Bottom-up effects of a no-take zone on endangered penguin demographics

Marine no-take zones can have positive impacts for target species and are increasingly important management tools. However, whether they indirectly benefit higher order predators remains unclear. The endangered African penguin (Spheniscus demersus) depends on commercially exploited forage fish. We examined how chick survival responded to an experimental 3-year fishery closure around Robben Island, South Africa, controlling for variation in prey biomass and fishery catches. Chick survival increased by 18% when the closure was initiated, which alone led to a predicted 27% higher population compared with continued fishing. However, the modelled population continued to decline, probably because of high adult mortality linked to poor prey availability over larger spatial scales. Our results illustrate that small no-take zones can have bottom-up benefits for highly mobile marine predators, but are only one component of holistic, ecosystem-based management regimes.     

Efficient Bayesian analysis of occupancy models with logit link functions

Occupancy models (Ecology, 2002; 83: 2248) were developed to infer the probability that a species under investigation occupies a site. Bayesian analysis of these models can be undertaken using statistical packages such as WinBUGS, OpenBUGS, JAGS, and more recently Stan, however, since these packages were not developed specifically to fit occupancy models, one often experiences long run times when undertaking an analysis. Bayesian spatial single‐season occupancy models can also be fit using the R package stocc. The approach assumes that the detection and occupancy regression effects are modeled using probit link functions. The use of the logistic link function, however, is algebraically more tractable and allows one to easily interpret the coefficient effects of an estimated model by using odds ratios, which is not easily done for a probit link function for models that do not include spatial random effects. We develop a Gibbs sampler to obtain posterior samples from the posterior distribution of the parameters of various occupancy models (nonspatial and spatial) when logit link functions are used to model the regression effects of the detection and occupancy processes. We apply our methods to data extracted from the 2nd Southern African Bird Atlas Project to produce a species distribution map of the Cape weaver (Ploceus capensis) and helmeted guineafowl (Numida meleagris) for South Africa. We found that the Gibbs sampling algorithm developed produces posterior samples that are identical to those obtained when using JAGS and Stan and that in certain cases the posterior chains mix much faster than those obtained when using JAGS, stocc, and Stan. Our algorithms are implemented in the R package, Rcppocc. The software is freely available and stored on GitHub ( https://github.com/AllanClark/Rcppocc ).     

Demographic effects of extreme winter weather in the barn owl

Extreme weather events can lead to immediate catastrophic mortality. Due to their rare occurrence, however, the long-term impacts of such events for ecological processes are unclear. We examined the effect of extreme winters on barn owl (Tyto alba) survival and reproduction in Switzerland over a 68-year period (∼20 generations). This long-term data set allowed us to compare events that occurred only once in several decades to more frequent events. Winter harshness explained 17 and 49% of the variance in juvenile and adult survival, respectively, and the two harshest winters were associated with major population crashes caused by simultaneous low juvenile and adult survival. These two winters increased the correlation between juvenile and adult survival from 0.63 to 0.69. Overall, survival decreased non-linearly with increasing winter harshness in adults, and linearly in juveniles. In contrast, brood size was not related to the harshness of the preceding winter. Our results thus reveal complex interactions between climate and demography. The relationship between weather and survival observed during regular years is likely to underestimate the importance of climate variation for population dynamics.     

Consequences of a changing environment on the breeding phenology and reproductive success components in a long-distance migratory bird

Migratory birds have a narrow time window to breed, especially in the Arctic, where early nesting typically yields the highest reproductive success. We assessed temporal changes (1991–2015) in reproductive success components in relation to timing of breeding in greater snow geese (Chen caerulescens atlantica). This species breeds in the Canadian Arctic, a region that has experienced a strong warming trend. We tested the effect of laying or hatching date, year and their interaction on six reproductive components: Total clutch laid, nesting success, egg survival, hatching success, prefledging, and postfledging survival. Over 25 years, mean laying date changed little, even though it advanced 1.8 days in early breeders and was delayed 3 days in late breeders. Likewise, the number of eggs in nests initiated early in the season decreased by 0.6 egg, whereas in late nests it increased by 0.3 egg. Success of nests initiated early and late in the season was lower than nests initiated near the population mean, and consistently increased over time. The proportion of eggs surviving to partial predation and postfledging survival decreased with laying date but the pattern did not change over time. In contrast, prefledging survival was not affected by laying date initially but declined in nests initiated late in the season toward the end of the study. Overall, nests initiated close to the population mean showed little temporal change for most components of reproductive success and seem to be less affected by environmental change than nests initiated early and late in the season.     

