Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles

<p>Abstract</p> <p>Background</p> <p>Phylogenies often contain both well-supported and poorly supported nodes. Determining how much additional data might be required to eventually recover most or all nodes with high support is an important pragmatic goal, and simulations have been used to examine this question. Most simulations have been based on few empirical loci, and suggest that well supported phylogenies can be determined with a very modest amount of data. Here we report the results of an empirical phylogenetic analysis of all 10 genera and 25 of 48 species of the new world pond turtles (family Emydidae) based on one mitochondrial (1070 base pairs) and seven nuclear loci (5961 base pairs), and a more biologically realistic simulation analysis incorporating variation among gene trees, aimed at determining how much more data might be necessary to recover weakly-supported nodes with strong support.</p> <p>Results</p> <p>Our mitochondrial-based phylogeny was well resolved, and congruent with some previous mitochondrial results. For example, all genera, and all species except <it>Pseudemys concinna</it>, <it>P. peninsularis</it>, and <it>Terrapene carolina </it>were monophyletic with strong support from at least one analytical method. The Emydinae was recovered as monophyletic, but the Deirochelyinae was not. Based on nuclear data, all genera were monophyletic with strong support except <it>Trachemys</it>, and all species except <it>Graptemys pseudogeographica</it>, <it>P. concinna</it>, <it>T. carolina</it>, and <it>T. coahuila </it>were monophyletic, generally with strong support. However, the branches subtending most genera were relatively short, and intergeneric relationships within subfamilies were mostly unsupported.</p> <p>Our simulations showed that relatively high bootstrap support values (i.e. ≥ 70) for all nodes were reached in all datasets, but an increase in data did not necessarily equate to an increase in support values. However, simulations based on a single empirical locus reached higher overall levels of support with less data than did the simulations that were based on all seven empirical nuclear loci, and symmetric tree distances were much lower for single versus multiple gene simulation analyses.</p> <p>Conclusion</p> <p>Our empirical results provide new insights into the phylogenetics of the Emydidae, but the short branches recovered deep in the tree also indicate the need for additional work on this clade to recover all intergeneric relationships with confidence and to delimit species for some problematic groups. Our simulation results suggest that moderate (in the few-to-tens of kb range) amounts of data are necessary to recover most emydid relationships with high support values. They also suggest that previous simulations that do not incorporate among-gene tree topological variance probably underestimate the amount of data needed to recover well supported phylogenies.</p

Wireless aquatic navigator for detection and analysis (WANDA)

The cost of monitoring and detecting pollutants in natural waters is of major concern. Current and forthcoming bodies of legislation will continue to drive demand for spatial and selective monitoring of our environment, as the focus increasingly moves towards effective enforcement of legislation through detection of events, and unambiguous identification of perpetrators. However, these monitoring demands are not being met due to the infrastructure and maintenance costs of conventional sensing models. Advanced autonomous platforms capable of performing complex analytical measurements at remote locations still require individual power, wireless communication, processor and electronic transducer units, along with regular maintenance visits. Hence the cost base for these systems is prohibitively high, and the spatial density and frequency of measurements are insufficient to meet requirements. In this paper we present a more cost effective approach for water quality monitoring using a low cost mobile sensing/communications platform together with very low cost stand-alone ‘satellite’ indicator stations that have an integrated colorimetric sensing material. The mobile platform is equipped with a wireless video camera that is used to interrogate each station to harvest information about the water quality. In simulation experiments, the first cycle of measurements is carried out to identify a ‘normal’ condition followed by a second cycle during which the platform successfully detected and communicated the presence of a chemical contaminant that had been localised at one of the satellite stations

WANDA: A Radically New Approach for Low-Cost Environmental Monitoring

The cost of monitoring pollutants within natural waters is of major concern. Existing and forthcoming bodies of legislation continually drive the demand for spatial and selective monitoring of key pollutants within our environment. Although research and commercial entities continue to drive down the cost of the infrastructure involved in environmental sensing systems (with an aim to increase scalability), the realisation of deploying a number of such systems even now remains out of reach. High cost and maintenance continue to persist as the major limiting factors. The aim of this work is to combine recent advances in robotics with chemical sensing techniques to remove all but the chemo-responsive material from each sensing node, and package the sensing element within a low cost, mobile, biomimetic robotic fish for effective water quality monitoring. Consequently, this approach is believed to radically reduce the systemic cost and maintenance per node and in doing so it will increase the scalability for spatial and selective monitoring of key pollutants within our environment

Patterning of polypyrrole trilayer actuators working in air for microrobotics

Within the areas of cell biology, biomedicine and minimal invasive surgery, there is a need for soft and flexible manipulators for handling biological objects, such as single cells and tissues. Polypyrrole (PPy) trilayer actuators are an attracting option since they use low power, are soft and can be operated without the need of an external electrolyte. The PPy trilayer actuator is made of three layers laminated together: two outer two layers of PPy and a middle, insulating layer of polyvinylidene difluoride (PVDF) to separate the two electrodes and contain the electrolyte. To date, only simple, individual actuators as have been fabricated and characterized. For the applications mentioned previously there is a need to be able to also fabricate complex structures, comprising individual addressable microactuators, for instance, in the form of multi-degree of freedom legs and microrobotic grippers. We have developed different microfabrication and patterning methods for both thick, membrane PVDF- and thin film PVDF-based trilayer actuators, which require different processing steps, thus extendeding our processing capabilities. We will present these new processing methods and initial articulated microactuator devices, i.e. actuators comprising individually controllable actuators/segments.</p

Coaxing Predictable Behaviour from Unstable (Intelligent) Polymer Systems: Processing Dynamic Systems

The development of intelligent polymeric materials is a multidimensional task. It requires the design of processing systems that retain dynamic properties meaning that the material produced is inherently "unstable". It also requires the design of communication tools that can be used to study, manipulate and control this dynamic character so as predictable, intelligent behaviour can be coaxed from these "unstable" systems. </jats:p