesian Approach for Inferring Diet in Aquatic Consumers

We modified the stable isotope mixing model MixSIR to infer primary producer contributions to consumer diets based on their fatty acid composition. To parameterize the algorithm, we generated a ‘consumer-resource library’ of FA signatures of Daphnia fed different algal diets, using 34 feeding trials representing diverse phytoplankton lineages. This library corresponds to the resource or producer file in classic Bayesian mixing models such as MixSIR or SIAR. Because this library is based on the FA profiles of zooplankton consuming known diets, and not the FA profiles of algae directly, trophic modification of consumer lipids is directly accounted for. To test the model, we simulated hypothetical Daphnia comprised of 80% diatoms, 10% green algae, and 10% cryptophytes and compared the FA signatures of these known pseudo-mixtures to outputs generated by the mixing model. The algorithm inferred these simulated consumers were comprised of 82% (63-92%) [median (2.5th to 97.5th percentile credible interval)] diatoms, 11% (4-22%) green algae, and 6% (0-25%) cryptophytes. We used the same model with published phytoplankton stable isotope (SI) data for δ¹³C and δ¹⁵N to examine how a SI based approach resolved a similar scenario. With SI, the algorithm inferred that the simulated consumer assimilated 52% (4-91%) diatoms, 23% (1-78%) green algae, and 18% (1-73%) cyanobacteria. The accuracy and precision of SI based estimates was extremely sensitive to both resource and consumer uncertainty, as well as the trophic fractionation assumption. These results indicate that when using only two tracers with substantial uncertainty for the putative resources, as is often the case in this class of analyses, the underdetermined constraint in consumer-resource SI analyses may be intractable. The FA based approach alleviated the underdetermined constraint because many more FA biomarkers were utilized (n < 20), different primary producers (e.g., diatoms, green algae, and cryptophytes) have very characteristic FA compositions, and the FA profiles of many aquatic primary consumers are strongly influenced by their diets.     

Cost-Benefit Analysis in a Regulatory Setting

The purpose of requiring cost-benefit analysis is to produce better out-comes from regulatory processes. If implemented well, cost-benefit analysis and risk assessment can produce improvements at several levels, by encouraging regulators to consider unintended effects of regulations and thereby avoid making things worse, to find the least burdensome approach to a goal, and to balance the pluses and minuses involved in choosing a goal. Whether these improvements will occur depends in large part on how cost-benefit analysis is implemented. Guidelines for conducting cost-benefit analysis and procedures for considering evidence on costs and benefits play an important role. This article describes how guidelines and rules of process can affect outcomes, and the issues that cost-benefit guidelines need to cover. Guidelines can affect the bias of a regulatory process toward one set of stakeholders or another, make outcomes more predictable, define the information needed for decisions, and provide a basis for legal challenges. The questions that guidelines should address include: what are costs and benefits, what constitutes good economics, what are standards of proof, how should unquantified costs and benefits be treated, how should uncertainties of cost-benefit estimates be dealt with, and how should alternatives be generated? The article concludes with recommen dations about how the adoption of cost-benefit analysis can be made most effective and beneficial in regulatory processes.     

Gene therapy in the clinic: whose risks?

Current experience with gene therapy for X-linked severe combined immunodeficiency disorder (X-SCID) suggests that we might now be at the point where it can be considered the 'standard of care'. This therapy carries an unquantified risk of leukaemia, raising important questions for regulators. How dangerous does a potentially curative therapy for a fatal illness need to be before we call it unsafe. How uncertain does a risk need to be for us to regard a therapy as still 'experimental'? Whose interests should prevail? Here I argue that in X-SCID it is the parents and children whom we should listen to first and foremost. How far does this patient-centred approach to licensing therapies extend? Can it be given a rational basis?     

Contaminated liquid nitrogen vapour as a risk factor in pathogen transfer

Liquid nitrogen in storage containers will gather particulate matter from the atmosphere, or the surfaces of containers placed into it, with time. Some of these accumulating particles may be pathogenic organisms and it can be demonstrated that their viability may be conserved by immersion in the liquid nitrogen. This contamination constitutes a risk to the status of stored samples that can, largely, be avoided by the use of appropriate techniques for sealing sample containers and sterilizing their outer surfaces. The present study uses fungal spores and organic crystals to demonstrate that such particles contained in liquid nitrogen are released back into the environment when nitrogen vapour cools programmable freezers or dry shippers. This demonstrates that storage in the vapour phase above liquid nitrogen still carries a real risk of sample, or facility, contamination. Regardless of the safety of the stored sample, this is a potential source of cross-contamination between repositories or experimental sites, both locally and internationally, that could have serious consequences in clinical and agricultural situations. This study provides evidence to suggest that this possibility, as yet unquantified, should be included in risk analysis of storage protocols for reproductive materials. The risk becomes diverse when, for example, semen and embryos are frozen at an agricultural site and the dry shipper can co-transport spores of contaminating crop plant pathogens to the destination site.     

