What are the genomic drivers of the rapid evolution of PRDM9?

Mammalian Prdm9 has been proposed to be a key determinant of the positioning of chromosome double-strand breaks during meiosis, a contributor to speciation processes, and the most rapidly evolving gene in human, and other animal, genomes. Prdm9 genes often exhibit substantial variation in their numbers of encoded zinc fingers (ZFs), not only between closely related species but also among individuals of a species. The near-identity of these ZF sequences appears to render them very unstable in copy number. The rare sequence differences, however, cluster within ZF sites that determine the DNA-binding specificity of PRDM9, and these substitutions are frequently positively selected. Here, possible drivers of the rapid evolution of Prdm9 are discussed, including selection for efficient pairing of homologous chromosomes or for recombination of deleterious linked alleles, and selection against depletion of recombination hotspots or against disease-associated genome rearrangement.     

Disentangling the paradox of insect phenology: are temporal trends reflecting the response to warming?

The strength and direction of phenological responses to changes in climate have been shown to vary significantly both among species and among populations of a species, with the overall patterns not fully resolved. Here, we studied the temporal and spatial variability associated with the response of several insect species to recent global warming. We use hierarchical models within a model comparison framework to analyze phenological data gathered over 40 years by the Japan Meteorological Agency on the emergence dates of 14 insect species at sites across Japan. Contrary to what has been predicted with global warming, temporal trends of annual emergence showed a later emergence day for some species and sites over time, even though temperatures are warming. However, when emergence data were analyzed as a function of temperature and precipitation, the overall response pointed out an earlier emergence day with warmer conditions. The apparent contradiction between the response to temperature and trends over time indicates that other factors, such as declining populations, may be affecting the date phenological events are being recorded. Overall, the responses by insects were weaker than those found for plants in previous work over the same time period in these ecosystems, suggesting the potential for ecological mismatches with deleterious effects for both suites of species. And although temperature may be the major driver of species phenology, we should be cautious when analyzing phenological datasets as many other factors may also be contributing to the variability in phenology.     

Avian communities’ preferences in recently created agricultural wetlands in irrigated landscapes of semi-arid areas

Numerous wetlands have been created spontaneously in the Ebro river basin as a consequence of new irrigation developments over the last 50 years. Water used for irrigating farmland drains into the lower parts of small valleys to form wetlands that are mostly dominated by common reed (Phragmites australis). Bird communities established in these wetlands are still simple, partly due to the lack of management to enable their ecological functions to improve. A knowledge of which environmental features favor these bird communities is essential in order to improve the design of newly created or restored wetlands associated to future irrigation developments. For this purpose, the habitat and vegetation features of 15 wetlands have been sampled. The structure of bird communities (richness, abundance and diversity) was monitored over 3 years during the breeding season and in winter at foraging and nocturnal roosting. The presence of bushes, height of stems and distance from large wetlands (>1 ha) proved to be the most influential variables on bird community structure and on most abundant species during the breeding season. Wetland area and compactness influenced species richness and the most abundant species during winter foraging and roosting. There was a maximum stem height at which only reed-dwelling birds remained. Uncontrolled winter burning had a severe negative effect upon these recently established populations. The ecological functions of newly created or restored wetlands, including those for run-off treatment in agricultural catchments, could be substantially improved taking into account simple guidelines from these results which relate bird community characteristics to wetland features.     

Does fire increase the spatial heterogeneity of bird communities in Mediterranean landscapes?

The occurrence of large burnt areas has increased considerably in southern Europe in recent years. In order to design management plans to prevent large wildfires while preserving biodiversity, understanding of the ways in which birds respond to these fires is required. We investigated the spatial variability of both avifauna and habitat structure in three zones: unburnt, burnt in 1982, and burnt in 1994. The habitat structure of the unburnt zone was the most variable spatially. However, bird species composition between sampling points was very homogeneous in space. In contrast, the bird communities inhabiting burnt zones were more spatially heterogeneous. This pattern was caused by distinct specific responses to variations in habitat structure. Open-space species responded to small changes in habitat structure with large changes in local abundance, whereas the response of forest species to these structural variations was much less. We suggest that land managers should select specific zones with limited vegetation recovery within large burnt areas and maintain them as open space to keep combustibility low and provide an appropriate habitat for several open space species that are of conservation concern.     

Bird community responses to habitat fragmentation: how consistent are they across landscapes?