Implementation of intensity modulated radiotherapy for prostate cancer in a private radiotherapy service in Mexico

Intensity modulated radiation therapy (IMRT) allows physicians to deliver higher conformal doses to the tumour, while avoiding adjacent structures. As a result the probability of tumour control is higher and toxicity may be reduced. However, implementation of IMRT is highly complex and requires a rigorous quality assurance (QA) program both before and during treatment. The present article describes the process of implementing IMRT for localized prostate cancer in a radiation therapy department. In our experience, IMRT implementation requires careful planning due to the need to simultaneously implement specialized software, multifaceted QA programs, and training of the multidisciplinary team. Establishing standardized protocols and ensuring close collaboration between a multidisciplinary team is challenging but essential.     

Medium and temperature dependence of decarboxylase reactions inAeromonas spp.

Decarboxylase/dihydrolase activities inAeromonas spp. are important as diagnostic tools and indicators of enterotoxin production. We have analyzed the following media at 25°C, 29°C, and 37°C, respectively, for their ability to detect such activities: Møller's, Falkow's, and Fay and Barry's (F&B) containing ornithine, lysine, and arginine, respectively, as well as motility-indole-ornithine (MIO) medium and lysine decarboxylase broth with 0.1% agar (LDC). In order to retain ornithine negativity, but to get as much positivity as possible for arginine, optimal incubation conditions were 29°C for 96 h (Møller), 48 h (Falkow, MIO, and LDC), and 24 h (F&B). The F&B medium proved to be the most sensitive for the detection of lysine decarboxylase, a positive test being highly correlated with the two speciesA. hydrophila andA. sobria, and we suggest its use for routine detection of decarboxylase/dihydrolase activities.In memory of Dr. Sally Jo Rubin.     

Value of rRNA gene restriction patterns ofAeromonas spp. for epidemiological investigations

We have investigated the value of rRNA gene restriction (rDNA) patterns for strain discrimination in aeromonads isolated from clinical and environmental sources. Chromosomal DNA was purified and digested with restriction enzymesPst I andSma I, and the resulting fragments were separated by agarose gel electrophoresis and stained with ethidium bromide. The DNA was transferred to membranes (Southern blotting), where it was probed with biotinylated plasmid pKK3535 DNA. Hybridization bands were developed with the BluGene (BRL) kit. The resulting rDNA patterns were visually analyzed for similarities between epidemiologically related strains. Pattern heterogeneity was observed among unrelated strains of aeromonads of clinical and environmental origin, whereas homology was observed amongAeromonas caviae isolates from three siblings with gastroenteritis and between an infant and foster mother with acute gastroenteritis caused byA. caviae. Multiple isolates ofA. caviae from the same patient over more than 3 years produced homologous rDNA patterns which remained stable after 20 consecutive subcultures. Serotyping results for typable strains were consistent with strain designations derived by analysis of rDNA patterns. The specificity, reproducibility, stability, and ease of performance, especially with the nonisotopic probe, make ribotyping a valuable method for epidemiological investigations ofAeromonas infections.     

Is climate change causing the range contraction of Cape Rock-jumpers (Chaetops frenatus)?

Species distribution models often suggest strong links between climate and species' distribution boundaries and project large distribution shifts in response to climate change. However, attributing distribution shifts to climate change requires more than correlative models. One idea is to examine correlates of the processes that cause distribution shifts, namely colonization and local extinction, by using dynamic occupancy models. The Cape Rock-jumper (Chaetops frenatus) has disappeared over most of its distribution where temperatures are the highest. We used dynamic occupancy models to analyse Cape Rock-jumper distribution with respect to climate (mean temperature and precipitation over the warmest annual quarter), vegetation (proportion of natural vegetation, fynbos) and land-use type (protected areas). Detection/non-detection data were collected over two phases of the Southern African Bird Atlas Project (SABAP): 1987–1991 (SABAP1) and 2008–2014 (SABAP2). The model described the contraction of the Cape Rock-jumper's distribution between SABAP1 and SABAP2 well. Occupancy probability during SABAP1 increased with the proportion of fynbos and protected area per grid cell, and decreased with increases in mean temperature and precipitation over the warmest annual quarter. Mean extinction probability increased with mean temperature and precipitation over the warmest annual quarter, although the associated confidence intervals were wide. Nonetheless, our results showed a clear correlation between climate and the distribution boundaries of the Cape Rock-jumper, and in particular, the species' aversion for higher temperatures. The data were less conclusive on whether the observed range contraction was linked to climate change or not. Examining the processes underlying distribution shifts requires large datasets and should lead to a better understanding of the drivers of these shifts.