Do habitat shifts drive diversification in teleost fishes? An example from the pufferfishes (Tetraodontidae)

Habitat shifts are implicated as the cause of many vertebrate radiations, yet relatively few empirical studies quantify patterns of diversification following colonization of new habitats in fishes. The pufferfishes (family Tetraodon‐tidae) occur in several habitats, including coral reefs and freshwater, which are thought to provide ecological opportunity for adaptive radiation, and thus provide a unique system for testing the hypothesis that shifts to new habitats alter diversification rates. To test this hypothesis, we sequenced eight genes for 96 species of pufferfishes and closely related porcupine fishes, and added 19 species from sequences available in GenBank. We time‐calibrated the molecular phylogeny using three fossils, and performed several comparative analyses to test whether colonization of novel habitats led to shifts in the rate of speciation and body size evolution, central predictions of clades experiencing ecological adaptive radiation. Colonization of freshwater is associated with lower rates of cladogenesis in pufferfishes, although these lineages also exhibit accelerated rates of body size evolution. Increased rates of cladogenesis are associated with transitions to coral reefs, but reef lineages surprisingly exhibit significantly lower rates of body size evolution. These results suggest that ecological opportunity afforded by novel habitats may be limited for pufferfishes due to competition with other species, constraints relating to pufferfish life history and trophic ecology, and other factors.     

A probabilistic model for secondary structure prediction from protein chemical shifts

Protein chemical shifts encode detailed structural information that is difficult and computationally costly to describe at a fundamental level. Statistical and machine learning approaches have been used to infer correlations between chemical shifts and secondary structure from experimental chemical shifts. These methods range from simple statistics such as the chemical shift index to complex methods using neural networks. Notwithstanding their higher accuracy, more complex approaches tend to obscure the relationship between secondary structure and chemical shift and often involve many parameters that need to be trained. We present hidden Markov models (HMMs) with Gaussian emission probabilities to model the dependence between protein chemical shifts and secondary structure. The continuous emission probabilities are modeled as conditional probabilities for a given amino acid and secondary structure type. Using these distributions as outputs of first‐ and second‐order HMMs, we achieve a prediction accuracy of 82.3%, which is competitive with existing methods for predicting secondary structure from protein chemical shifts. Incorporation of sequence‐based secondary structure prediction into our HMM improves the prediction accuracy to 84.0%. Our findings suggest that an HMM with correlated Gaussian distributions conditioned on the secondary structure provides an adequate generative model of chemical shifts. Proteins 2013; © 2012 Wiley Periodicals, Inc.     

IMPLEMENTATION OF 12-HOUR SHIFTS IN A BRAZILIAN PETROCHEMICAL PLANT: IMPACT ON SLEEP AND ALERTNESS

A recent worldwide trend in chemical and petrochemical industries is to extend the duration of shifts. Optimization of the labor force to reduce costs is one reason to increase the length of working time in a shift. Implementation of 12h shifts is a controversial decision for managers and scientists. Literature reviews show alertness is lower during the nighttime hours, and sleep duration is reduced and worse during the daytime. The main objective of this study was to evaluate the impacts of 12h shifts on alertness and sleep. To evaluate the duration and quality of sleep and alertness during work, 22 male shift workers on a continuous rotating schedule at a petrochemical plant completed activity logs and estimated alertness using analog 10-cm scales for 30 consecutive days, three times (at 2h, 6h, and 10h of the shift) every work shift. Statistical tests (analysis of variance [ANOVA] and Tukey) were performed to detect differences between workdays and off days. The shift schedule was 2 days/3 nights/4 off days, followed by 3 days/2 nights/5 off days, followed by 2 days/2 nights/5 off days. Sleep duration varied significantly (p <. 001) among the work shifts and off days. Comparing work nights, the shortest mean sleep occurred after the second night (mean = 311.4 minutes, SD = 101.7 minutes), followed by the third night (mean = 335.3 minutes, SD = 151.2 minutes). All but one shift (sleep after the first work night) were significantly different from sleep after the first 2 workdays (p <. 002). Tukey tests showed no significant differences in sleep quality between workdays and nights, with the exception of sleep after the third day compared to sleep after night shifts. However, significant differences were detected between off days and work nights (p <. 01). ANOVA analysis showed borderline differences among perceived alertness during day shifts (p =. 073) and significant differences among the hours of theshifts(p =. 0005), especially when comparing the 2nd hour of the first day with the 10th hour of all the day shifts. There were no significant differences in perceived alertness during night work among the first, second, and third nights (p =. 573), but there were significant differences comparing the times (2nd, 6th, 10th hour) of the night shifts (p ≤. 001). The evaluation of sleep (duration and quality) and level of alertness have been extensively used in the literature as indicators of possible performance decrements at work. The results of this study show poorer sleep after and significantly decreased alertness during night work. Shifts of 12h are usually implemented for technical and economic reasons. These results point out the necessity of a careful trade-off between the financial and technical gains longer shifts might bring and the possible losses due to incidents or accidents from performance decrements during work. (Chronobiology International, 17(4), 521–537, 2000)     

Nymphal feeding habits of Perla madritensis Rambur 1842 (Plecoptera: Perlidae)

The diet of Perla madritensis, endemic species of the northern half of the Iberian Peninsula, is described for the first time by means of a study carried out in north-western Spain. As other species of the genus Perla, this taxon behaves mainly as predator, with Chironomidae, followed by Baetidae, being the most abundant prey in its gut. Shifts in diet composition were detected in relation to size in this species, with smaller prey being replaced by larger ones such as Simuliidae and Leptophlebiidae when the nymphs become larger.     