Preliminary assessment of Greenland halibut diet in Cumberland Sound using stable isotopes

We provide preliminary carbon (δ¹³C) and nitrogen (δ¹⁵N) stable isotope assessment of the Greenland halibut (Reinhardtius hippoglossoides) diet in Cumberland Sound, with focus on two possible prey sources: pelagic represented by capelin (Mallotus villosus) and epibenthic represented by shrimp (Lebbeus polaris). The δ¹³C for the Greenland halibut stock indicated a pelagic carbon source in Cumberland Sound while stable isotope mixing models, IsoSource and MixSIR, indicated a 99% dietary composition of capelin relative to the shrimp. The δ¹⁵N did not vary across Greenland halibut size ranges and placed them at a fourth trophic position relative to a primary herbivore. This study provides the starting point for more elaborate Cumberland Sound research on the local Greenland halibut feeding ecology by confirming pelagic feeding and establishing relative trophic position as well as identifying stable isotopes as a useful tool for the study of diet in cold water fish species.     

Rapid evolution in a fraction of theDrosophila nuclear genome

Summary Previous observations have indicated thatDrosophila DNA contains a component that evolves so rapidly that it fails to hybridize between the DNAs of sibling species. To establish the reality of this component and study its properties, the fraction (about 20%) ofDrosophila simulans (Dsim) DNA that fails to hybridize toDrosophila melanogaster (Dmel) DNA has been isolated. The majority of the hybridizable part of this isolated fraction (based on control tests on Dsim DNA) fails to hybridize with Dmel DNA under the conditions used for the initial fractionation. Clones of this fraction do hybridize with Dmel DNA at open criterion producing duplexes with greatly reduced thermal stability, indicating that the underlying process is rapid sequence divergence rather than loss of the homologous sequences by relatively large deletions.Cloned fragments from the nonhybridizing fraction from Dsim are more than 15% divergent from the Dmel homologues, whereas the fraction that does hybridize is only 3–5% divergent. In comparison, synonymous substitutions in the coding regions of five genes show a 9% average divergence between Dsim and Dmel. They appear to be intermediate in their degree of divergence between the hybridizing and nonhybridizing components.     

To See or Not to See: Investigating Detectability of Ganges River Dolphins Using a Combined Visual-Acoustic Survey

Detection of animals during visual surveys is rarely perfect or constant, and failure to account for imperfect detectability affects the accuracy of abundance estimates. Freshwater cetaceans are among the most threatened group of mammals, and visual surveys are a commonly employed method for estimating population size despite concerns over imperfect and unquantified detectability. We used a combined visual-acoustic survey to estimate detectability of Ganges River dolphins (Platanista gangetica gangetica) in four waterways of southern Bangladesh. The combined visual-acoustic survey resulted in consistently higher detectability than a single observer-team visual survey, thereby improving power to detect trends. Visual detectability was particularly low for dolphins close to meanders where these habitat features temporarily block the view of the preceding river surface. This systematic bias in detectability during visual-only surveys may lead researchers to underestimate the importance of heavily meandering river reaches. Although the benefits of acoustic surveys are increasingly recognised for marine cetaceans, they have not been widely used for monitoring abundance of freshwater cetaceans due to perceived costs and technical skill requirements. We show that acoustic surveys are in fact a relatively cost-effective approach for surveying freshwater cetaceans, once it is acknowledged that methods that do not account for imperfect detectability are of limited value for monitoring.     

The biofuel potential of municipal solid waste

The world in the 21st century is facing a dual crisis of increasing waste and global climate change. Substituting fossil fuels with waste biomass‐derived cellulosic ethanol is a promising strategy to simultaneously meet part of our energy needs, mitigate greenhouse gas (GHG) emissions, and manage municipal solid waste (MSW). However, the global potential of MSW as an energy source is as yet unquantified. Here, we report increasing trends of MSW generation, and waste biomass‐derived cellulosic ethanol potentials in relation to socio‐economic development across 173 countries, and show that globally, up to 82.9 billion litres of waste paper‐derived cellulosic ethanol can be produced worldwide, replacing 5.36% of gasoline consumption, with accompanying GHG emissions savings of between 29.2% and 86.1%.     

Outflow distribution at the distal anastomosis of infrainguinal bypass grafts

Outflow distribution at the distal anastomosis of infrainguinal bypass grafts remains unquantified in vivo, but is likely to influence flow patterns and haemodynamics, thereby impacting upon graft patency. This study measured the ratio of distal to proximal outflow in 30 patients undergoing infrainguinal bypass for lower limb ischaemia, using a flow probe and a transit-time ultrasonic flow meter. The mean outflow distribution was approximately 75% distal to 25% proximal, with above knee anastomoses having a greater proportion of distal flow (84%) compared to below knee grafts (73%). These in vivo flow characteristics differ significantly from those used in theoretical models studying flow phenomena (50:50 and/or 100:0), and should be incorporated into future research.     

