Faster evolution of highly conserved DNA in tropical plants

A faster rate of nuclear DNA evolution has recently been found for plants occupying warmer low latitudes relative to those in cooler high latitudes. That earlier study by our research group compared substitution rates within the variable internal transcribed spacer (ITS) region of the ribosomal gene complex amongst 45 congeneric species pairs, each member of which differed in their latitudinal distributions. To determine whether this rate differential might also occur within highly conserved DNA, we sequenced the 18S ribosomal gene in the same 45 pairs of plants. We found that the rate of evolution in 18S was 51% faster in the tropical plant species relative to their temperate sisters and that the substitution rate in 18S correlated positively with that in the more variable ITS. This result, with a gene coding for ribosomal structure, suggests that climatic influences on evolution extend to functionally important regions of the genome.     

Community persistence in Broadstone Stream (U.K.) over three decades

1. Few detailed long-term data sets exist for fresh waters with which to examine large-scale temporal changes in community composition. Consequently, insight into community persistence has been restricted to a few, contingent case studies. We collated and analysed data for the aquatic macroinvertebrate community of Broadstone Stream in south-east England, spanning three decades. The pH of this naturally acid stream has risen progressively since the 1970s, and we sought to examine the potential effects of this environmental change upon the community.
2. Persistence within Broadstone was high when compared with other systems that have been analysed using similar methods. The stream was characterised by a `core' community of eight taxa that were always present, and contributed 75–97% of total invertebrate abundance, with a trailing limb of progressively rarer and more acid-sensitive taxa. There was little species turnover, although the time-series exceeded 20 generations for most species.
3. Despite this high persistence, a long-term response to rising pH was detected: species indicating profound acidity (identified a priori from independent studies) have declined since the 1970s, whereas indicators of moderate acidity increased. The structure of the community food web has also changed since the 1970s, with increased predator diversity and abundance, and a lengthening of food chains following the invasion of a new top predator.
4. These changes in the community appeared to be driven by an interaction between pH and climate. The unusually hot, dry summers characteristic of the 1990s may have raised pH during the more sensitive (i.e. early) stages of the life-cycle, and thus provided a window of opportunity for less acid-tolerant taxa to colonise and become established. Changes in pH appeared to set the boundaries of the available local species pool, within which biotic interactions ultimately shaped the community.     

In vitro assessment of the toxicity of metal compounds

A review of in vitro mutagenesis assessment of metal compounds in mammalian and nonmammalian test systems has been compiled. Prokaryotic assays are ineffective or inconsistent in their detection of most metals as mutagens, with the notable exception of hexavalent chromium. Mammalian assay systems appear to be similarly inappropriate for the screening of metal compounds based upon the limited number of studies that have employed those compounds having known carcinogenic activity. Although of limited value as screening tests for the detection of potentially carcinogenic metal compounds, the well-characterized in vitro mutagenesis systems may prove to be of significant value as a means to elucidate mechanisms of metal genotoxicity.     

Review: Assessment of completeness of reporting in intervention studies using livestock: an example from pain mitigation interventions in neonatal piglets

Accurate and complete reporting of study methods, results and interpretation are essential components for any scientific process, allowing end-users to evaluate the internal and external validity of a study. When animals are used in research, excellence in reporting is expected as a matter of continued ethical acceptability of animal use in the sciences. Our primary objective was to assess completeness of reporting for a series of studies relevant to mitigation of pain in neonatal piglets undergoing routine management procedures. Our second objective was to illustrate how authors can report the items in the Reporting guidElines For randomized controLled trials for livEstoCk and food safety (REFLECT) statement using examples from the animal welfare science literature. A total of 52 studies from 40 articles were evaluated using a modified REFLECT statement. No single study reported all REFLECT checklist items. Seven studies reported specific objectives with testable hypotheses. Six studies identified primary or secondary outcomes. Randomization and blinding were considered to be partially reported in 21 and 18 studies, respectively. No studies reported the rationale for sample sizes. Several studies failed to report key design features such as units for measurement, means, standard deviations, standard errors for continuous outcomes or comparative characteristics for categorical outcomes expressed as either rates or proportions. In the discipline of animal welfare science, authors, reviewers and editors are encouraged to use available reporting guidelines to ensure that scientific methods and results are adequately described and free of misrepresentations and inaccuracies. Complete and accurate reporting increases the ability to apply the results of studies to the decision-making process and prevent wastage of financial and animal resources.     

