Nile perch (Lates niloticus,L.) and cichlids (Haplochromis spp.) in Lake Victoria: could prey mortality promote invasion of its predator?

The invasion of Nile perch into Lake Victoria is one of the iconic examples of the destructive effect of an introduced species on an ecosystem but no convincing explanation exists of why Nile perch only increased dramatically after a 25 year lag. Here, we consider this problem using a mathematical model that takes into account interactions between Nile perch and its cichlid prey. We examined competing hypotheses to explain Nile perch invasion and show that suppression of juvenile Nile perch by cichlids may cause the system to have two alternative stable states: one with only cichlids and one with coexistence of cichlids and Nile perch. Without cichlid predation on Nile perch, alternative stable states did not occur. Our analysis indicates that cichlid mortality, for example fishing mortality, may have induced the observed shift between the states.     

Was the Late Ordovician mass extinction truly exceptional?

The Late Ordovician mass extinction event is the oldest of the five great extinction events in the fossil record. It has long been regarded as an outlier among mass extinctions, primarily due to its association with a cooling climate. However, recent temporally better resolved fossil biodiversity estimates complicate this view, providing growing evidence for a prolonged but punctuated biodiversity decline modulated by changes in atmospheric composition, ocean chemistry, and viable habitat area. This evolving view invokes extinction drivers similar to those that occurred during other major extinctions; some are even factors in the current human-induced biodiversity crisis. Even this very ancient and, at first glance, exceptional event conveys important lessons about the intensifying ‘sixth mass extinction’.     

Did the loss of phytoplanktivorous fish contribute to algal blooms in the Mwanza Gulf of Lake Victoria?

Possible causes of the increased algal blooms in Lake Victoria in the 1980s have been disputed by several authors; some suggested a top-down effect by the introduced Nile perch, whereas others suggested a bottom-up effect due to eutrophication. In this article the potential impact is established of grazing by fish on phytoplankton densities, before the Nile perch upsurge and the concomitant algal blooms in the Mwanza Gulf. The biomass and trophic composition of fish in the sublittoral area of the Mwanza Gulf were calculated based on catch data from bottom trawls, and from gill nets covering the whole water column. Estimates of phytoplankton production in the same area were made from Secchi values and chlorophyll concentrations. The total phytoplankton intake by fish was estimated at 230 mg DW m⁻² day⁻¹. The daily gross production ranged from 6,200 to 7,100 mg DW m⁻² day⁻¹ and the net production from 1,900 to 2,200 mg DW m⁻² day⁻¹. Thus, losses of phytoplankton through grazing by fish were about 3–4% of daily gross and 10–12% of daily net phytoplankton production. As a consequence it is unlikely that the phytoplankton blooms in the second half of the 1980s were due to a top-down effect caused by a strong decline in phytoplankton grazing by fish.     

Heritability and heterochrony of polychromatism in a Lake Victoria Cichlid fish: Stepping stones for speciation?

In many haplochromine cichlid fish, male nuptial coloration is subject to female mate choice and plays a central role in the evolution of reproductive isolation between incipient species. Intraspecific variation in male coloration may serve as a target for diversifying sexual selection and provide a starting point for species divergence. Here, we investigated a polychromatism in Neochromis omnicaeruleus, a haplochromine from Lake Victoria, East-Africa. In this species, male coloration ranges from skyblue to yellow-red and females are grey-blue to yellow. We found that both genetic and environmental factors influence the expression of these colours during individual development. In a natural population, we found that male colour was associated with size and sexual maturity: yellow males were smaller than blue males and tended to be sexually immature. In females, size and maturity did not differ between colour types. Laboratory crosses revealed that there is a heritable component to the observed colour variation: yellow parents produced more yellow offspring than blue parents. Together with repeated aquarium observations of yellow individuals that gradually become blue, these data suggest that yellow males change to blue as they approach sexual maturity, and that the occurrence and timing of this transition is influenced by both environmental and genetic effects. The significance of this mechanism of colour expression as a possible target for divergent selection remains to be evaluated.     