Eucalypts face increasing climate stress

Global climate change is already impacting species and ecosystems across the planet. Trees, although long‐lived, are sensitive to changes in climate, including climate extremes. Shifts in tree species' distributions will influence biodiversity and ecosystem function at scales ranging from local to landscape; dry and hot regions will be especially vulnerable. The Australian continent has been especially susceptible to climate change with extreme heat waves, droughts, and flooding in recent years, and this climate trajectory is expected to continue. We sought to understand how climate change may impact Australian ecosystems by modeling distributional changes in eucalypt species, which dominate or codominate most forested ecosystems across Australia. We modeled a representative sample of Eucalyptus and Corymbia species (n = 108, or 14% of all species) using newly available Representative Concentration Pathway (RCP) scenarios developed for the 5th Assessment Report of the IPCC, and bioclimatic and substrate predictor variables. We compared current, 2025, 2055, and 2085 distributions. Overall, Eucalyptus and Corymbia species in the central desert and open woodland regions will be the most affected, losing 20% of their climate space under the mid‐range climate scenario and twice that under the extreme scenario. The least affected species, in eastern Australia, are likely to lose 10% of their climate space under the mid‐range climate scenario and twice that under the extreme scenario. Range shifts will be lateral as well as polewards, and these east–west transitions will be more significant, reflecting the strong influence of precipitation rather than temperature changes in subtropical and midlatitudes. These net losses, and the direction of shifts and contractions in range, suggest that many species in the eastern and southern seaboards will be pushed toward the continental limit and that large tracts of currently treed landscapes, especially in the continental interior, will change dramatically in terms of species composition and ecosystem structure.     

The influence of variability in species trait data on community‐level ecological prediction and inference

Species trait data have been used to predict and infer ecological processes and the responses of biological communities to environmental changes. It has also been suggested that, in lieu of trait, data niche differences can be inferred from phylogenetic distance. It remains unclear how variation in trait data may influence the strength and character of ecological inference. Using species‐level trait data in community ecology assumes intraspecific variation is small in comparison with interspecific variation. Intraspecific variation across species ranges or within populations may lead to variability in trait data derived from different scales (i.e., local or regional) and methods (i.e., mean or maximum values). Variation in trait data across species can affect community‐level relationships. I examined variability in body size, a key trait often measured across taxa. I collected 12 metrics of fish species length (including common and maximum values) for 40 species from literature, online databases, museum collections, and field data. I then tested whether different metrics of fish length could consistently predict observed species range boundary shifts and the impacts of an introduced predator on inland lake fish communities across Ontario, Canada. I also investigated whether phylogenetic signal, an indicator of niche‐conservativism, changed among measures. I found strong correlations between length metrics and limited variation across metrics. Accordingly, length was a consistently significant predictor of the response of fish communities to environmental change. Additionally, I found significant evidence of phylogenetic signal in fish length across metrics. Limited variation in length across metrics (within species), in comparison with variation within metrics (across species), made fish species length a reliable predictor at a community‐level. When considering species‐level trait data from different sources, researchers should examine the potential influence of intraspecific trait variation on data derived by different metrics and at different scales.     

Seasonal variation in understorey bird species diversity and abundance in the Uluguru Nature Reserve,Tanzania

The Uluguru Mountains form a component block of the Eastern Arc Mountains of Tanzania and Kenya and are known for a high degree of endemic vertebrate and plant taxa. Among the Eastern Arc Mountains, the Uluguru Mountains rank second in the number of endemic species. Although the forests in these mountains have received considerable ornithological attention, studies on how forest bird communities in the available low elevation forests are affected by seasons remain patchy and sporadic. Such studies are important because in the Uluguru Mountains, forest destruction in the lower slopes has been severe to an extent that there is very little substantial forest survives below 900 m above sea level. Using mist netting, seasonal variation in understorey bird communities in the remaining low elevation forests in the Uluguru Nature Reserve was assessed between 2005 and 2011. Species diversity and relative abundance of the birds were higher during the cold season in comparison with the hot season possibly due to seasonal elevational movements of some species. Elevational migrants made a large proportion of the avifauna in the study area. The results suggest that low altitude forests are important cold season refugia of elevational migrants and these forests need continual protection.     

Midpoint attractors and species richness: Modelling the interaction between environmental drivers and geometric constraints

We introduce a novel framework for conceptualising, quantifying and unifying discordant patterns of species richness along geographical gradients. While not itself explicitly mechanistic, this approach offers a path towards understanding mechanisms. In this study, we focused on the diverse patterns of species richness on mountainsides. We conjectured that elevational range midpoints of species may be drawn towards a single midpoint attractor – a unimodal gradient of environmental favourability. The midpoint attractor interacts with geometric constraints imposed by sea level and the mountaintop to produce taxon‐specific patterns of species richness. We developed a Bayesian simulation model to estimate the location and strength of the midpoint attractor from species occurrence data sampled along mountainsides. We also constructed midpoint predictor models to test whether environmental variables could directly account for the observed patterns of species range midpoints. We challenged these models with 16 elevational data sets, comprising 4500 species of insects, vertebrates and plants. The midpoint predictor models generally failed to predict the pattern of species midpoints. In contrast, the midpoint attractor model closely reproduced empirical spatial patterns of species richness and range midpoints. Gradients of environmental favourability, subject to geometric constraints, may parsimoniously account for elevational and other patterns of species richness.