A simulation approach for power calculation in large cohort studies based on multistate models

Realistic power calculations for large cohort studies and nested case control studies are essential for successfully answering important and complex research questions in epidemiology and clinical medicine. For this, we provide a methodical framework for general realistic power calculations via simulations that we put into practice by means of an R‐based template. We consider staggered recruitment and individual hazard rates, competing risks, interaction effects, and the misclassification of covariates. The study cohort is assembled with respect to given age‐, gender‐, and community distributions. Nested case‐control analyses with a varying number of controls enable comparisons of power with a full cohort analysis. Time‐to‐event generation under competing risks, including delayed study‐entry times, is realized on the basis of a six‐state Markov model. Incidence rates, prevalence of risk factors and prefixed hazard ratios allow for the assignment of age‐dependent transition rates given in the form of Cox models. These provide the basis for a central simulation‐algorithm, which is used for the generation of sample paths of the underlying time‐inhomogeneous Markov processes. With the inclusion of frailty terms into the Cox models the Markov property is specifically biased. An “individual Markov process given frailty” creates some unobserved heterogeneity between individuals. Different left‐truncation‐ and right‐censoring patterns call for the use of Cox models for data analysis. p‐values are recorded over repeated simulation runs to allow for the desired power calculations. For illustration, we consider scenarios with a “testing” character as well as realistic scenarios. This enables the validation of a correct implementation of theoretical concepts and concrete sample size recommendations against an actual epidemiological background, here given with possible substudy designs within the German National Cohort.     

Impact of the Arundo scale Rhizaspidiotus donacis (Hemiptera: Diaspididae) on the weight of Arundo donax (Poaceae: Arundinoideae) rhizomes in Languedoc southern France and Mediterranean Spain

Arundo donax L. (Poaceae) is native to Mediterranean Europe and invasive in the Rio Grande Basin of North America. Rhizomes from nine sites in France and Spain infested with a candidate control agent, the armoured scale Rhizaspidiotus donacis (Hemiptera: Diaspididae) weighed 50% less than those from nine sites without scale.     

Fish population structuring in the North Sea: understanding processes and mechanisms from studies of the movements of adults

Few fish species form single, panmictic populations throughout their geographic range, most form subpopulations or 'stocks' with differing levels of interconnectivity. Different patterns of interconnectivity between subpopulations will give rise to different responses to exploitation and management, but they will also have different capacities to generate the genetic and phenotypic differences often used to discriminate between stocks. Consequently, knowledge of ontogenetic and seasonal patterns in the distribution, movement and behaviour of individuals is crucial to identifying population substructure. This paper considers the evidence gathered about movements and behaviour of adult fishes from mark-recapture and electronic tagging studies for a number of fish species in the North Sea and elsewhere in U.K. waters in an attempt to understand population structure and the processes that may give rise to it.     

Reply to the first systematic response by the Global Footprint Network to criticism: A real debate finally?

We respond to a reaction of the Global Footprint Network/GFN on our 8-point criticism of the ecological footprint. We also refer to, and comment on, an associated debate in this journal between Giampietro and Saltelli, 2014a, Giampietro and Saltelli, 2014b, on the one hand, and Goldfinger et al. (2014), on the other. We conclude that criticism on the footprint is accumulating and coherent across the various studies and disciplines and among the different authors. This was the first time that Wackernagel/GFN systematically responded to our criticisms. Hence, our response contains several original elements and the resulting exchange can be seen to add value to the existing literature. It ultimately allows readers to better make up their mind about the different viewpoints on the ecological footprint.     

Epilogue — Demography and anthropology

As a conclusion, this paper reviews briefly the content of the volume. The wealth of demographic data has not been adequately exploited in anthropology; this is why this publication is valuable in showing attempts to apply demographic data in a variety of anthropological problems. This symposium has explored many interesting points which we recall here. Yet it has also opened up a whole range of further questions on the material presented as well as in this broad field. Several directions of research could be developed, for instance, testing among human populations, over long periods, the ecological thoughts of ecosystems evolving as a cascade of instabilities, rather than a succession of equilibrium states. Let us also recall the pervasive nature of demographic facts in topics such as the energy cycle or the genetic structure and evolution of human populations.