Adaptive responses in resurgent Lake Victoria cichlids over the past 30 years

Textbook examples of adaptive radiation like the Galapagos finches and the East-African cichlids form a subject of major interest in evolutionary biology. Many of these species often show rapid morphological changes in response to a perturbed environment. The dramatic ecological changes in Lake Victoria during the past three decades, e.g. Nile perch predation and eutrophication, provide a unique opportunity to study environmental effects on cichlid morphology. Preliminary research has revealed that the lake’s haplochromines tend to be extremely plastic and sensitive to these environmental changes. So far, long-term ecomorphological studies at short-term intervals are extremely rare. In this study, we examined morphological changes over a 30 year period in six haplochromine species. Geometric morphometric analyses at intervals of approximately 3 years revealed adaptive responses. Three out of four resurgent haplochromines had a smaller head surface/caudal peduncle area (HS/CPA) ratio during the upsurge of the predatory Nile perch. During the same period, all four resurgent species had a larger cheek depth and a smaller eye size. The smaller HS/CPA ratio and larger cheek depth are likely to be adaptive responses to a high predation pressure and a diet shift to larger prey. The smaller eye size seems to be the result of a trade off between the eyes and other morphological structures in the smaller head of these species. Interestingly, the direction of the morphological changes was different between the four resurgent cichlid species and two species that became extremely rare or even may have gone extinct. The HS/CPA ratio increased in the extinct species where it decreased in the resurgent species. This study suggests that predation is a major driver of these morphological changes, which may be due to either phenotypic plasticity or adaptive changes.     

A microbial role in the construction of Mono Lake carbonate chimneys?

Lacustrine carbonate chimneys are striking, metre‐scale constructions. If these were bioinfluenced constructions, they could be priority targets in the search for early and extraterrestrial microbial life. However, there are questions over whether such chimneys are built on a geobiological framework or are solely abiotic geomorphological features produced by mixing of lake and spring waters. Here, we use correlative microscopy to show that microbes were living around Pleistocene Mono Lake carbonate chimneys during their growth. A plausible interpretation, in line with some recent works by others on other lacustrine carbonates, is that benthic cyanobacteria and their associated extracellular organic material (EOM) formed tubular biofilms around rising sublacustrine spring vent waters, binding calcium ions and trapping and binding detrital silicate sediment. Decay of these biofilms would locally have increased calcium and carbonate ion activity, inducing calcite precipitation on and around the biofilms. Early manganese carbonate mineralisation was directly associated with cell walls, potentially related to microbial activity though the precise mechanism remains to be elucidated. Much of the calcite crystal growth was likely abiotic, and no strong evidence for either authigenic silicate growth or a clay mineral precursor framework was observed. Nevertheless, it seems likely that the biofilms provided initial sites for calcite nucleation and encouraged the primary organised crystal growth. We suggest that the nano‐, micro‐ and macroscale fabrics of these Pleistocene Mono Lake chimneys were affected by the presence of centimetre‐thick tubular and vertically stacked calcifying microbial mats. Such carbonate chimneys represent a promising macroscale target in the exploration for ancient or extraterrestrial life.     

A Novel Implicit Solvent Model for Simulating the Molecular Dynamics of?RNA

Although molecular dynamics simulations can be accelerated by more than an order of magnitude by implicitly describing the influence of the solvent with a continuum model, most currently available implicit solvent simulations cannot robustly simulate the structure and dynamics of nucleic acids. The difficulties become exacerbated especially for RNAs, suggesting the presence of serious physical flaws in the prior continuum models for the influence of the solvent and counter ions on the nucleic acids. We present a novel, to our knowledge, implicit solvent model for simulating nucleic acids by combining the Langevin–Debye model and the Poisson–Boltzmann equation to provide a better estimate of the electrostatic screening of both the water and counter ions. Tests of the model involve comparisons of implicit and explicit solvent simulations for three RNA targets with 20, 29, and 75 nucleotides. The model provides reasonable agreement with explicit solvent simulations, and directions for future improvement are noted.     