Aim The woodland ecosystems of south‐eastern Australia have been extensively disturbed by agriculture and urbanization. Herein, the occurrence of birds in woodland remnants in three distinct landscapes was analysed to examine the effects of different types of landscape matrices on species richness vs. area and species richness vs. isolation relationships and individual species responses to woodland fragmentation. Location The study system comprised three distinct woodland landscapes of the northern Australian Capital Territory and bordering areas of New South Wales. These landscapes (termed agricultural, peri‐urban and urban) are located within 50 km of each other, have remnant fragments of similar age, size, isolation, woodland cover, elevation and climates. The major distinguishing feature of the three landscapes was the properties of the habitats surrounding the numerous woodland remnants. Methods Bird surveys, using an area‐search methodology, were conducted in 1999 and 2000 in 127 remnants in the three landscapes to determine bird species presence/absence. Each remnant was characterized by measures of remnant area, isolation and habitat complexity. To characterize differences between each landscape, we conducted an analysis of the amount of tree cover and human disturbance in each landscape using SPOT imagery and aerial photographs. Linear regressions of woodland‐dependent species richness vs. remnant area and remnant isolation for the three different landscapes were calculated to see if there were any apparent differences. Binomial logistic regressions were used to determine the relationships between the occurrence of each species and the size and isolation of woodland habitat, in each landscape. Results All the landscapes displayed a significant (P < 0.01) species vs. area relationship, but the slope of the urban relationship was significantly greater than those of the other landscapes. In contrast, only the agricultural landscape displayed a significant (P < 0.01) species richness vs. isolation relationship. When individual species were investigated, we found species that were: (1) apparently insensitive to reduction in remnant area and increase in isolation across all landscapes, (2) absent in small remnants in all landscapes, (3) absent in small remnants in all landscapes and also absent in isolated remnants in the agricultural landscape, (4) absent in isolated remnants in the agricultural landscape, and (5) absent in small remnants in the urban landscape. Threshold values (50% probability of occurrence) for area and isolation for individual species were highly variable across the three landscapes. Main conclusions These results indicate that woodland bird communities have a varying response to habitat fragmentation in different landscapes. Whilst we cannot be sure how representative our chosen landscapes are of other similarly composed landscapes, these results suggest that the type of landscape matrix may have a considerable influence on how bird species are affected by woodland fragmentation in the region. For instance, the properties of a matrix may influence both the resources available in the landscape as a whole for different bird species, and the connectivity (dispersal of birds), between woodland remnants. We encourage further research that examines these hypotheses and argue that the management of the matrix should be included in conservation strategies for fragmented landscapes.     

Visualization of the interactome: What are we looking at?

Network visualization of the interactome has been become routine in systems biology research. Not only does it serve as an illustration on the cellular organization of protein-protein interactions, it also serves as a biological context for gaining insights from high-throughput data. However, the challenges to produce an effective visualization have been great owing to the fact that the scale, biological context and dynamics of any given interactome are too large and complex to be captured by a single visualization. Visualization design therefore requires a pragmatic trade-off between capturing biological concept and being comprehensible. In this review, we focus on the biological interpretation of different network visualizations. We will draw on examples predominantly from our experiences but elaborate them in the context of the broader field. A rich variety of networks will be introduced including interactomes and the complexome in 2D, interactomes in 2.5D and 3D and dynamic networks.     

How heterogeneous are the cloud forest communities in the mountains of central Veracruz, Mexico?

The montane forest in central Veracruz, Mexico is a hotspot of biodiversity. We asked whether lower and upper montane forests could be distinguished in this ecoregion. Variables of vegetation and seasonality in precipitation were tested across 14 sites between 1,250- and 2,550-m elevations. A total of 1,639 individuals and 128 tree species was recorded. There was a unimodal pattern in the richness of species, genera, and families; their richness was positively correlated with precipitation in the wettest quarter of the year, though there were no differences in the basal area and density. Rarefaction, species turnover, nonmetric multidimensional scaling, and a cluster histogram suggest two major groups: lower elevation forests that are less diverse, have low beta diversity and are more similar in composition, with Clethra macrophylla, Liquidambar styraciflua, and Quercus lancifolia as indicator species; and higher elevation forests that are more diverse, have high species turnover, and include forests with Quercus corrugata and Prunus rhamnoides, and forests with Fagus grandifolia, Persea americana, and Ternstroemia sylvatica as indicator species. However, other communities (an Oreomunnea mexicana at the upper site, and a limestone site in the lower forests), exemplify the high regional heterogeneity. We conclude that elevation and seasonality in precipitation produce a directional change in richness and indicator species, but not in vegetation structure. Lower montane forests differed from cloud forests at upper elevations. However, other factors should be included—mainly biogeographic affinities, historic and recent anthropogenic disturbance—to conclusively distinguish them. Montane forest can still be considered very heterogeneous and very high in beta diversity.     

