The virtual ecologist approach: simulating data and observers

Ecologists carry a well‐stocked toolbox with a great variety of sampling methods, statistical analyses and modelling tools, and new methods are constantly appearing. Evaluation and optimisation of these methods is crucial to guide methodological choices. Simulating error‐free data or taking high‐quality data to qualify methods is common practice. Here, we emphasise the methodology of the ‘virtual ecologist’ (VE) approach where simulated data and observer models are used to mimic real species and how they are ‘virtually’ observed. This virtual data is then subjected to statistical analyses and modelling, and the results are evaluated against the ‘true’ simulated data. The VE approach is an intuitive and powerful evaluation framework that allows a quality assessment of sampling protocols, analyses and modelling tools. It works under controlled conditions as well as under consideration of confounding factors such as animal movement and biased observer behaviour. In this review, we promote the approach as a rigorous research tool, and demonstrate its capabilities and practical relevance. We explore past uses of VE in different ecological research fields, where it mainly has been used to test and improve sampling regimes as well as for testing and comparing models, for example species distribution models. We discuss its benefits as well as potential limitations, and provide some practical considerations for designing VE studies. Finally, research fields are identified for which the approach could be useful in the future. We conclude that VE could foster the integration of theoretical and empirical work and stimulate work that goes far beyond sampling methods, leading to new questions, theories, and better mechanistic understanding of ecological systems.     

Limpets break Dollo's Law

A new molecular phylogeny of the limpet molluscs (Calyptraeidae) reveals that coiled shells have independently re-evolved at least once in this family, which is a violation of Dollo's Law that complex ancestral states, once lost, are never reacquired. Reacquisition of the coiled ancestral state is remarkable in that uncoiled shells have been the most recent ancestral state for 20 million-100 million years. Adult coiling might have re-evolved by the mechanism of prolonging the period during which genes for coiling are expressed in larvae. This and other developmental mechanisms could provide general routes for maintaining the potential to produce traits lost in distant ancestors.     

Inferring the origins of state-dependent courtship traits

We examine a simple model of state-dependent (indicator) traits that focuses on their evolutionary origins as courtship signals. A necessary condition for the initial evolution of signals was found: the marginal female preference for minimal traits must exceed a certain threshold, where that threshold is proportional to the marginal male fitness costs for minimal traits. We interpret a positive threshold as implying a need for preexisting sensory bias in order to overcome the threshold if indicator signals are to start to evolve. We extend the model to allow for the possibility that signal costs and female preferences may vary over evolutionary time. If there is independent information on the way that signaling costs have evolved, then one may use measurements of contemporary female preferences to make inferences concerning the presence of the ancestral threshold. It is the marginal female preferences for minimal male traits that are important, whereas reconstructing ancestral origins from measurement of average size signals is not informative. Our analyses suggest two foci for future studies: measurement of the marginal response of contemporary females to minimal male signals and reconstruction of how signaling costs have changed over evolutionary time.     

High-performance liquid chromatographic separation and measurement of various biogenic compounds possibly involved in the pathomechanism of Parkinson’s disease

The work presented here describes an optimised, reversed-phase high-performance liquid chromatographic (RP-HPLC) method for separating 46 biogenic compounds, which, as neurotoxins or as their precursors or derivatives, may be relevant in the pathomechanism of Parkinson’s disease. In some cases, the physico–chemical properties of these substances are very similar, in other cases they differ greatly. In order to facilitate their detection in one chromatographic run, ion-pair chromatography was uniquely combined with a gradient elution. A diode array or a dual wavelength detector was used in combination with a fluorescence detector to verify the identity of the compounds.     

The MIPS mammalian protein-protein interaction database

SUMMARY: The MIPS mammalian protein-protein interaction database (MPPI) is a new resource of high-quality experimental protein interaction data in mammals. The content is based on published experimental evidence that has been processed by human expert curators. We provide the full dataset for download and a flexible and powerful web interface for users with various requirements.