HIV Infection in Fishing Communities of Lake Victoria Basin of Uganda – A Cross-Sectional Sero-Behavioral Survey

Background

Uganda''s first AIDS case was reported in a fishing village. Thereafter, due to varying risk factors, the epidemic spread heterogeneously to all regions, with some populations more affected. Given the recent rising trends in HIV infection in Uganda, it is crucial to know the risk factors in different populations. The aim of this study was to determine the prevalence and risk factors of HIV infection among fishing communities.

Methodology

A cross-sectional survey of 46 fishing communities was conducted in 2010. Following written consent, 911 randomly selected respondents age 15–59 years were interviewed and gave blood for HIV testing. HIV testing was conducted in the field and central laboratory according to national algorithm. Survey protocol was approved by the Science and Ethics Committee of Uganda Virus Research Institute, and cleared by Uganda National Council for Science and Technology. Data was captured by EPIINFO and statistical analysis done in SPSS.

Findings

Overall HIV prevalence was 22%; there was no difference by sex (x ² test, p>0.05). Association with HIV infection was determined by x ² test, p<0.5. Never married respondents had lower HIV prevalence (6.2%) than the ever married (24.1%). HIV prevalence was lower in younger respondents, age 15–24 years (10.8%) than in age group 25 years and above (26.1%). Muslims had lower HIV prevalence (14.4%) than Christians (25.2%). HIV prevalence was higher among respondents reporting 3 or more lifetime sexual partners (25.3%) than in those reporting less numbers (10.8%). HIV prevalence was higher among uncircumcised men (27%) than in circumcised men (11%). Multivariate analysis identified 4 risk factors for HIV infection; age, religion, ever condom use and number of lifetime sexual partners.

Conclusions

HIV prevalence in the surveyed communities was three times higher than of general population. This underscores the need for tailor made HIV combination prevention interventions targeting fishing communities.     

Effects of interspecific gene flow on the phenotypic variance–covariance matrix in Lake Victoria Cichlids

Rotifers are ubiquitous freshwater animals for which many complexes of cryptic species (i.e. distinct species that are morphologically difficult to distinguish) are described. Keratella cochlearis occurs globally and shows a wide phenotypic diversity indicating the potential presence of a species complex. We sampled lakes of the Trentino-South Tyrol region (Italy) and investigated mitochondrial genetic diversity in K. cochlearis in relation to detailed lorica measurements. We sequenced the mitochondrial cytochrome c oxidase subunit I and used the generalised mixed Yule coalescent approach, Poisson tree process model and automatic barcode gap discovery to delimit mitochondrial groups, associated with putative evolutionary significant units (ESUs). Based on 248 sequences, eight putative ESUs were indicated that could only partially be delimited by lorica morphology. Specifically, several morphological characteristics (i.e. spinelets, bended median ridge, and posterior spine) were found in specimens of different putative ESUs, and thus, these characters seem to be of poor discriminatory value. Furthermore, different putative ESUs of K. cochlearis were found in the same lake. We conclude that the high mitochondrial genetic diversity may be linked to tolerance of K. cochlearis to varying environmental conditions.     

Charles Bonnet Syndrome: Evidence for a Generative Model in the Cortex?

Several theories propose that the cortex implements an internal model to explain, predict, and learn about sensory data, but the nature of this model is unclear. One condition that could be highly informative here is Charles Bonnet syndrome (CBS), where loss of vision leads to complex, vivid visual hallucinations of objects, people, and whole scenes. CBS could be taken as indication that there is a generative model in the brain, specifically one that can synthesise rich, consistent visual representations even in the absence of actual visual input. The processes that lead to CBS are poorly understood. Here, we argue that a model recently introduced in machine learning, the deep Boltzmann machine (DBM), could capture the relevant aspects of (hypothetical) generative processing in the cortex. The DBM carries both the semantics of a probabilistic generative model and of a neural network. The latter allows us to model a concrete neural mechanism that could underlie CBS, namely, homeostatic regulation of neuronal activity. We show that homeostatic plasticity could serve to make the learnt internal model robust against e.g. degradation of sensory input, but overcompensate in the case of CBS, leading to hallucinations. We demonstrate how a wide range of features of CBS can be explained in the model and suggest a potential role for the neuromodulator acetylcholine. This work constitutes the first concrete computational model of CBS and the first application of the DBM as a model in computational neuroscience. Our results lend further credence to the hypothesis of a generative model in the brain.     