Genetic Prediction: What are the Limits?

The spectre of determinism stalks many of the concerns surrounding the impact of genetic research into both disease and normal behaviour. The ability accurately to predict a person's actions would certainly have profound implications for notions of individuality and free will. But to what extent will the current explosion in genetic research provide more accurate predictors than have been available for millennia in the form of wealth, social status and perceived family resemblance? The genetic research program is at too early a stage to answer this question with confidence, but various indicators tend to point in the same direction: the predictive ability of genetic analysis will generally be low. This conclusion runs counter to widely perceived popular notions. The deconstruction of genetic determinism is an essential safeguard against the real concern that genetic information may be used for discrimination by unscrupulous powers.     

What are 60 warblers worth? Killing in the name of conservation

Ecological research sometimes entails animal suffering and even animal killing. The ethical appropriateness of animal suffering and killing in conservation research may entail considerations that differ from many other kinds of research. This is true, insomuch as conservation research is specifically motivated by an ethical premise: an appreciation for non-human life. In striking contrast with other academic fields (e.g. medicine), however, the ethical dimension of conservation research is only rarely discussed. When it is discussed, it tends to be characterized by logical errors. These errors are important because they are general (i.e. both common and with far-reaching implications), and they are easily made by intelligent people; especially those with no formal training in ethics or logic. Failure to recognize these errors could stymie efforts to increase the ethical quality of ecological research conducted in the name of conservation.
We take advantage of a recently published dialogue concerning the ethical appropriateness of a specific field experiment that entailed killing black-throated blue warblers, Dendroica caerulescens . Both sides of this debate exemplify the kinds of errors to which we refer. In this paper we briefly review the arguments presented on each side of this debate, highlight their mistakes, and indicate necessary corrections. We argue that: (1) compliance with animal research regulations, while important, inadequately accommodates the ethical aspects of animal research, and (2) individual ecologists ought to understand themselves what does and does not represent sound and valid arguments for ethical decisions. Finally, we discuss how any ecological researcher might begin to apply our analysis to his or her own research.     

What are the characteristics of cycling cells in the adult central nervous system?

Many regions of the adult central nervous system contain cycling cells. Such cells comprise a relatively small fraction of the total population of the CNS. Work over decades has attempted to determine the normal fates of these cells and their fates under pathological conditions. The recent interest in "stem" cells and "progenitors" in the adult CNS has sparked a much revived exploration into the nature of these cells and in the signals by which they may be induced to differentiate into mature neurons or glia. This population has not yet been fully characterized, although it has become clear that this is a heterogeneous group of cells, differing in morphology, antigen expression, migratory capacity, and potential fates.     

Impact of antimicrobial residues on gut communities: are the new regulations effective?

Veterinary medicines are subject to a rigorous evaluation with regard to safety, efficacy and quality before they are licensed. For drugs used in food producing animals, it is necessary to establish what is referred to as the acceptable daily intake (ADI), this is defined as an estimate of the amount of a substance, expressed on a body weight basis, that can be ingested daily over a lifetime without appreciable risk to human health. It is necessary to determine a toxicological, pharmacological and microbiological ADI. This article describes a recently harmonized guideline that outlines the process for determining the need for a microbiological ADI and discusses the test systems that take into account the complexity of the human intestinal flora. The described process is used to address the effects of antimicrobial drug residues on human intestinal flora for regulatory purposes. The guideline does not recommend any one particular system for use in regulatory decision making but provides recommendations for a harmonized approach to establish a microbiological ADI and offers test options rather than specifying a testing regimen. The process and the challenges of this new guideline are discussed.     

What are the genuine action potentials in plants?

This is a comment on the paper by Pyatygin in this issue [Biophysics 53(1), 81–86 (2008)], indicating some points that should be clarified to comprehensively assess the apparent diversity of plant electrical signaling.