Mating system of the Eurasian badger, Meles meles, in a high density population

Badgers are facultatively social, forming large groups at high density. Group-living appears to have high reproductive costs for females, and may lead to increased levels of inbreeding. The extent of female competition for reproduction has been estimated from field data, but knowledge of male reproductive success and the extent of extra-group paternity remains limited. Combining field data with genetic data (16 microsatellite loci), we studied the mating system of 10 badger social groups across 14 years in a high-density population. From 923 badgers, including 425 cubs, we were able to assign maternity to 307 cubs, with both parents assigned to 199 cubs (47%) with 80% confidence, and 14% with 95% confidence. Age had a significant effect on the probability of reproduction, seemingly as a result of a deficit of individuals aged two years and greater than eight years attaining parentage. We estimate that approximately 30% of the female population successfully reproduced in any given year, with a similar proportion of the male population gaining paternity across the same area. While it was known there was a cost to female reproduction in high density populations, it appears that males suffer similar, but not greater, costs. Roughly half of assigned paternity was attributed to extra-group males, the majority of which were from neighbouring social groups. Few successful matings occurred between individuals born in the same social group (22%). The high rate of extra-group mating, previously unquantified, may help reduce inbreeding, potentially making philopatry a less costly strategy.     

Each of the activities of signal recognition particle (SRP) is contained within a distinct domain: analysis of biochemical mutants of SRP

Signal recognition particle (SRP), a small ribonucleoprotein required for targeting secretory proteins to the ER, has three known functions: signal recognition, elongation arrest, and translocation promotion. Because SRP is inactivated by the sulfhydryl alkylating reagent N-ethylmaleimide (NEM), we have attempted to establish structure-function relationships within SRP by assembling particles in which a single protein is modified. Alkylation of the 68/72 kd protein of SRP yields a particle that arrests elongation but fails to promote translocation and no longer interacts with SRP receptor. Alkylation of the 54 kd protein yields a particle that fails to recognize signal sequences. This approach has allowed us to map activities to specific protein domains on SRP, and should be generally useful for analyzing other ribonucleoproteins.     

Model-building with interpolated temporal data

Ecological data can be difficult to collect, and as a result, some important temporal ecological datasets contain irregularly sampled data. Since many temporal modelling techniques require regularly spaced data, one common approach is to linearly interpolate the data, and build a model from the interpolated data. However, this process introduces an unquantified risk that the data is over-fitted to the interpolated (and hence more typical) instances. Using one such irregularly-sampled dataset, the Lake Kasumigaura algal dataset, we compare models built on the original sample data, and on the interpolated data, to evaluate the risk of mis-fitting based on the interpolated data.     

MECHANISMS OF FLUID SHEAR‐INDUCED INHIBITION OF POPULATION GROWTH IN A RED‐TIDE DINOFLAGELLATE1

Net population growth of some dinoflagellates is inhibited by fluid shear at shear stresses comparable with those generated during oceanic turbulence. Decreased net growth may occur through lowered cell division, increased mortality, or both. The dominant mechanism under various flow conditions was determined for the red‐tide dinoflagellate Lingulodinium polyedrum (Stein) Dodge. Cell division and mortality were determined by direct observation of isolated cells in 0.5‐mL cultures that were shaken to generate unquantified fluid shear. Larger volume cultures were exposed to quantified laminar shear in Couette‐flow chambers (0.004–0.019 N·m ^{? 2} shear stress) and to unquantified flow in shaken flasks. In these larger cultures, cell division frequency was calculated from flow cytometric measurements of DNA·cell^?1. The mechanism by which shear inhibits net growth of L. polyedrum depends on shear stress level and growth conditions. Observations on the isolated cells showed that shaking inhibited growth by lowering cell division without increased mortality. Similar results were found for early exponential‐phase cultures exposed to the lowest experimental shear stress in Couette‐flow chambers. However, mortality occurred when a late exponential‐phase culture was exposed to the same low shear stress and was inferred to occur in cultures exposed to higher shear stresses. Elevated mortality in those treatments was confirmed using behavioral, morphological, and physiological assays. The results predict that cell division in L. polyedrum populations will be inhibited by levels of oceanic turbulence common for near‐surface waters. Shear‐induced mortality is not expected unless shear‐stress levels are unusually high or when cellular condition resembles late exponential/stationary phase cultures.     

The use of a novel plate assay in a search for yeast mutants defective in deoxyribonucleases.

Methods by which the intracellular enzymes deoxyribonuclease, ribonuclease and protease can be assayed in whole colonies of Saccharomyces cerevisiae on agar plates are described. A search for mutants deficient in deoxyribonuclease has been carried out. Two types of mutant are described. One apparently fails to produce deoxyribonuclease, ribonuclease or protease on agar plates and the other apparently fails to produce deoxyribonuclease and ribonuclease.