What are the policy priorities for sustaining ecological processes? A case study from Victoria,Australia

Summary Developments in ecological theory indicate that ecological processes have major implications for sustaining biodiversity and the provision of ecosystem services. Consequently, conservation actions that focus solely on particular species, vegetation communities, habitats or sites (‘assets’) are unlikely to be effective over the long term unless the ecological processes that support them continue to function. Efforts to sustain biodiversity must embrace both ‘assets’ and ‘process‐oriented’ approaches. Existing knowledge about ecological processes, incomplete though it is, has not been adequately considered in government decision making. It is, therefore, necessary to consider how to build consideration of ecological processes into legislative and institutional frameworks, policy and planning processes, and on‐ground environmental management. Drawing on insights from interviews, a facilitated workshop, and a literature review, this paper identifies a suite of policy priorities and associated reforms which should assist in ensuring that ecological processes are given more attention in policy‐making processes. It is concluded that a multi‐pronged approach is required, because there are no ‘silver bullets’ for sustaining ecological processes.     

Principles of Biofouling Protection in Marine Sponges: A Model for the Design of Novel Biomimetic and Bio-inspired Coatings in the Marine Environment?

The process of biofouling of marine structures and substrates, such as platforms or ship hulls, proceeds in multiple steps. Soon after the formation of an initial conditioning film, formed via the adsorption of organic particles to natural or man-made substrates, a population of different bacterial taxa associates under the formation of a biofilm. These microorganisms communicate through a complex quorum sensing network. Macro-foulers, e.g., barnacles, then settle and form a fouling layer on the marine surfaces, a process that globally has severe impacts both on the economy and on the environment. Since the ban of tributyltin, an efficient replacement of this antifouling compound by next-generation antifouling coatings that are environmentally more acceptable and also showing longer half-lives has not yet been developed. The sponges, as sessile filter-feeder animals, have evolved antifouling strategies to protect themselves against micro- and subsequent macro-biofouling processes. Experimental data are summarized and suggest that coating of the sponge surface with bio-silica contributes to the inhibition of the formation of a conditioning film. A direct adsorption of the surfaces by microorganisms can be impaired through poisoning the organisms with direct-acting secondary metabolites or toxic peptides. In addition, first, compounds from sponges have been identified that interfere with the anti-quorum sensing network. Sponge secondary metabolites acting selectively on diatom colonization have not yet been identified. Finally, it is outlined that direct-acting secondary metabolites inhibiting the growth of macro-fouling animals and those that poison the multidrug resistance pump are available. It is concluded that rational screening programs for inhibitors of the complex and dynamic problem of biofilm production, based on multidisciplinary studies and using sponges as a model, are required in the future.     

Was the initiation of translation in early eukaryotes IRES-driven?

The initiation of translation in eukaryotes generally involves the recognition of a 'cap' structure at the 5' end of the mRNA. However, for some viral and cellular mRNAs, a cap-independent mechanism occurs through an mRNA structure known as the internal ribosome entry site (IRES). Here, I postulate that the first eukaryotic mRNAs were translated in a cap-independent, IRES-driven manner that was then superseded in evolution by the cap-dependent mechanism, rather than vice versa. This hypothesis is supported by the following observations: (i) IRES-dependent, but not cap-dependent, translation can take place in the absence of not only a cap, but also many initiation factors; (ii) eukaryotic initiation factor 4E (eIF4E) and eIF4G, molecules absolutely required for cap-dependent translation, are among the most recently evolved translation factors; and (iii) functional similarities suggest the evolution of IRESs from spliceosomal introns. Thus, the contemporary cellular IRESs might be relics of the past.