Population genomics of wild and laboratory zebrafish (Danio rerio)

Understanding a wider range of genotype–phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large‐scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1832 polymorphic EST‐based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among‐clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall F_ST of 0.170 (95% CI 0.105–0.254). These genetic groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4%) and nine loci (0.5%) with significantly low F_ST values. Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.     

Coordinated approaches to quantify long‐term ecosystem dynamics in response to global change

Many serious ecosystem consequences of climate change will take decades or even centuries to emerge. Long‐term ecological responses to global change are strongly regulated by slow processes, such as changes in species composition, carbon dynamics in soil and by long‐lived plants, and accumulation of nutrient capitals. Understanding and predicting these processes require experiments on decadal time scales. But decadal experiments by themselves may not be adequate because many of the slow processes have characteristic time scales much longer than experiments can be maintained. This article promotes a coordinated approach that combines long‐term, large‐scale global change experiments with process studies and modeling. Long‐term global change manipulative experiments, especially in high‐priority ecosystems such as tropical forests and high‐latitude regions, are essential to maximize information gain concerning future states of the earth system. The long‐term experiments should be conducted in tandem with complementary process studies, such as those using model ecosystems, species replacements, laboratory incubations, isotope tracers, and greenhouse facilities. Models are essential to assimilate data from long‐term experiments and process studies together with information from long‐term observations, surveys, and space‐for‐time studies along environmental and biological gradients. Future research programs with coordinated long‐term experiments, process studies, and modeling have the potential to be the most effective strategy to gain the best information on long‐term ecosystem dynamics in response to global change.     

Physical illness in patients with severe mental disorders. II. Barriers to care, monitoring and treatment guidelines, plus recommendations at the system and individual level

Physical disorders are, compared to the general population, more prevalent in people with severe mental illness (SMI). Although this excess morbidity and mortality is largely due to modifiable lifestyle risk factors, the screening and assessment of physical health aspects remains poor, even in developed countries. Moreover, specific patient, provider, treatment and system factors act as barriers to the recognition and to the management of physical diseases in people with SMI. Psychiatrists can play a pivotal role in the improvement of the physical health of these patients by expanding their task from clinical psychiatric care to the monitoring and treatment of crucial physical parameters. At a system level, actions are not easy to realize, especially for developing countries. However, at an individual level, even simple and very basic monitoring and treatment actions, undertaken by the treating clinician, can already improve the problem of suboptimal medical care in this population. Adhering to monitoring and treatment guidelines will result in a substantial enhancement of physical health outcomes. Furthermore, psychiatrists can help educate and motivate people with SMI to address their suboptimal lifestyle, including smoking, unhealthy diet and lack of exercise. The adoption of the recommendations presented in this paper across health care systems throughout the world will contribute to a significant improvement in the medical and related psychiatric health outcomes of patients with SMI.     

Correlated geographic variation in predation risk and antipredator behaviour within a wide‐ranging snake species (Notechis scutatus,Elapidae)

Geographic variation in antipredator behaviour within wide‐ranging species may be driven by both genetic and environmental influences. We quantified antipredator responses in neonatal (laboratory born, n = 555) and adult (field caught, n = 346) tiger snakes (Notechis scutatus) from 11 mainland and island sites in southern Australia. We used these data to test predictions from Bonnet et al.'s hypothesis that the vigour of antipredator responses in this species reflects behavioural plasticity (in turn, driven by an individual snake's exposure to predators during its lifetime) rather than by genetic variation in this trait. We used the number of predator taxa in each area as an index of predator risk. As predicted, adult snakes from predator‐rich areas had more vigorous defensive responses when handled, whereas neonatal behaviour (although also variable among populations) was unrelated to predator species richness. Adult males bit more readily than adult females (as expected from the greater predation exposure of males during mate searching) but no such sex difference was evident in neonates. Although alternative models remain possible, our data are most consistent with the hypothesis that geographic divergence in antipredator tactics within this species primarily reflects developmentally plastic responses to local predation risk.     

Spatial population genetic structure reveals strong natal site fidelity in Echinocladius martini (Diptera: Chironomidae) in northeast Queensland,Australia

1. A diverse array of patterns has been reported regarding the spatial extent of population genetic structure and effective dispersal in freshwater macroinvertebrates. In river systems, the movements of many taxa can be restricted to varying degrees by the natural stream channel hierarchy. 2. In this study, we sampled populations of the non‐biting freshwater midge Echinocladius martini in the Paluma bioregion of tropical northeast Queensland to investigate fine scale patterns of within‐ and among‐stream dispersal and gene flow within a purported historical refuge. We amplified a 639‐bp fragment of mitochondrial cytochrome c oxidase subunit I and analysed genetic structure using pairwise Φ_ST, hierarchical amova , Mantel tests and a parsimony network. Genetic variation was partitioned among stream sections, using Streamtree , to investigate the effect of potential instream dispersal barriers. 3. The data revealed strong natal site fidelity and significant differentiation among neighbouring, geographically proximate streams. We found evidence for only episodic adult flight among sites on separate stream reaches. Overall, however, our data suggested that both larval and adult dispersal was largely limited to within a stream channel. 4. This may arise from a combination of the high density of riparian vegetation physically restricting dispersal and from the joint effects of habitat stability and large population sizes. Together these latter may make it more likely that upstream populations will persist, even in the absence of regular compensatory upstream flight, and will thus reduce the adaptive value of dispersal among streams. Taken together, these data suggest that dispersal of E. martini is highly restricted, to the scale of only a few kilometres, and hence occurs predominantly within the natal stream.     

Global Standard Stratotype-section and Point (GSSP) of the Furongian Series and Paibian Stage (Cambrian)

The Global Standard Stratotype-section and Point (GSSP) of the Furongian Series (uppermost series of the Cambrian System) and the Paibian Stage (lowermost stage of the Furongian Series), has been recently defined and ratified by the International Union of Geological Sciences (IUGS). The boundary stratotype is 369 metres above the base of the Huaqiao Formation in the Paibi section, northwestern Hunan Province, China. This point coincides with the first appearance of the cosmopolitan agnostoid trilobite Glyptagnostus reticulatus, and occurs near the base of a large positive carbon isotopic excursion (SPICE excursion).